#CCP4I VERSION CCP4Interface 1.4.4.2 #CCP4I SCRIPT LOG buccaneer_ref #CCP4I DATE 20 Nov 2007 15:08:07 #CCP4I USER cowtan #CCP4I PROJECT PROJECT #CCP4I JOB_ID 393 #CCP4I SCRATCH /tmp/cowtan #CCP4I HOSTNAME setsuko.chem.york.ac.uk #CCP4I PID 8526 # /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/cbuccaneer -stdin
 
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 ### CCP4 6.0: cbuccaneer         version 1.0.0     : 04/10/07##
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 User: cowtan  Run date: 20/11/2007 Run time: 15:08:08 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2007 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$

title 	[No title given]
pdbin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	/*/*/[FP.F_sigF.F,FP.F_sigF.sigF]
colin-ref-hl 	/*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D]
seqin-wrk 	/home/cowtan/test/1vjf.seq
mtzin-wrk 	/home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
colin-wrk-fo 	/*/*/[FP,SIGFP]
colin-wrk-free 	/*/*/[FreeR_flag]
colin-wrk-hl 	/*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]
pdbout-wrk 	/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
find
grow
join
link
sequence
correct
filter
ncsbuild
prune
rebuild
cycles 	3
sequence-reliability 	0.95
new-residue-name 	UNK
resolution 	2.0

Cycle: 1

 C-alphas after finding:    24
 C-alphas after growing:    337
 C-alphas after joining:    211
 C-alphas linked:           0
 C-alphas sequenced:        115
 C-alphas corrected:        0
 C-alphas after filtering:  211
 C-alphas after NCS build:  211
 C-alphas after pruning:    146
 C-alphas after rebuilding: 146


Internal cycle   1
  146 residues were built in  6 chains, the longest having   33 residues.
  108 residues were sequenced, after pruning.



Cycle: 2

 C-alphas after finding:    170
 C-alphas after growing:    421
 C-alphas after joining:    218
 C-alphas linked:           0
 C-alphas sequenced:        146
 C-alphas corrected:        0
 C-alphas after filtering:  196
 C-alphas after NCS build:  196
 C-alphas after pruning:    170
 C-alphas after rebuilding: 170


Internal cycle   2
  170 residues were built in  5 chains, the longest having   73 residues.
  128 residues were sequenced, after pruning.



Cycle: 3

 C-alphas after finding:    194
 C-alphas after growing:    311
 C-alphas after joining:    211
 C-alphas linked:           1
 C-alphas sequenced:        133
 C-alphas corrected:        0
 C-alphas after filtering:  199
 C-alphas after NCS build:  199
 C-alphas after pruning:    165
 C-alphas after rebuilding: 165


Internal cycle   3
  165 residues were built in  3 chains, the longest having   73 residues.
  125 residues were sequenced, after pruning.


$TEXT:Result: $$ $$
  165 residues were built in  3 chains, the longest having   73 residues.
  125 residues were sequenced, after pruning.
$$


cbuccaneer: Normal termination
Times: User:     197.1s System:    0.4s Elapsed:     3:19  
# /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
 
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 ### CCP4 6.0: Refmac_5.3.0037    version 5.3.0037  : 03/29/06##
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 User: cowtan  Run date: 20/11/2007 Run time: 15:11:28 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Data line--- title [No title given]
 TITL
 Data line--- weight MATRIX 0.1
 WEIG
 Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
 LABI
 Data line--- make check NONE
 MAKE
 Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
 MAKE
 Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
 REFI
 Data line--- ncyc 10
 NCYC
 Data line--- scal type SIMP LSSC ANISO EXPE
 SCAL
 Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
 SOLV
 Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
 MONI
 Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
 LABO
 Data line--- PNAME buccaneer
 PNAM
 Data line--- DNAME buccaneer
 DNAM
 Data line--- RSIZE 80
 RSIZ
 Data line--- END
 END 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/cowtan/test/1vjf-3.2A.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib

 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
 
Cell from mtz :    50.903    50.903   121.411    90.000    90.000    90.000
Space group from mtz: number -   96; name - P43212
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens in input coordinate file will be kept
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0049
  Refinement of individual isotropic Bfactors
  Refinement resln        :    46.9323  3.2002
  Estimated number of reflections :       3404
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.1000
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian
  using working set of reflns and experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation
 
  Scaling and SigmaA resln:    46.9323  3.2002
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.12
 _lib_update       20/09/07
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2436
                with complete description    :   454
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib


  Number of atoms    :    1138
  Number of residues :     165
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.389 ideal_dist=   1.500
            ch:AA   res: 137  ASP      at:CG  .->ch:BB   res:  98  UNK      at:CB  .
  INFO:     link is found (not be used) dist=   1.386 ideal_dist=   1.337
            ch:AA   res: 137  ASP      at:OD1 .->ch:BB   res:  98  UNK      at:CB  .
  INFO:     link is found (not be used) dist=   1.364 ideal_dist=   1.337
            ch:AA   res: 137  ASP      at:OD2 .->ch:BB   res:  98  UNK      at:CB  .
  INFO:     link is found (not be used) dist=   1.510 ideal_dist=   1.410
            ch:BB   res:  65  LYS      at:NZ  .->ch:BB   res:  92  ARG      at:NH1 .
  INFO:     link is found (not be used) dist=   1.444 ideal_dist=   1.530
            ch:CC   res:  13  UNK      at:CB  .->ch:CC   res:  18  UNK      at:CB  .
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CB   UNK       116  AA   is missing in the structure
  ATTENTION: atom:CB   UNK       123  AA   is missing in the structure
  ATTENTION: atom:O    VAL       179  AA   is missing in the structure
  ATTENTION: atom:CB   UNK        63  BB   is missing in the structure
  ATTENTION: atom:O    UNK       100  BB   is missing in the structure
  ATTENTION: atom:O    UNK        26  CC   is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     165
  Number of atoms                   :    1144
  Number of missing atoms           :       6
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1154
  Number of angles restraints   :    1568
  Number of torsions restraints :     769
  Number of chiralities         :     191
  Number of planar groups       :     205
 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
 
 
 Number of reflections in file       2948
 Number of reflection read           2948
 
 
     CGMAT cycle number =      1
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    107 UNK CA  . - A    107 UNK C   . mod.= 1.273 id.= 1.525 dev=  0.252 sig.= 0.021
A    108 UNK C   . - A    109 UNK N   . mod.= 1.082 id.= 1.329 dev=  0.247 sig.= 0.014
A    119 ILE C   . - A    120 ASN N   . mod.= 1.098 id.= 1.329 dev=  0.231 sig.= 0.014
A    143 PRO CD  . - A    143 PRO N   . mod.= 2.054 id.= 1.473 dev= -0.581 sig.= 0.014
A    143 PRO C   . - A    144 LEU N   . mod.= 1.157 id.= 1.329 dev=  0.172 sig.= 0.014
A    164 LEU C   . - A    165 GLY N   . mod.= 1.065 id.= 1.329 dev=  0.264 sig.= 0.014
A    168 PRO CD  . - A    168 PRO N   . mod.= 2.067 id.= 1.473 dev= -0.594 sig.= 0.014
B     36 UNK C   . - B     37 UNK N   . mod.= 1.077 id.= 1.329 dev=  0.252 sig.= 0.014
B     38 UNK C   . - B     39 VAL N   . mod.= 1.063 id.= 1.329 dev=  0.266 sig.= 0.014
B     53 PRO CD  . - B     53 PRO N   . mod.= 2.070 id.= 1.473 dev= -0.597 sig.= 0.014
B     56 HIS C   . - B     57 THR N   . mod.= 1.135 id.= 1.329 dev=  0.194 sig.= 0.014
B     58 LYS C   . - B     59 ASN N   . mod.= 0.920 id.= 1.329 dev=  0.409 sig.= 0.014
B     65 LYS C   . - B     66 GLY N   . mod.= 1.115 id.= 1.329 dev=  0.214 sig.= 0.014
B     74 LEU C   . - B     75 GLY N   . mod.= 0.684 id.= 1.329 dev=  0.645 sig.= 0.014
B     75 GLY C   . - B     76 GLU N   . mod.= 1.066 id.= 1.329 dev=  0.263 sig.= 0.014
B     86 HIS C   . - B     87 VAL N   . mod.= 1.089 id.= 1.329 dev=  0.240 sig.= 0.014
B     89 GLY C   . - B     90 SER N   . mod.= 1.137 id.= 1.329 dev=  0.192 sig.= 0.014
B     91 GLY N   . - B     91 GLY CA  . mod.= 1.200 id.= 1.458 dev=  0.258 sig.= 0.021
C     18 UNK C   . - C     19 UNK N   . mod.= 1.187 id.= 1.329 dev=  0.142 sig.= 0.014
C     19 UNK N   . - C     19 UNK CA  . mod.= 1.144 id.= 1.458 dev=  0.314 sig.= 0.021
C     19 UNK C   . - C     20 UNK N   . mod.= 1.117 id.= 1.329 dev=  0.212 sig.= 0.014
C     23 UNK C   . - C     24 UNK N   . mod.= 0.967 id.= 1.329 dev=  0.362 sig.= 0.014
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    110 UNK O     - A    111 PRO N     mod.=  95.24 id.= 123.00 dev= 27.757 sig.=  1.600
A    110 UNK CA    - A    111 PRO N     mod.= 143.93 id.= 116.90 dev=-27.030 sig.=  1.500
A    110 UNK C     - A    111 PRO CD    mod.=  57.78 id.= 125.00 dev= 67.217 sig.=  4.100
A    137 ASP C     - A    138 PRO CD    mod.=  82.23 id.= 125.00 dev= 42.771 sig.=  4.100
A    143 PRO CA    - A    143 PRO CD    mod.=  87.18 id.= 112.00 dev= 24.816 sig.=  1.400
A    143 PRO N     - A    143 PRO CG    mod.=  80.17 id.= 103.20 dev= 23.033 sig.=  1.500
A    144 LEU C     - A    145 LYS CA    mod.= 140.79 id.= 121.70 dev=-19.093 sig.=  1.800
A    164 LEU O     - A    165 GLY N     mod.= 100.92 id.= 123.00 dev= 22.076 sig.=  1.600
A    164 LEU CA    - A    165 GLY N     mod.= 138.22 id.= 116.20 dev=-22.020 sig.=  2.000
A    164 LEU C     - A    165 GLY CA    mod.= 148.71 id.= 121.70 dev=-27.006 sig.=  1.800
A    168 PRO CA    - A    168 PRO CD    mod.=  85.51 id.= 112.00 dev= 26.489 sig.=  1.400
A    168 PRO N     - A    168 PRO CG    mod.=  80.58 id.= 103.20 dev= 22.618 sig.=  1.500
B     53 PRO CA    - B     53 PRO CD    mod.=  85.32 id.= 112.00 dev= 26.676 sig.=  1.400
B     53 PRO N     - B     53 PRO CG    mod.=  80.58 id.= 103.20 dev= 22.625 sig.=  1.500
B     58 LYS O     - B     59 ASN N     mod.=  93.56 id.= 123.00 dev= 29.442 sig.=  1.600
B     58 LYS CA    - B     59 ASN N     mod.= 145.52 id.= 116.20 dev=-29.320 sig.=  2.000
B     58 LYS C     - B     59 ASN CA    mod.= 148.69 id.= 121.70 dev=-26.988 sig.=  1.800
B     74 LEU O     - B     75 GLY N     mod.= 100.90 id.= 123.00 dev= 22.099 sig.=  1.600
B     74 LEU CA    - B     75 GLY N     mod.= 138.20 id.= 116.20 dev=-22.001 sig.=  2.000
B     74 LEU C     - B     75 GLY CA    mod.= 151.95 id.= 121.70 dev=-30.253 sig.=  1.800
B     90 SER C     - B     91 GLY CA    mod.= 154.09 id.= 121.70 dev=-32.390 sig.=  1.800
B     91 GLY N     - B     91 GLY C     mod.= 147.32 id.= 112.50 dev=-34.817 sig.=  2.900
C     19 UNK N     - C     19 UNK C     mod.= 141.21 id.= 111.20 dev=-30.009 sig.=  2.800
C     19 UNK O     - C     20 UNK N     mod.= 106.68 id.= 123.00 dev= 16.315 sig.=  1.600
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A    111 PRO N     deviation=   0.25 sigma.=   0.02
Atom: A    138 PRO N     deviation=  -0.35 sigma.=   0.02
Atom: A    143 PRO N     deviation=  -0.29 sigma.=   0.02
Atom: A    168 PRO N     deviation=   0.33 sigma.=   0.02
Atom: B     52 MET C     deviation=   0.21 sigma.=   0.02
Atom: B     53 PRO N     deviation=  -0.42 sigma.=   0.02
 
    ****                    VDW outliers                    ****
 
VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored
 
A    122 THR CB  . - B     65 LYS NZ  . mod.= 1.140 id.= 3.550 dev= -2.41 sig.= 0.20 sym.=  4  0 -1  0
A    122 THR CB  . - B     65 LYS CE  . mod.= 1.632 id.= 3.870 dev= -2.24 sig.= 0.20 sym.=  4  0 -1  0
A    122 THR CG2 . - B     65 LYS NZ  . mod.= 1.286 id.= 3.540 dev= -2.25 sig.= 0.20 sym.=  4  0 -1  0
A    137 ASP CG  . - B     98 UNK CB  . mod.= 1.389 id.= 3.690 dev= -2.30 sig.= 0.20 sym.=  1  0  0  0
A    137 ASP OD1 . - B     98 UNK CB  . mod.= 1.386 id.= 3.460 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0
A    137 ASP OD2 . - B     98 UNK CB  . mod.= 1.364 id.= 3.460 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0
C     13 UNK CB  . - C     18 UNK CB  . mod.= 1.444 id.= 3.880 dev= -2.44 sig.= 0.20 sym.=  1  0  0  0
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.338314    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.055     0.022
Bond angles  : refined atoms                   1568     4.884     1.952
Torsion angles, period  1. refined              162     4.652     5.000
Torsion angles, period  2. refined               37    40.119    23.514
Torsion angles, period  3. refined              163     6.804    15.000
Torsion angles, period  4. refined                6     8.389    15.000
Chiral centres: refined atoms                   191     0.179     0.200
Planar groups: refined atoms                    861     0.031     0.020
VDW repulsions: refined atoms                   668     0.563     0.200
VDW; torsion: refined atoms                     815     0.350     0.200
HBOND: refined atoms                             48     0.248     0.200
VDW repulsions; symmetry: refined atoms          89     0.703     0.200
HBOND; symmetry: refined atoms                    4     0.364     0.200
M. chain bond B values: refined atoms           810     0.000     1.500
M. chain angle B values: refined atoms         1256     0.000     2.000
S. chain bond B values: refined atoms           344     0.000     3.000
S. chain angle B values: refined atoms          312     0.000     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.518, B  = -41.796
Partial structure    1: scale =    0.289, B  =   1.832
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   516.0   431.4  0.43  0.49       5   601.5   556.7  0.62  0.71
 0.008      70  98.63   768.0   621.3  0.38  0.44       2   450.6   291.3  0.35  0.38
 0.013      80 100.00   698.3   604.0  0.39  0.39       9   593.0   462.6  0.35  0.37
 0.017      93 100.00   497.0   525.5  0.44  0.42       6   534.3   360.5  0.61  0.64
 0.022     102 100.00   479.9   535.6  0.44  0.45       4   658.6   580.2  0.44  0.39
 0.027     129 100.00   499.1   499.1  0.43  0.43       2   771.5   358.8  0.60  0.58
 0.032     112  98.41   494.6   472.2  0.46  0.45      12   559.9   415.0  0.48  0.43
 0.037     125 100.00   633.2   565.5  0.43  0.43       9   674.1   479.8  0.47  0.39
 0.042     141 100.00   699.4   613.7  0.44  0.44       5   803.5   334.9  0.58  0.57
 0.047     148 100.00   678.1   600.1  0.41  0.42       3   618.1   489.3  0.77  0.74
 0.051     159 100.00   680.3   598.2  0.40  0.41       6   823.6   566.0  0.51  0.49
 0.056     159 100.00   768.1   591.9  0.40  0.39       4   602.3   555.9  0.48  0.47
 0.061     158 100.00   686.6   551.0  0.44  0.43       9   679.9   289.6  0.66  0.58
 0.066     167 100.00   608.9   518.6  0.47  0.46       6   664.6   554.7  0.43  0.49
 0.071     181 100.00   628.0   522.2  0.46  0.44       5   820.1   702.5  0.30  0.33
 0.076     180 100.00   636.7   570.9  0.48  0.45      11   650.4   455.0  0.37  0.35
 0.081     178 100.00   611.6   508.9  0.42  0.43      14   487.6   457.2  0.64  0.53
 0.085     185 100.00   549.9   498.8  0.54  0.50       8   439.0   457.9  0.64  0.46
 0.090     194 100.00   516.8   465.5  0.48  0.47      11   688.3   512.9  0.39  0.38
 0.095     192 100.00   542.7   456.1  0.47  0.46      12   393.7   432.5  0.53  0.48
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    1. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.901    46   0.923  0.821
  0.0077    30   0.944    40   0.956    70   0.951  0.824
  0.0126    41   0.917    39   0.875    80   0.897  0.827
  0.0175    56   0.936    37   0.819    93   0.889  0.829
  0.0223    64   0.919    38   0.852   102   0.894  0.831
  0.0272    81   0.922    48   0.816   129   0.882  0.833
  0.0320    73   0.919    39   0.845   112   0.893  0.834
  0.0369    86   0.915    39   0.814   125   0.883  0.836
  0.0418   100   0.945    41   0.842   141   0.915  0.837
  0.0466   109   0.920    39   0.840   148   0.899  0.839
  0.0515   113   0.917    46   0.825   159   0.891  0.840
  0.0563   114   0.932    45   0.874   159   0.916  0.841
  0.0612   122   0.928    36   0.811   158   0.902  0.842
  0.0661   124   0.886    43   0.796   167   0.863  0.843
  0.0709   141   0.891    40   0.699   181   0.848  0.844
  0.0758   133   0.902    47   0.658   180   0.838  0.845
  0.0806   140   0.884    38   0.816   178   0.870  0.846
  0.0855   145   0.875    40   0.762   185   0.851  0.847
  0.0904   152   0.856    42   0.741   194   0.831  0.848
  0.0952   151   0.876    41   0.735   192   0.846  0.849
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.4435
Free R factor                        =     0.5000
Overall weighted R factor            =     0.4392
Free weighted R factor               =     0.4651
Overall correlation coefficient      =     0.5028
Free correlation coefficient         =     0.3590
DPI based on free R factor           =     1.0380
Overall figure of merit              =     0.8772
ML based su of positional parameters =     0.9914
ML based su of thermal parameters    =    54.7370
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Not converging with gamma equal   0.0000000E+00
 Trying gamma equal   5.5000003E-02
 Gamma decreased to   4.4000003E-02
 
 
     CGMAT cycle number =      2
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.612395    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.063     0.022
Bond angles  : refined atoms                   1568     4.546     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.504, B  = -11.506
Partial structure    1: scale =    0.294, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3782
Free R factor                        =     0.4797
Overall figure of merit              =     0.8844
-----------------------------------------------------------------------------
 Trying gamma equal   4.4000003E-02
 Gamma decreased to   3.4000002E-02
 
 
     CGMAT cycle number =      3
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.069     0.022
Bond angles  : refined atoms                   1568     4.618     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.503, B  = -11.736
Partial structure    1: scale =    0.298, B  =  -9.111
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3564
Free R factor                        =     0.4762
Overall figure of merit              =     0.8857
-----------------------------------------------------------------------------
 Trying gamma equal   3.4000002E-02
 Gamma decreased to   2.4909092E-02
 
 
     CGMAT cycle number =      4
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.072     0.022
Bond angles  : refined atoms                   1568     4.715     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.503, B  = -11.962
Partial structure    1: scale =    0.297, B  =  -9.771
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3437
Free R factor                        =     0.4699
Overall figure of merit              =     0.8860
-----------------------------------------------------------------------------
 Trying gamma equal   2.4909092E-02
 Gamma decreased to   1.6644629E-02
 
 
     CGMAT cycle number =      5
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.073     0.022
Bond angles  : refined atoms                   1568     4.787     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.503, B  = -12.135
Partial structure    1: scale =    0.298, B  =  -8.520
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3362
Free R factor                        =     0.4677
Overall figure of merit              =     0.8860
-----------------------------------------------------------------------------
 Trying gamma equal   1.6644629E-02
 Gamma decreased to   9.1314809E-03
 
 
     CGMAT cycle number =      6
 
 weigth matrix   9.9999994E-02
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.074     0.022
Bond angles  : refined atoms                   1568     4.826     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.502, B  = -12.606
Partial structure    1: scale =    0.298, B  =  -6.905
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3302
Free R factor                        =     0.4636
Overall figure of merit              =     0.8861
-----------------------------------------------------------------------------
 Trying gamma equal   9.1314809E-03
 Gamma decreased to   2.3013467E-03
 
 
     CGMAT cycle number =      7
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.074     0.022
Bond angles  : refined atoms                   1568     4.851     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.505, B  = -12.493
Partial structure    1: scale =    0.311, B  =  -2.434
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3259
Free R factor                        =     0.4576
Overall figure of merit              =     0.8864
-----------------------------------------------------------------------------
 Trying gamma equal   2.3013467E-03
 Gamma decreased to   0.0000000E+00
 
 
     CGMAT cycle number =      8
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.074     0.022
Bond angles  : refined atoms                   1568     4.872     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.505, B  = -12.666
Partial structure    1: scale =    0.312, B  =  -0.640
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3222
Free R factor                        =     0.4524
Overall figure of merit              =     0.8868
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 
 
     CGMAT cycle number =      9
 
 weigth matrix   9.9999994E-02
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.073     0.022
Bond angles  : refined atoms                   1568     4.890     1.952
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.508, B  = -12.231
Partial structure    1: scale =    0.312, B  =  -4.475
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3205
Free R factor                        =     0.4512
Overall figure of merit              =     0.8876
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 
 
     CGMAT cycle number =     10
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    127 PHE CE1 . - A    127 PHE CZ  . mod.= 1.788 id.= 1.382 dev= -0.406 sig.= 0.030
A    137 ASP CB  . - A    137 ASP CG  . mod.= 1.916 id.= 1.516 dev= -0.400 sig.= 0.025
A    137 ASP C   . - A    137 ASP O   . mod.= 1.521 id.= 1.231 dev= -0.290 sig.= 0.020
A    145 LYS CB  . - A    145 LYS CG  . mod.= 1.896 id.= 1.520 dev= -0.376 sig.= 0.030
B     35 UNK C   . - B     35 UNK O   . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020
B     35 UNK C   . - B     36 UNK N   . mod.= 0.765 id.= 1.329 dev=  0.564 sig.= 0.014
B     36 UNK N   . - B     36 UNK CA  . mod.= 1.769 id.= 1.458 dev= -0.311 sig.= 0.021
B     36 UNK C   . - B     36 UNK O   . mod.= 1.478 id.= 1.231 dev= -0.247 sig.= 0.020
B     36 UNK C   . - B     37 UNK N   . mod.= 1.186 id.= 1.329 dev=  0.143 sig.= 0.014
B     37 UNK C   . - B     37 UNK O   . mod.= 1.660 id.= 1.231 dev= -0.429 sig.= 0.020
B     38 UNK CA  . - B     38 UNK C   . mod.= 2.086 id.= 1.525 dev= -0.561 sig.= 0.021
B     38 UNK C   . - B     39 VAL N   . mod.= 1.120 id.= 1.329 dev=  0.209 sig.= 0.014
B     39 VAL N   . - B     39 VAL CA  . mod.= 1.719 id.= 1.458 dev= -0.261 sig.= 0.021
B     60 LEU CG  . - B     60 LEU CD2 . mod.= 2.005 id.= 1.521 dev= -0.484 sig.= 0.033
B     63 UNK N   . - B     63 UNK CA  . mod.= 1.678 id.= 1.458 dev= -0.220 sig.= 0.021
B     63 UNK C   . - B     64 ALA N   . mod.= 1.548 id.= 1.329 dev= -0.219 sig.= 0.014
B     92 ARG CG  . - B     92 ARG CD  . mod.= 1.841 id.= 1.520 dev= -0.321 sig.= 0.030
C     16 UNK CA  . - C     16 UNK CB  . mod.= 1.865 id.= 1.521 dev= -0.344 sig.= 0.033
C     24 UNK C   . - C     24 UNK O   . mod.= 0.986 id.= 1.231 dev=  0.245 sig.= 0.020
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    111 PRO CA    - A    111 PRO CD    mod.=  97.38 id.= 112.00 dev= 14.622 sig.=  1.400
B     36 UNK N     - B     36 UNK C     mod.=  69.35 id.= 111.20 dev= 41.847 sig.=  2.800
B     37 UNK N     - B     37 UNK C     mod.=  81.76 id.= 111.20 dev= 29.442 sig.=  2.800
B     65 LYS O     - B     66 GLY N     mod.= 105.51 id.= 123.00 dev= 17.492 sig.=  1.600
C     25 UNK N     - C     25 UNK C     mod.=  80.83 id.= 111.20 dev= 30.367 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    118 LEU CA    - A    119 ILE CA    mod.= 111.01 id.= 180.00 per.= 1 dev=  68.99 sig.=   5.00
A    136 SER CA    - A    137 ASP CA    mod.=-119.95 id.= 180.00 per.= 1 dev= -60.05 sig.=   5.00
B     35 UNK CA    - B     36 UNK CA    mod.= 116.07 id.= 180.00 per.= 1 dev=  63.93 sig.=   5.00
B     53 PRO CA    - B     54 GLY CA    mod.=-124.71 id.= 180.00 per.= 1 dev= -55.29 sig.=   5.00
B     54 GLY CA    - B     55 GLY CA    mod.=-118.21 id.= 180.00 per.= 1 dev= -61.79 sig.=   5.00
B     90 SER CA    - B     91 GLY CA    mod.= -99.86 id.= 180.00 per.= 1 dev= -80.14 sig.=   5.00
B     98 UNK CA    - B     99 UNK CA    mod.=-129.80 id.= 180.00 per.= 1 dev= -50.20 sig.=   5.00
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A    111 PRO N     deviation=   0.23 sigma.=   0.02
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.082     0.022
Bond angles  : refined atoms                   1568     5.176     1.952
Torsion angles, period  1. refined              162    18.727     5.000
Torsion angles, period  2. refined               37    39.096    23.514
Torsion angles, period  3. refined              163    24.335    15.000
Torsion angles, period  4. refined                6    22.756    15.000
Chiral centres: refined atoms                   191     0.300     0.200
Planar groups: refined atoms                    861     0.020     0.020
VDW repulsions: refined atoms                   552     0.406     0.200
VDW; torsion: refined atoms                     793     0.393     0.200
HBOND: refined atoms                             39     0.259     0.200
VDW repulsions; symmetry: refined atoms          82     0.576     0.200
HBOND; symmetry: refined atoms                    1     0.134     0.200
M. chain bond B values: refined atoms           855     0.117     1.500
M. chain angle B values: refined atoms         1256     0.155     2.000
S. chain bond B values: refined atoms           367     1.545     3.000
S. chain angle B values: refined atoms          312     1.954     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.505, B  = -12.824
Partial structure    1: scale =    0.313, B  =  -1.678
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   528.6   428.2  0.48  0.54       5   616.2   516.3  0.54  0.59
 0.008      70  98.63   786.7   678.0  0.36  0.41       2   461.7    48.4  0.90  0.86
 0.013      80 100.00   715.4   602.5  0.34  0.35       9   607.5   468.2  0.34  0.34
 0.017      93 100.00   509.2   535.0  0.35  0.35       6   547.4   392.2  0.57  0.58
 0.022     102 100.00   491.7   491.6  0.38  0.39       4   674.7   551.2  0.37  0.41
 0.027     129 100.00   511.3   495.4  0.40  0.40       2   790.4   532.1  0.39  0.39
 0.032     112  98.41   506.7   474.1  0.45  0.44      12   573.6   447.2  0.52  0.50
 0.037     125 100.00   648.7   621.1  0.35  0.36       9   690.5   567.1  0.51  0.49
 0.042     141 100.00   716.5   672.5  0.31  0.31       5   823.1   472.9  0.43  0.43
 0.047     148 100.00   694.7   637.7  0.31  0.33       3   633.2   385.3  0.46  0.37
 0.051     159 100.00   696.9   652.3  0.28  0.28       6   843.7   689.4  0.30  0.29
 0.056     159 100.00   786.8   703.6  0.27  0.27       4   617.0   595.7  0.58  0.56
 0.061     158 100.00   703.4   611.1  0.29  0.29       9   696.5   519.0  0.45  0.40
 0.066     167 100.00   623.7   591.6  0.31  0.30       6   680.8   540.4  0.66  0.68
 0.071     181 100.00   643.3   583.0  0.31  0.30       5   840.1   767.6  0.33  0.38
 0.076     180 100.00   652.2   611.4  0.30  0.29      11   666.3   568.3  0.33  0.37
 0.081     178 100.00   626.6   580.5  0.28  0.28      14   499.6   521.2  0.46  0.41
 0.085     185 100.00   563.3   555.9  0.30  0.29       8   449.8   401.2  0.61  0.49
 0.090     194 100.00   529.4   493.7  0.32  0.29      11   705.1   534.0  0.43  0.40
 0.095     192 100.00   556.0   537.9  0.31  0.29      12   403.4   442.3  0.46  0.39
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   10. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.880    46   0.908  0.885
  0.0077    30   0.950    40   0.945    70   0.947  0.885
  0.0126    41   0.925    39   0.893    80   0.909  0.884
  0.0175    56   0.938    37   0.823    93   0.892  0.884
  0.0223    64   0.921    38   0.845   102   0.893  0.884
  0.0272    81   0.928    48   0.825   129   0.890  0.884
  0.0320    73   0.926    39   0.860   112   0.903  0.883
  0.0369    86   0.921    39   0.828   125   0.892  0.883
  0.0418   100   0.947    41   0.830   141   0.913  0.883
  0.0466   109   0.929    39   0.858   148   0.910  0.883
  0.0515   113   0.925    46   0.841   159   0.901  0.883
  0.0563   114   0.943    45   0.865   159   0.921  0.882
  0.0612   122   0.937    36   0.786   158   0.903  0.882
  0.0661   124   0.904    43   0.826   167   0.884  0.882
  0.0709   141   0.899    40   0.702   181   0.856  0.882
  0.0758   133   0.914    47   0.657   180   0.847  0.882
  0.0806   140   0.897    38   0.824   178   0.881  0.882
  0.0855   145   0.894    40   0.801   185   0.874  0.882
  0.0904   152   0.877    42   0.753   194   0.850  0.881
  0.0952   151   0.885    41   0.790   192   0.864  0.881
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.3194
Free R factor                        =     0.4564
Overall weighted R factor            =     0.3215
Free weighted R factor               =     0.4437
Overall correlation coefficient      =     0.7458
Free correlation coefficient         =     0.5074
DPI based on free R factor           =     0.9476
Overall figure of merit              =     0.8869
ML based su of positional parameters =     0.7466
ML based su of thermal parameters    =    40.9093
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Gamma decreased to   0.0000000E+00
 
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    118 LEU C   . - A    119 ILE N   . mod.= 1.058 id.= 1.329 dev=  0.271 sig.= 0.014
A    119 ILE N   . - A    119 ILE CA  . mod.= 1.820 id.= 1.458 dev= -0.362 sig.= 0.021
A    119 ILE CA  . - A    119 ILE C   . mod.= 1.837 id.= 1.525 dev= -0.312 sig.= 0.021
A    119 ILE C   . - A    120 ASN N   . mod.= 1.530 id.= 1.329 dev= -0.201 sig.= 0.014
A    120 ASN CA  . - A    120 ASN C   . mod.= 1.242 id.= 1.525 dev=  0.283 sig.= 0.021
A    120 ASN C   . - A    120 ASN O   . mod.= 0.973 id.= 1.231 dev=  0.258 sig.= 0.020
A    121 ASP CG  . - A    121 ASP OD2 . mod.= 1.598 id.= 1.249 dev= -0.349 sig.= 0.019
A    127 PHE CE1 . - A    127 PHE CZ  . mod.= 1.795 id.= 1.382 dev= -0.413 sig.= 0.030
A    137 ASP CB  . - A    137 ASP CG  . mod.= 1.924 id.= 1.516 dev= -0.408 sig.= 0.025
A    137 ASP C   . - A    137 ASP O   . mod.= 1.517 id.= 1.231 dev= -0.286 sig.= 0.020
A    145 LYS CB  . - A    145 LYS CG  . mod.= 1.879 id.= 1.520 dev= -0.359 sig.= 0.030
B     35 UNK N   . - B     35 UNK CA  . mod.= 1.988 id.= 1.491 dev= -0.497 sig.= 0.021
B     35 UNK C   . - B     35 UNK O   . mod.= 1.540 id.= 1.231 dev= -0.309 sig.= 0.020
B     35 UNK C   . - B     36 UNK N   . mod.= 1.096 id.= 1.329 dev=  0.233 sig.= 0.014
B     38 UNK CA  . - B     38 UNK C   . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021
B     60 LEU CG  . - B     60 LEU CD2 . mod.= 1.929 id.= 1.521 dev= -0.408 sig.= 0.033
B     63 UNK C   . - B     64 ALA N   . mod.= 1.534 id.= 1.329 dev= -0.205 sig.= 0.014
B     65 LYS CD  . - B     65 LYS CE  . mod.= 2.084 id.= 1.520 dev= -0.564 sig.= 0.030
B     65 LYS CE  . - B     65 LYS NZ  . mod.= 1.930 id.= 1.489 dev= -0.441 sig.= 0.030
B     65 LYS C   . - B     66 GLY N   . mod.= 1.826 id.= 1.329 dev= -0.497 sig.= 0.014
B     66 GLY CA  . - B     66 GLY C   . mod.= 1.754 id.= 1.516 dev= -0.238 sig.= 0.018
B     69 TRP NE1 . - B     69 TRP CE2 . mod.= 1.535 id.= 1.370 dev= -0.165 sig.= 0.011
B     89 GLY N   . - B     89 GLY CA  . mod.= 1.685 id.= 1.458 dev= -0.227 sig.= 0.021
B     92 ARG CG  . - B     92 ARG CD  . mod.= 1.876 id.= 1.520 dev= -0.356 sig.= 0.030
C     16 UNK CA  . - C     16 UNK CB  . mod.= 1.868 id.= 1.521 dev= -0.347 sig.= 0.033
C     23 UNK C   . - C     23 UNK O   . mod.= 1.444 id.= 1.231 dev= -0.213 sig.= 0.020
C     23 UNK C   . - C     24 UNK N   . mod.= 1.495 id.= 1.329 dev= -0.166 sig.= 0.014
C     24 UNK C   . - C     25 UNK N   . mod.= 1.562 id.= 1.329 dev= -0.233 sig.= 0.014
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    107 UNK N     - A    107 UNK C     mod.=  78.94 id.= 111.20 dev= 32.261 sig.=  2.800
A    118 LEU N     - A    118 LEU CB    mod.=  91.27 id.= 110.50 dev= 19.226 sig.=  1.700
A    118 LEU CA    - A    118 LEU O     mod.= 103.70 id.= 120.80 dev= 17.102 sig.=  1.700
A    119 ILE CA    - A    120 ASN N     mod.=  92.64 id.= 116.20 dev= 23.559 sig.=  2.000
A    119 ILE C     - A    120 ASN CA    mod.= 100.90 id.= 121.70 dev= 20.805 sig.=  1.800
A    120 ASN CA    - A    120 ASN O     mod.=  99.49 id.= 120.80 dev= 21.307 sig.=  1.700
B     35 UNK N     - B     35 UNK CB    mod.= 133.52 id.= 110.40 dev=-23.116 sig.=  1.500
B     65 LYS CG    - B     65 LYS CE    mod.=  87.48 id.= 111.30 dev= 23.816 sig.=  2.300
B     65 LYS O     - B     66 GLY N     mod.= 106.62 id.= 123.00 dev= 16.382 sig.=  1.600
B     65 LYS CA    - B     66 GLY N     mod.= 136.28 id.= 116.20 dev=-20.084 sig.=  2.000
B     66 GLY CA    - B     66 GLY O     mod.= 149.47 id.= 120.80 dev=-28.674 sig.=  1.700
C     25 UNK N     - C     25 UNK C     mod.=  82.47 id.= 111.20 dev= 28.734 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    118 LEU CA    - A    119 ILE CA    mod.= 118.93 id.= 180.00 per.= 1 dev=  61.07 sig.=   5.00
A    136 SER CA    - A    137 ASP CA    mod.=-119.72 id.= 180.00 per.= 1 dev= -60.28 sig.=   5.00
B     35 UNK CA    - B     36 UNK CA    mod.= 117.71 id.= 180.00 per.= 1 dev=  62.29 sig.=   5.00
B     53 PRO CA    - B     54 GLY CA    mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.=   5.00
B     54 GLY CA    - B     55 GLY CA    mod.=-119.84 id.= 180.00 per.= 1 dev= -60.16 sig.=   5.00
B     90 SER CA    - B     91 GLY CA    mod.= -99.24 id.= 180.00 per.= 1 dev= -80.76 sig.=   5.00
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A    111 PRO N     deviation=   0.23 sigma.=   0.02
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz 

 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1154     0.087     0.022
Bond angles  : refined atoms                   1568     5.566     1.952
Torsion angles, period  1. refined              162    19.402     5.000
Torsion angles, period  2. refined               37    39.300    23.514
Torsion angles, period  3. refined              163    24.091    15.000
Torsion angles, period  4. refined                6    25.144    15.000
Chiral centres: refined atoms                   191     0.283     0.200
Planar groups: refined atoms                    861     0.024     0.020
VDW repulsions: refined atoms                   562     0.418     0.200
VDW; torsion: refined atoms                     779     0.393     0.200
HBOND: refined atoms                             39     0.293     0.200
VDW repulsions; symmetry: refined atoms          75     0.565     0.200
HBOND; symmetry: refined atoms                    1     0.085     0.200
M. chain bond B values: refined atoms           857     0.090     1.500
M. chain angle B values: refined atoms         1256     0.124     2.000
S. chain bond B values: refined atoms           365     1.340     3.000
S. chain angle B values: refined atoms          312     1.822     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.510, B  = -12.100
Partial structure    1: scale =    0.312, B  =  -8.977
Overall anisotropic scale factors
   B11 =  0.01 B22 =  0.01 B33 = -0.03 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   524.1   428.4  0.47  0.53       5   610.8   527.1  0.54  0.60
 0.008      70  98.63   779.9   674.7  0.36  0.41       2   457.7    30.3  0.93  0.91
 0.013      80 100.00   709.2   601.4  0.34  0.35       9   602.3   453.5  0.35  0.36
 0.017      93 100.00   504.8   533.4  0.37  0.36       6   542.7   387.9  0.47  0.49
 0.022     102 100.00   487.4   497.5  0.41  0.42       4   668.8   531.0  0.38  0.43
 0.027     129 100.00   506.9   495.4  0.42  0.42       2   783.6   531.5  0.43  0.46
 0.032     112  98.41   502.3   470.2  0.43  0.42      12   568.6   445.0  0.53  0.51
 0.037     125 100.00   643.1   619.8  0.33  0.34       9   684.6   562.0  0.55  0.53
 0.042     141 100.00   710.3   649.7  0.32  0.33       5   816.0   431.9  0.47  0.48
 0.047     148 100.00   688.7   627.0  0.31  0.33       3   627.8   361.4  0.47  0.29
 0.051     159 100.00   690.9   634.4  0.29  0.30       6   836.4   689.2  0.27  0.26
 0.056     159 100.00   780.0   702.2  0.27  0.27       4   611.7   568.3  0.48  0.47
 0.061     158 100.00   697.3   601.3  0.31  0.30       9   690.5   535.0  0.50  0.42
 0.066     167 100.00   618.4   581.3  0.31  0.31       6   675.0   573.9  0.59  0.61
 0.071     181 100.00   637.7   583.7  0.33  0.32       5   832.9   784.3  0.34  0.39
 0.076     180 100.00   646.6   615.1  0.31  0.30      11   660.6   620.4  0.34  0.37
 0.081     178 100.00   621.2   577.1  0.28  0.28      14   495.2   509.8  0.44  0.38
 0.085     185 100.00   558.5   550.7  0.32  0.31       8   445.9   372.1  0.67  0.55
 0.090     194 100.00   524.8   488.3  0.33  0.31      11   699.0   522.9  0.47  0.46
 0.095     192 100.00   551.2   527.3  0.31  0.31      12   399.9   416.5  0.41  0.34
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   11. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.880    46   0.908  0.883
  0.0077    30   0.947    40   0.944    70   0.945  0.883
  0.0126    41   0.927    39   0.893    80   0.911  0.883
  0.0175    56   0.938    37   0.829    93   0.895  0.884
  0.0223    64   0.922    38   0.850   102   0.895  0.884
  0.0272    81   0.929    48   0.830   129   0.892  0.884
  0.0320    73   0.926    39   0.858   112   0.903  0.884
  0.0369    86   0.920    39   0.825   125   0.890  0.884
  0.0418   100   0.947    41   0.831   141   0.913  0.884
  0.0466   109   0.929    39   0.864   148   0.912  0.884
  0.0515   113   0.924    46   0.840   159   0.900  0.884
  0.0563   114   0.944    45   0.867   159   0.922  0.885
  0.0612   122   0.937    36   0.789   158   0.904  0.885
  0.0661   124   0.903    43   0.818   167   0.881  0.885
  0.0709   141   0.900    40   0.697   181   0.855  0.885
  0.0758   133   0.914    47   0.656   180   0.847  0.885
  0.0806   140   0.901    38   0.826   178   0.885  0.885
  0.0855   145   0.897    40   0.797   185   0.876  0.885
  0.0904   152   0.879    42   0.760   194   0.853  0.885
  0.0952   151   0.883    41   0.807   192   0.866  0.885
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.3264
Free R factor                        =     0.4581
Overall weighted R factor            =     0.3301
Free weighted R factor               =     0.4436
Overall correlation coefficient      =     0.7417
Free correlation coefficient         =     0.5118
DPI based on free R factor           =     0.9509
Overall figure of merit              =     0.8877
ML based su of positional parameters =     0.7466
ML based su of thermal parameters    =    40.9093
-----------------------------------------------------------------------------
  Time in seconds: CPU =         5.34
             Elapsed =           6.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LLG vs cycle :N:1,5:
:Geometry vs cycle:N:1,6,7,8:
$$
      Ncyc   Rfact   Rfree     FOM         LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
         0   0.443   0.500    0.877        1296.8    0.055    4.884    0.179
         1   0.378   0.480    0.884         642.8    0.063    4.546    0.209
         2   0.356   0.476    0.886         439.1    0.069    4.618    0.258
         3   0.344   0.470    0.886         323.4    0.072    4.715    0.267
         4   0.336   0.468    0.886         257.8    0.073    4.787    0.259
         5   0.330   0.464    0.886         223.0    0.074    4.826    0.259
         6   0.326   0.458    0.886         165.7    0.074    4.851    0.260
         7   0.322   0.452    0.887         129.1    0.074    4.872    0.260
         8   0.321   0.451    0.888          86.6    0.073    4.890    0.259
         9   0.319   0.456    0.887         121.7    0.082    5.176    0.300
        10   0.326   0.458    0.888         111.4    0.087    5.566    0.283
 $$

 Refmac_5.3.0037:  End of Refmac_5.3.0037
Times: User:       7.5s System:    0.3s Elapsed:     0:09  
# /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/cbuccaneer -stdin
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.0: cbuccaneer         version 1.0.0     : 04/10/07##
 ###############################################################
 User: cowtan  Run date: 20/11/2007 Run time: 15:11:37 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2007 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$

title 	[No title given]
pdbin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	/*/*/[FP.F_sigF.F,FP.F_sigF.sigF]
colin-ref-hl 	/*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D]
seqin-wrk 	/home/cowtan/test/1vjf.seq
mtzin-wrk 	/home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
colin-wrk-fo 	/*/*/[FP,SIGFP]
colin-wrk-free 	/*/*/[FreeR_flag]
colin-wrk-phifom 	/*/*/[PHCOMB,FOM]
pdbin-wrk 	/home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
pdbout-wrk 	/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
find
grow
join
link
sequence
correct
filter
ncsbuild
prune
rebuild
cycles 	1
correlation-mode
sequence-reliability 	0.95
new-residue-name 	UNK
resolution 	2.0

Cycle: 1

 C-alphas after finding:    189
 C-alphas after growing:    355
 C-alphas after joining:    213
 C-alphas linked:           0
 C-alphas sequenced:        149
 C-alphas corrected:        2
 C-alphas after filtering:  210
 C-alphas after NCS build:  210
 C-alphas after pruning:    175
 C-alphas after rebuilding: 175


Internal cycle   1
  175 residues were built in  3 chains, the longest having   84 residues.
  141 residues were sequenced, after pruning.


$TEXT:Result: $$ $$
  175 residues were built in  3 chains, the longest having   84 residues.
  141 residues were sequenced, after pruning.
$$


cbuccaneer: Normal termination
Times: User:     110.4s System:    0.3s Elapsed:     1:50  
# /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.0: Refmac_5.3.0037    version 5.3.0037  : 03/29/06##
 ###############################################################
 User: cowtan  Run date: 20/11/2007 Run time: 15:13:27 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Data line--- title [No title given]
 TITL
 Data line--- weight MATRIX 0.1
 WEIG
 Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
 LABI
 Data line--- make check NONE
 MAKE
 Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
 MAKE
 Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
 REFI
 Data line--- ncyc 10
 NCYC
 Data line--- scal type SIMP LSSC ANISO EXPE
 SCAL
 Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
 SOLV
 Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
 MONI
 Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
 LABO
 Data line--- PNAME buccaneer
 PNAM
 Data line--- DNAME buccaneer
 DNAM
 Data line--- RSIZE 80
 RSIZ
 Data line--- END
 END 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/cowtan/test/1vjf-3.2A.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib

 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
 
Cell from mtz :    50.903    50.903   121.411    90.000    90.000    90.000
Space group from mtz: number -   96; name - P43212
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens in input coordinate file will be kept
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0049
  Refinement of individual isotropic Bfactors
  Refinement resln        :    46.9323  3.2002
  Estimated number of reflections :       3404
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.1000
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian
  using working set of reflns and experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation
 
  Scaling and SigmaA resln:    46.9323  3.2002
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.12
 _lib_update       20/09/07
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2436
                with complete description    :   454
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib


  Number of atoms    :    1236
  Number of residues :     175
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.447 ideal_dist=   1.450
            ch:AA   res:  97  UNK      at:N   .->ch:AA   res: 124  ARG      at:CG  .
  INFO:     link is found (not be used) dist=   0.948 ideal_dist=   1.450
            ch:AA   res:  97  UNK      at:N   .->ch:AA   res: 124  ARG      at:CD  .
  INFO:     link is found (not be used) dist=   1.290 ideal_dist=   1.524
            ch:AA   res:  97  UNK      at:CA  .->ch:AA   res: 124  ARG      at:CD  .
  INFO:     link is found (not be used) dist=   1.643 ideal_dist=   1.510
            ch:AA   res:  97  UNK      at:C   .->ch:AA   res: 124  ARG      at:CD  .
  INFO:     link is found (not be used) dist=   0.991 ideal_dist=   1.339
            ch:AA   res:  97  UNK      at:C   .->ch:AA   res: 124  ARG      at:NE  .
  INFO:     link is found (not be used) dist=   1.589 ideal_dist=   1.460
            ch:AA   res:  97  UNK      at:C   .->ch:AA   res: 124  ARG      at:CZ  .
  INFO:     link is found (not be used) dist=   1.146 ideal_dist=   1.240
            ch:AA   res:  97  UNK      at:O   .->ch:AA   res: 124  ARG      at:NE  .
  INFO:     link is found (not be used) dist=   0.881 ideal_dist=   1.330
            ch:AA   res:  97  UNK      at:O   .->ch:AA   res: 124  ARG      at:CZ  .
  INFO:     link is found (not be used) dist=   1.207 ideal_dist=   1.240
            ch:AA   res:  97  UNK      at:O   .->ch:AA   res: 124  ARG      at:NH1 .
  INFO:     link is found (not be used) dist=   1.275 ideal_dist=   1.337
            ch:AA   res:  99  UNK      at:CB  .->ch:AA   res: 103  GLU      at:OE1 .
  INFO:     link is found (not be used) dist=   1.666 ideal_dist=   1.420
            ch:AA   res: 111  SER      at:CB  .->ch:AA   res: 146  ASN      at:OD1 .
  INFO:     link is found (not be used) dist=   1.365 ideal_dist=   1.462
            ch:AA   res: 124  ARG      at:NH1 .->ch:BB   res:  68  LEU      at:CD1 .
  INFO:     link is found (not be used) dist=   1.396 ideal_dist=   1.337
            ch:BB   res:  40  ARG      at:CG  .->ch:BB   res:  42  GLU      at:OE1 .
  INFO:     link is found (not be used) dist=   1.515 ideal_dist=   1.337
            ch:BB   res:  40  ARG      at:CD  .->ch:BB   res:  42  GLU      at:OE1 .
  INFO:     link is found (not be used) dist=   1.289 ideal_dist=   1.339
            ch:BB   res:  40  ARG      at:NE  .->ch:BB   res:  42  GLU      at:CD  .
  INFO:     link is found (not be used) dist=   1.479 ideal_dist=   1.275
            ch:BB   res:  40  ARG      at:NE  .->ch:BB   res:  42  GLU      at:OE1 .
  INFO:     link is found (not be used) dist=   0.773 ideal_dist=   1.510
            ch:BB   res:  40  ARG      at:CZ  .->ch:BB   res:  42  GLU      at:CG  .
  INFO:     link is found (not be used) dist=   1.181 ideal_dist=   1.460
            ch:BB   res:  40  ARG      at:CZ  .->ch:BB   res:  42  GLU      at:CD  .
  INFO:     link is found (not be used) dist=   0.497 ideal_dist=   1.457
            ch:BB   res:  40  ARG      at:NH1 .->ch:BB   res:  42  GLU      at:CB  .
  INFO:     link is found (not be used) dist=   1.076 ideal_dist=   1.457
            ch:BB   res:  40  ARG      at:NH1 .->ch:BB   res:  42  GLU      at:CG  .
  INFO:     link is found (not be used) dist=   1.278 ideal_dist=   1.457
            ch:BB   res:  40  ARG      at:NH2 .->ch:BB   res:  42  GLU      at:CG  .
  INFO:     link is found (not be used) dist=   1.416 ideal_dist=   1.275
            ch:BB   res:  63  ASP      at:OD1 .->ch:BB   res:  67  GLN      at:N   .
  INFO:     link is found (not be used) dist=   1.628 ideal_dist=   1.413
            ch:BB   res:  35  UNK      at:CB  .->ch:CC   res:  24  UNK      at:O   .
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:O    UNK       180  AA   is missing in the structure
  ATTENTION: atom:O    GLN        98  BB   is missing in the structure
  ATTENTION: atom:O    UNK        26  CC   is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     175
  Number of atoms                   :    1239
  Number of missing atoms           :       3
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1254
  Number of angles restraints   :    1703
  Number of torsions restraints :     838
  Number of chiralities         :     208
  Number of planar groups       :     221
 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
 
 
 Number of reflections in file       2948
 Number of reflection read           2948
 
 
     CGMAT cycle number =      1
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A     99 UNK C   . - A    100 UNK N   . mod.= 1.170 id.= 1.329 dev=  0.159 sig.= 0.014
A    107 VAL C   . - A    108 THR N   . mod.= 1.157 id.= 1.329 dev=  0.172 sig.= 0.014
A    108 THR C   . - A    109 PRO N   . mod.= 1.088 id.= 1.341 dev=  0.253 sig.= 0.016
A    109 PRO N   . - A    109 PRO CA  . mod.= 1.240 id.= 1.458 dev=  0.218 sig.= 0.021
A    109 PRO CD  . - A    109 PRO N   . mod.= 1.933 id.= 1.473 dev= -0.460 sig.= 0.014
A    120 ASP CA  . - A    120 ASP C   . mod.= 1.260 id.= 1.525 dev=  0.265 sig.= 0.021
A    120 ASP C   . - A    121 THR N   . mod.= 1.139 id.= 1.329 dev=  0.190 sig.= 0.014
B     34 UNK N   . - B     34 UNK CA  . mod.= 1.987 id.= 1.491 dev= -0.496 sig.= 0.021
B     34 UNK C   . - B     35 UNK N   . mod.= 1.095 id.= 1.329 dev=  0.234 sig.= 0.014
B     37 PRO CD  . - B     37 PRO N   . mod.= 2.196 id.= 1.473 dev= -0.723 sig.= 0.014
B     37 PRO CA  . - B     37 PRO C   . mod.= 1.805 id.= 1.525 dev= -0.280 sig.= 0.021
B     52 PRO CD  . - B     52 PRO N   . mod.= 1.953 id.= 1.473 dev= -0.480 sig.= 0.014
B     56 THR N   . - B     56 THR CA  . mod.= 1.245 id.= 1.458 dev=  0.213 sig.= 0.021
B     56 THR C   . - B     57 LYS N   . mod.= 1.186 id.= 1.329 dev=  0.143 sig.= 0.014
B     65 LYS C   . - B     66 GLY N   . mod.= 0.983 id.= 1.329 dev=  0.346 sig.= 0.014
B     75 GLY C   . - B     76 GLU N   . mod.= 1.181 id.= 1.329 dev=  0.148 sig.= 0.014
B     89 GLY N   . - B     89 GLY CA  . mod.= 1.684 id.= 1.458 dev= -0.226 sig.= 0.021
C     12 UNK C   . - C     13 UNK N   . mod.= 1.112 id.= 1.329 dev=  0.217 sig.= 0.014
C     20 UNK C   . - C     21 UNK N   . mod.= 1.006 id.= 1.329 dev=  0.323 sig.= 0.014
C     21 UNK C   . - C     22 UNK N   . mod.= 1.060 id.= 1.329 dev=  0.269 sig.= 0.014
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    106 GLY O     - A    107 VAL N     mod.=  94.73 id.= 123.00 dev= 28.266 sig.=  1.600
A    106 GLY CA    - A    107 VAL N     mod.= 144.33 id.= 116.20 dev=-28.132 sig.=  2.000
A    106 GLY C     - A    107 VAL CA    mod.= 145.83 id.= 121.70 dev=-24.129 sig.=  1.800
A    107 VAL O     - A    108 THR N     mod.=  99.42 id.= 123.00 dev= 23.579 sig.=  1.600
A    107 VAL CA    - A    108 THR N     mod.= 139.62 id.= 116.20 dev=-23.421 sig.=  2.000
A    108 THR C     - A    109 PRO CD    mod.=  68.32 id.= 125.00 dev= 56.682 sig.=  4.100
A    109 PRO N     - A    109 PRO CG    mod.=  78.82 id.= 103.20 dev= 24.380 sig.=  1.500
A    120 ASP O     - A    121 THR N     mod.= 100.87 id.= 123.00 dev= 22.132 sig.=  1.600
A    120 ASP CA    - A    121 THR N     mod.= 138.24 id.= 116.20 dev=-22.039 sig.=  2.000
B     37 PRO CA    - B     37 PRO CD    mod.=  81.71 id.= 112.00 dev= 30.292 sig.=  1.400
B     37 PRO N     - B     37 PRO CG    mod.=  79.63 id.= 103.20 dev= 23.565 sig.=  1.500
B     52 PRO CA    - B     52 PRO CD    mod.=  88.44 id.= 112.00 dev= 23.556 sig.=  1.400
B     52 PRO N     - B     52 PRO CG    mod.=  81.54 id.= 103.20 dev= 21.657 sig.=  1.500
B     67 GLN N     - B     67 GLN C     mod.= 150.46 id.= 111.20 dev=-39.264 sig.=  2.800
C     25 UNK N     - C     25 UNK C     mod.=  82.46 id.= 111.20 dev= 28.740 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    136 SER CA    - A    137 ASP CA    mod.=-119.67 id.= 180.00 per.= 1 dev= -60.33 sig.=   5.00
B     34 UNK CA    - B     35 UNK CA    mod.= 117.72 id.= 180.00 per.= 1 dev=  62.28 sig.=   5.00
B     52 PRO CA    - B     53 GLY CA    mod.=-125.50 id.= 180.00 per.= 1 dev= -54.50 sig.=   5.00
B     53 GLY CA    - B     54 GLY CA    mod.=-119.90 id.= 180.00 per.= 1 dev= -60.10 sig.=   5.00
B     90 SER CA    - B     91 GLY CA    mod.= -99.30 id.= 180.00 per.= 1 dev= -80.70 sig.=   5.00
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A    108 THR C     deviation=   0.21 sigma.=   0.02
Atom: A    109 PRO N     deviation=  -0.38 sigma.=   0.02
Atom: B     36 UNK C     deviation=   0.20 sigma.=   0.02
Atom: B     37 PRO N     deviation=  -0.44 sigma.=   0.02
Atom: B     52 PRO N     deviation=  -0.26 sigma.=   0.02
 
    ****                    VDW outliers                    ****
 
VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored
 
A     97 UNK N   . - A    124 ARG CG  . mod.= 1.447 id.= 3.520 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0
A     97 UNK N   . - A    124 ARG CD  . mod.= 0.948 id.= 3.520 dev= -2.57 sig.= 0.20 sym.=  1  0  0  0
A     97 UNK CA  . - A    124 ARG CD  . mod.= 1.290 id.= 3.870 dev= -2.58 sig.= 0.20 sym.=  1  0  0  0
A     97 UNK C   . - A    124 ARG CD  . mod.= 1.643 id.= 3.670 dev= -2.03 sig.= 0.20 sym.=  1  0  0  0
A     97 UNK C   . - A    124 ARG NE  . mod.= 0.991 id.= 3.350 dev= -2.36 sig.= 0.20 sym.=  1  0  0  0
A     97 UNK O   . - A    124 ARG CZ  . mod.= 0.881 id.= 3.270 dev= -2.39 sig.= 0.20 sym.=  1  0  0  0
A     99 UNK CB  . - A    103 GLU OE1 . mod.= 1.275 id.= 3.460 dev= -2.19 sig.= 0.20 sym.=  1  0  0  0
A    105 LEU CD2 . - A    117 LEU CD2 . mod.= 1.792 id.= 3.880 dev= -2.09 sig.= 0.20 sym.=  1  0  0  0
A    124 ARG NH1 . - B     68 LEU CD1 . mod.= 1.365 id.= 3.540 dev= -2.18 sig.= 0.20 sym.=  1  0  0  0
A    137 ASP OD1 . - A    138 PRO CD  . mod.= 0.788 id.= 3.440 dev= -2.65 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG CG  . - B     42 GLU OE1 . mod.= 1.396 id.= 3.440 dev= -2.04 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG NE  . - B     42 GLU CD  . mod.= 1.289 id.= 3.350 dev= -2.06 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG CZ  . - B     42 GLU CG  . mod.= 0.773 id.= 3.670 dev= -2.90 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG CZ  . - B     42 GLU CD  . mod.= 1.181 id.= 3.500 dev= -2.32 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG NH1 . - B     42 GLU CG  . mod.= 1.076 id.= 3.520 dev= -2.44 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG NH1 . - B     42 GLU CB  . mod.= 0.497 id.= 3.520 dev= -3.02 sig.= 0.20 sym.=  1  0  0  0
B     40 ARG NH2 . - B     42 GLU CG  . mod.= 1.278 id.= 3.520 dev= -2.24 sig.= 0.20 sym.=  1  0  0  0
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.193648    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.050     0.022
Bond angles  : refined atoms                   1703     4.403     1.960
Torsion angles, period  1. refined              172    15.113     5.000
Torsion angles, period  2. refined               42    37.997    24.048
Torsion angles, period  3. refined              189     6.834    15.000
Torsion angles, period  4. refined                6     5.919    15.000
Chiral centres: refined atoms                   208     0.179     0.200
Planar groups: refined atoms                    928     0.025     0.020
VDW repulsions: refined atoms                   865     0.654     0.200
VDW; torsion: refined atoms                     867     0.362     0.200
HBOND: refined atoms                             53     0.563     0.200
VDW repulsions; symmetry: refined atoms          42     0.457     0.200
M. chain bond B values: refined atoms           863     0.000     1.500
M. chain angle B values: refined atoms         1350     0.000     2.000
S. chain bond B values: refined atoms           391     0.000     3.000
S. chain angle B values: refined atoms          353     0.000     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.480, B  = -47.873
Partial structure    1: scale =    0.311, B  =  21.740
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   556.8   466.7  0.44  0.52       5   649.0   553.1  0.28  0.32
 0.008      70  98.63   828.7   640.4  0.34  0.36       2   486.3   163.4  0.66  0.53
 0.013      80 100.00   753.5   689.7  0.33  0.34       9   639.9   540.4  0.46  0.54
 0.017      93 100.00   536.3   505.4  0.34  0.34       6   576.6   442.6  0.38  0.37
 0.022     102 100.00   517.9   499.2  0.45  0.46       4   710.6   514.3  0.62  0.50
 0.027     129 100.00   538.6   550.6  0.38  0.37       2   832.5   502.4  0.40  0.41
 0.032     112  98.41   533.7   556.9  0.49  0.47      12   604.1   504.3  0.40  0.34
 0.037     125 100.00   683.3   641.1  0.38  0.38       9   727.4   636.5  0.44  0.37
 0.042     141 100.00   754.7   735.3  0.35  0.36       5   867.0   668.5  0.23  0.27
 0.047     148 100.00   731.8   663.1  0.37  0.38       3   667.0   590.6  0.43  0.44
 0.051     159 100.00   734.1   667.4  0.35  0.35       6   888.7   650.7  0.27  0.23
 0.056     159 100.00   828.8   708.4  0.33  0.34       4   649.9   603.1  0.56  0.55
 0.061     158 100.00   740.9   607.3  0.37  0.36       9   733.7   360.5  0.58  0.57
 0.066     167 100.00   657.0   556.8  0.41  0.40       6   717.1   525.8  0.44  0.44
 0.071     181 100.00   677.6   578.2  0.42  0.40       5   884.9   582.9  0.40  0.41
 0.076     180 100.00   687.0   591.7  0.41  0.40      11   701.9   538.2  0.42  0.47
 0.081     178 100.00   660.0   598.2  0.38  0.37      14   526.2   535.4  0.49  0.47
 0.085     185 100.00   593.4   546.2  0.44  0.42       8   473.7   431.4  0.74  0.61
 0.090     194 100.00   557.6   503.9  0.44  0.43      11   742.7   517.0  0.39  0.40
 0.095     192 100.00   585.6   569.2  0.41  0.40      12   424.9   357.5  0.46  0.43
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    1. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.925    46   0.941  0.895
  0.0077    30   0.948    40   0.941    70   0.944  0.892
  0.0126    41   0.922    39   0.879    80   0.901  0.890
  0.0175    56   0.934    37   0.797    93   0.880  0.889
  0.0223    64   0.919    38   0.839   102   0.889  0.888
  0.0272    81   0.932    48   0.837   129   0.897  0.887
  0.0320    73   0.926    39   0.870   112   0.906  0.885
  0.0369    86   0.916    39   0.864   125   0.900  0.884
  0.0418   100   0.945    41   0.843   141   0.915  0.884
  0.0466   109   0.929    39   0.833   148   0.904  0.883
  0.0515   113   0.920    46   0.824   159   0.892  0.882
  0.0563   114   0.934    45   0.902   159   0.925  0.881
  0.0612   122   0.928    36   0.798   158   0.899  0.880
  0.0661   124   0.895    43   0.825   167   0.877  0.880
  0.0709   141   0.898    40   0.720   181   0.859  0.879
  0.0758   133   0.906    47   0.655   180   0.841  0.878
  0.0806   140   0.892    38   0.806   178   0.874  0.878
  0.0855   145   0.886    40   0.754   185   0.857  0.877
  0.0904   152   0.869    42   0.747   194   0.843  0.876
  0.0952   151   0.878    41   0.798   192   0.861  0.876
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.3896
Free R factor                        =     0.4406
Overall weighted R factor            =     0.3885
Free weighted R factor               =     0.4340
Overall correlation coefficient      =     0.6297
Free correlation coefficient         =     0.5329
DPI based on free R factor           =     0.9531
Overall figure of merit              =     0.8837
ML based su of positional parameters =     0.8548
ML based su of thermal parameters    =    47.1747
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      2
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.340322    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.065     0.022
Bond angles  : refined atoms                   1703     5.299     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.483, B  = -13.479
Partial structure    1: scale =    0.311, B  =  -6.884
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3314
Free R factor                        =     0.4055
Overall figure of merit              =     0.8893
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Not converging with gamma equal   0.0000000E+00
 Trying gamma equal   5.5000003E-02
 Gamma decreased to   4.4000003E-02
 
 
     CGMAT cycle number =      3
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.866606    
 special position -----------   3.413604    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.061     0.022
Bond angles  : refined atoms                   1703     4.758     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.483, B  = -13.581
Partial structure    1: scale =    0.312, B  =  -1.015
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.3105
Free R factor                        =     0.3929
Overall figure of merit              =     0.8917
-----------------------------------------------------------------------------
 Trying gamma equal   4.4000003E-02
 Gamma decreased to   3.4000002E-02
 
 
     CGMAT cycle number =      4
 
 weigth matrix   9.9999994E-02
 
 
 special position -----------   3.785506    
 special position -----------   3.482043    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.062     0.022
Bond angles  : refined atoms                   1703     4.654     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.484, B  = -13.679
Partial structure    1: scale =    0.312, B  =  -0.111
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2993
Free R factor                        =     0.3864
Overall figure of merit              =     0.8933
-----------------------------------------------------------------------------
 Trying gamma equal   3.4000002E-02
 Gamma decreased to   2.4909092E-02
 
 
     CGMAT cycle number =      5
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.820793    
 special position -----------   3.556735    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.063     0.022
Bond angles  : refined atoms                   1703     4.614     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.484, B  = -13.938
Partial structure    1: scale =    0.310, B  =   1.072
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2925
Free R factor                        =     0.3862
Overall figure of merit              =     0.8941
-----------------------------------------------------------------------------
 Trying gamma equal   2.4909092E-02
 Gamma decreased to   1.6644629E-02
 
 
     CGMAT cycle number =      6
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.717989    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.063     0.022
Bond angles  : refined atoms                   1703     4.574     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.484, B  = -14.011
Partial structure    1: scale =    0.310, B  =   0.654
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2874
Free R factor                        =     0.3847
Overall figure of merit              =     0.8947
-----------------------------------------------------------------------------
 Trying gamma equal   1.6644629E-02
 Gamma decreased to   9.1314809E-03
 
 
     CGMAT cycle number =      7
 
 weigth matrix   0.1000000    
 
 
 special position -----------   3.892307    
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.062     0.022
Bond angles  : refined atoms                   1703     4.537     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.484, B  = -14.207
Partial structure    1: scale =    0.310, B  =   1.120
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2835
Free R factor                        =     0.3827
Overall figure of merit              =     0.8949
-----------------------------------------------------------------------------
 Trying gamma equal   9.1314809E-03
 Gamma decreased to   2.3013467E-03
 
 
     CGMAT cycle number =      8
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.062     0.022
Bond angles  : refined atoms                   1703     4.500     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.485, B  = -14.339
Partial structure    1: scale =    0.310, B  =   2.082
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2801
Free R factor                        =     0.3849
Overall figure of merit              =     0.8950
-----------------------------------------------------------------------------
 Trying gamma equal   2.3013467E-03
 Not converging with gamma equal   2.3013467E-03
 Trying gamma equal   3.6452018E-02
 Gamma decreased to   2.9621884E-02
 
 
     CGMAT cycle number =      9
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.062     0.022
Bond angles  : refined atoms                   1703     4.462     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.485, B  = -14.313
Partial structure    1: scale =    0.308, B  =   0.494
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2781
Free R factor                        =     0.3841
Overall figure of merit              =     0.8953
-----------------------------------------------------------------------------
 Trying gamma equal   2.9621884E-02
 Gamma decreased to   2.3412671E-02
 
 
     CGMAT cycle number =     10
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    137 ASP C   . - A    138 PRO N   . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    106 GLY C     - A    107 VAL CA    mod.= 101.87 id.= 121.70 dev= 19.833 sig.=  1.800
A    107 VAL N     - A    107 VAL C     mod.= 141.06 id.= 111.20 dev=-29.859 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    137 ASP CA    - A    138 PRO CA    mod.= 114.58 id.= 180.00 per.= 1 dev=  65.42 sig.=   5.00
B     34 UNK CA    - B     35 UNK CA    mod.= 120.39 id.= 180.00 per.= 1 dev=  59.61 sig.=   5.00
B     52 PRO CA    - B     53 GLY CA    mod.=-123.26 id.= 180.00 per.= 1 dev= -56.74 sig.=   5.00
B     90 SER CA    - B     91 GLY CA    mod.= -93.50 id.= 180.00 per.= 1 dev= -86.50 sig.=   5.00
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A    109 PRO N     deviation=  -0.20 sigma.=   0.02
 
    ****                    VDW outliers                    ****
 
VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored
 
A    137 ASP OD1 . - A    138 PRO CD  . mod.= 1.371 id.= 3.440 dev= -2.07 sig.= 0.20 sym.=  1  0  0  0
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.061     0.022
Bond angles  : refined atoms                   1703     4.427     1.960
Torsion angles, period  1. refined              172    16.779     5.000
Torsion angles, period  2. refined               42    41.314    24.048
Torsion angles, period  3. refined              189    22.708    15.000
Torsion angles, period  4. refined                6    18.244    15.000
Chiral centres: refined atoms                   208     0.267     0.200
Planar groups: refined atoms                    928     0.016     0.020
VDW repulsions: refined atoms                   710     0.462     0.200
VDW; torsion: refined atoms                     863     0.388     0.200
HBOND: refined atoms                             54     0.340     0.200
VDW repulsions; symmetry: refined atoms          35     0.305     0.200
HBOND; symmetry: refined atoms                    1     0.110     0.200
M. chain bond B values: refined atoms           894     0.000     1.500
M. chain angle B values: refined atoms         1350     0.000     2.000
S. chain bond B values: refined atoms           413     0.799     3.000
S. chain angle B values: refined atoms          353     1.473     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.487, B  = -13.964
Partial structure    1: scale =    0.308, B  =  -2.091
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   547.9   470.8  0.39  0.47       5   638.6   521.6  0.38  0.46
 0.008      70  98.63   815.4   651.2  0.32  0.35       2   478.5   204.5  0.76  0.64
 0.013      80 100.00   741.4   686.9  0.27  0.29       9   629.6   514.2  0.30  0.33
 0.017      93 100.00   527.7   517.6  0.32  0.32       6   567.3   397.9  0.45  0.45
 0.022     102 100.00   509.5   496.7  0.39  0.40       4   699.2   413.4  0.44  0.36
 0.027     129 100.00   530.0   523.8  0.36  0.37       2   819.2   530.4  0.35  0.39
 0.032     112  98.41   525.1   536.5  0.38  0.38      12   594.4   490.1  0.41  0.38
 0.037     125 100.00   672.3   649.2  0.32  0.33       9   715.7   791.8  0.32  0.31
 0.042     141 100.00   742.6   732.5  0.26  0.26       5   853.1   632.6  0.26  0.27
 0.047     148 100.00   720.0   677.5  0.24  0.24       3   656.3   451.2  0.69  0.64
 0.051     159 100.00   722.3   698.7  0.25  0.25       6   874.4   736.8  0.18  0.17
 0.056     159 100.00   815.5   738.6  0.25  0.25       4   639.4   640.4  0.36  0.36
 0.061     158 100.00   729.0   664.2  0.25  0.26       9   721.9   390.2  0.51  0.53
 0.066     167 100.00   646.4   608.5  0.26  0.27       6   705.6   618.7  0.40  0.37
 0.071     181 100.00   666.7   612.3  0.26  0.27       5   870.7   792.7  0.16  0.18
 0.076     180 100.00   676.0   625.1  0.26  0.26      11   690.6   569.8  0.39  0.39
 0.081     178 100.00   649.4   607.2  0.25  0.25      14   517.7   559.2  0.41  0.39
 0.085     185 100.00   583.8   586.7  0.26  0.25       8   466.1   375.7  0.58  0.49
 0.090     194 100.00   548.7   527.7  0.27  0.26      11   730.8   582.7  0.35  0.32
 0.095     192 100.00   576.2   564.4  0.26  0.25      12   418.0   399.7  0.50  0.47
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   10. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.981    33   0.905    46   0.926  0.915
  0.0077    30   0.954    40   0.950    70   0.952  0.915
  0.0126    41   0.927    39   0.888    80   0.908  0.916
  0.0175    56   0.937    37   0.825    93   0.892  0.916
  0.0223    64   0.928    38   0.855   102   0.901  0.916
  0.0272    81   0.934    48   0.843   129   0.900  0.917
  0.0320    73   0.934    39   0.869   112   0.911  0.917
  0.0369    86   0.927    39   0.860   125   0.906  0.917
  0.0418   100   0.953    41   0.843   141   0.921  0.917
  0.0466   109   0.938    39   0.865   148   0.918  0.917
  0.0515   113   0.928    46   0.838   159   0.902  0.918
  0.0563   114   0.947    45   0.904   159   0.935  0.918
  0.0612   122   0.941    36   0.837   158   0.917  0.918
  0.0661   124   0.910    43   0.824   167   0.888  0.918
  0.0709   141   0.913    40   0.737   181   0.874  0.918
  0.0758   133   0.924    47   0.652   180   0.853  0.918
  0.0806   140   0.905    38   0.829   178   0.889  0.919
  0.0855   145   0.901    40   0.799   185   0.879  0.919
  0.0904   152   0.885    42   0.788   194   0.864  0.919
  0.0952   151   0.894    41   0.795   192   0.873  0.919
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.2761
Free R factor                        =     0.3848
Overall weighted R factor            =     0.2830
Free weighted R factor               =     0.3781
Overall correlation coefficient      =     0.8118
Free correlation coefficient         =     0.6305
DPI based on free R factor           =     0.8326
Overall figure of merit              =     0.8957
ML based su of positional parameters =     0.6276
ML based su of thermal parameters    =    34.2870
-----------------------------------------------------------------------------
 Trying gamma equal   2.3412671E-02
 Gamma decreased to   1.7767932E-02
 
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    137 ASP C   . - A    138 PRO N   . mod.= 1.517 id.= 1.341 dev= -0.176 sig.= 0.016
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     98 UNK C     - A     99 UNK CA    mod.= 103.32 id.= 121.70 dev= 18.377 sig.=  1.800
A    106 GLY C     - A    107 VAL CA    mod.= 101.45 id.= 121.70 dev= 20.248 sig.=  1.800
A    107 VAL N     - A    107 VAL C     mod.= 142.08 id.= 111.20 dev=-30.881 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A    137 ASP CA    - A    138 PRO CA    mod.= 114.78 id.= 180.00 per.= 1 dev=  65.22 sig.=   5.00
B     34 UNK CA    - B     35 UNK CA    mod.= 119.89 id.= 180.00 per.= 1 dev=  60.11 sig.=   5.00
B     52 PRO CA    - B     53 GLY CA    mod.=-123.53 id.= 180.00 per.= 1 dev= -56.47 sig.=   5.00
B     90 SER CA    - B     91 GLY CA    mod.= -93.13 id.= 180.00 per.= 1 dev= -86.87 sig.=   5.00
 
    ****                    VDW outliers                    ****
 
VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored
 
A    137 ASP OD1 . - A    138 PRO CD  . mod.= 1.361 id.= 3.440 dev= -2.08 sig.= 0.20 sym.=  1  0  0  0
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz 

 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1254     0.061     0.022
Bond angles  : refined atoms                   1703     4.388     1.960
Torsion angles, period  1. refined              172    16.834     5.000
Torsion angles, period  2. refined               42    42.053    24.048
Torsion angles, period  3. refined              189    22.766    15.000
Torsion angles, period  4. refined                6    19.290    15.000
Chiral centres: refined atoms                   208     0.271     0.200
Planar groups: refined atoms                    928     0.016     0.020
VDW repulsions: refined atoms                   705     0.457     0.200
VDW; torsion: refined atoms                     862     0.386     0.200
HBOND: refined atoms                             55     0.332     0.200
VDW repulsions; symmetry: refined atoms          33     0.317     0.200
HBOND; symmetry: refined atoms                    1     0.162     0.200
M. chain bond B values: refined atoms           893     0.000     1.500
M. chain angle B values: refined atoms         1350     0.000     2.000
S. chain bond B values: refined atoms           414     0.783     3.000
S. chain angle B values: refined atoms          353     1.412     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.487, B  = -14.084
Partial structure    1: scale =    0.307, B  =  -0.930
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   547.8   472.6  0.39  0.48       5   638.5   524.6  0.39  0.46
 0.008      70  98.63   815.3   655.6  0.32  0.35       2   478.4   212.3  0.74  0.63
 0.013      80 100.00   741.4   688.5  0.27  0.29       9   629.6   515.3  0.29  0.32
 0.017      93 100.00   527.7   516.7  0.33  0.32       6   567.3   397.4  0.45  0.45
 0.022     102 100.00   509.5   499.1  0.39  0.40       4   699.2   410.2  0.44  0.36
 0.027     129 100.00   529.9   523.4  0.36  0.37       2   819.1   533.6  0.35  0.39
 0.032     112  98.41   525.1   536.4  0.37  0.37      12   594.4   484.6  0.41  0.39
 0.037     125 100.00   672.3   650.6  0.31  0.33       9   715.6   798.5  0.32  0.32
 0.042     141 100.00   742.5   731.5  0.26  0.26       5   853.0   631.9  0.26  0.27
 0.047     148 100.00   719.9   676.3  0.23  0.24       3   656.2   443.0  0.70  0.65
 0.051     159 100.00   722.2   697.8  0.25  0.25       6   874.4   735.8  0.18  0.17
 0.056     159 100.00   815.4   738.9  0.25  0.25       4   639.4   632.5  0.34  0.34
 0.061     158 100.00   728.9   665.0  0.25  0.25       9   721.8   395.5  0.51  0.53
 0.066     167 100.00   646.4   609.9  0.26  0.27       6   705.6   613.2  0.40  0.37
 0.071     181 100.00   666.7   612.6  0.26  0.27       5   870.6   813.1  0.18  0.20
 0.076     180 100.00   675.9   625.6  0.26  0.26      11   690.5   570.2  0.39  0.39
 0.081     178 100.00   649.3   607.9  0.25  0.25      14   517.7   559.3  0.40  0.38
 0.085     185 100.00   583.8   589.1  0.26  0.25       8   466.1   358.9  0.60  0.52
 0.090     194 100.00   548.6   526.8  0.27  0.26      11   730.7   583.2  0.37  0.34
 0.095     192 100.00   576.2   564.4  0.25  0.24      12   418.0   403.7  0.48  0.45
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   11. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.903    46   0.925  0.915
  0.0077    30   0.953    40   0.950    70   0.951  0.915
  0.0126    41   0.926    39   0.891    80   0.909  0.915
  0.0175    56   0.937    37   0.826    93   0.893  0.915
  0.0223    64   0.928    38   0.855   102   0.901  0.916
  0.0272    81   0.934    48   0.843   129   0.900  0.916
  0.0320    73   0.934    39   0.869   112   0.911  0.916
  0.0369    86   0.927    39   0.861   125   0.906  0.916
  0.0418   100   0.953    41   0.841   141   0.920  0.916
  0.0466   109   0.937    39   0.864   148   0.918  0.916
  0.0515   113   0.928    46   0.836   159   0.901  0.916
  0.0563   114   0.947    45   0.903   159   0.934  0.916
  0.0612   122   0.941    36   0.839   158   0.918  0.916
  0.0661   124   0.910    43   0.825   167   0.888  0.916
  0.0709   141   0.913    40   0.736   181   0.874  0.916
  0.0758   133   0.924    47   0.652   180   0.853  0.916
  0.0806   140   0.905    38   0.836   178   0.890  0.916
  0.0855   145   0.901    40   0.798   185   0.879  0.916
  0.0904   152   0.885    42   0.795   194   0.865  0.916
  0.0952   151   0.894    41   0.797   192   0.874  0.916
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.2741
Free R factor                        =     0.3856
Overall weighted R factor            =     0.2809
Free weighted R factor               =     0.3788
Overall correlation coefficient      =     0.8143
Free correlation coefficient         =     0.6291
DPI based on free R factor           =     0.8343
Overall figure of merit              =     0.8958
ML based su of positional parameters =     0.6276
ML based su of thermal parameters    =    34.2870
-----------------------------------------------------------------------------
  Time in seconds: CPU =         5.42
             Elapsed =           5.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LLG vs cycle :N:1,5:
:Geometry vs cycle:N:1,6,7,8:
$$
      Ncyc   Rfact   Rfree     FOM         LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
         0   0.390   0.441    0.884         943.4    0.050    4.403    0.179
         1   0.331   0.405    0.889         279.2    0.065    5.299    0.245
         2   0.310   0.393    0.892          56.8    0.061    4.758    0.221
         3   0.299   0.386    0.893         -85.2    0.062    4.654    0.229
         4   0.292   0.386    0.894        -162.9    0.063    4.614    0.238
         5   0.287   0.385    0.895        -222.6    0.063    4.574    0.246
         6   0.284   0.383    0.895        -255.3    0.062    4.537    0.253
         7   0.280   0.385    0.895        -277.0    0.062    4.500    0.258
         8   0.278   0.384    0.895        -297.9    0.062    4.462    0.263
         9   0.276   0.385    0.896        -329.6    0.061    4.427    0.267
        10   0.274   0.386    0.896        -338.8    0.061    4.388    0.271
 $$

 Refmac_5.3.0037:  End of Refmac_5.3.0037
Times: User:       8.1s System:    0.4s Elapsed:     0:09  
# /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/cbuccaneer -stdin
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.0: cbuccaneer         version 1.0.0     : 04/10/07##
 ###############################################################
 User: cowtan  Run date: 20/11/2007 Run time: 15:13:36 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2007 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$

title 	[No title given]
pdbin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	/*/*/[FP.F_sigF.F,FP.F_sigF.sigF]
colin-ref-hl 	/*/*/[FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D]
seqin-wrk 	/home/cowtan/test/1vjf.seq
mtzin-wrk 	/home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
colin-wrk-fo 	/*/*/[FP,SIGFP]
colin-wrk-free 	/*/*/[FreeR_flag]
colin-wrk-phifom 	/*/*/[PHCOMB,FOM]
pdbin-wrk 	/home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
pdbout-wrk 	/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
find
grow
join
link
sequence
correct
filter
ncsbuild
prune
rebuild
cycles 	1
correlation-mode
sequence-reliability 	0.95
new-residue-name 	UNK
resolution 	2.0

Cycle: 1

 C-alphas after finding:    199
 C-alphas after growing:    273
 C-alphas after joining:    193
 C-alphas linked:           0
 C-alphas sequenced:        169
 C-alphas corrected:        0
 C-alphas after filtering:  179
 C-alphas after NCS build:  179
 C-alphas after pruning:    170
 C-alphas after rebuilding: 170


Internal cycle   1
  170 residues were built in  2 chains, the longest having  127 residues.
  165 residues were sequenced, after pruning.


$TEXT:Result: $$ $$
  170 residues were built in  2 chains, the longest having  127 residues.
  165 residues were sequenced, after pruning.
$$


cbuccaneer: Normal termination
Times: User:      90.1s System:    0.3s Elapsed:     1:31  
# /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/bin/refmac5 HKLIN /home/cowtan/test/1vjf-3.2A.mtz XYZIN /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb HKLOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz XYZOUT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.0: Refmac_5.3.0037    version 5.3.0037  : 03/29/06##
 ###############################################################
 User: cowtan  Run date: 20/11/2007 Run time: 15:15:07 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ comment $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 Data line--- title [No title given]
 TITL
 Data line--- weight MATRIX 0.1
 WEIG
 Data line--- labin HLA=pirate.ABCD.A HLB=pirate.ABCD.B HLC=pirate.ABCD.C HLD=pirate.ABCD.D FREE=FreeR_flag FP=FP SIGFP=SIGFP
 LABI
 Data line--- make check NONE
 MAKE
 Data line--- make hydrogen YES hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
 MAKE
 Data line--- refi type REST PHASE SCBL 1.0 BBLU 0.0 resi MLKF meth CGMAT bref ISOT
 REFI
 Data line--- ncyc 10
 NCYC
 Data line--- scal type SIMP LSSC ANISO EXPE
 SCAL
 Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
 SOLV
 Data line--- monitor MEDIUM torsion 10.0 distance 10.0 angle 10.0 plane 10.0 chiral 10.0 bfactor 10.0 bsphere 10.0 rbond 10.0 ncsr 10.0
 MONI
 Data line--- labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB
 LABO
 Data line--- PNAME buccaneer
 PNAM
 Data line--- DNAME buccaneer
 DNAM
 Data line--- RSIZE 80
 RSIZ
 Data line--- END
 END 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /home/cowtan/test/1vjf-3.2A.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/syminfo.lib

 
    ****           Input and Default parameters#            ****
 
 
Input coordinate file.  Logical name - XYZIN actual file name  - /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /home/cowtan/test/1vjf-3.2A.mtz
Output reflection file. Logical name - HKLOUT actual file name - /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz
 
Cell from mtz :    50.903    50.903   121.411    90.000    90.000    90.000
Space group from mtz: number -   96; name - P43212
 
  Refinement type                        : Restrained
 
 
    ****                 Makecif parameters                 ****
 
Dictionary files for restraints : /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens in input coordinate file will be kept
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically
 
 
  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00
 
    ****          Least-square scaling parameters           ****
 
Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800
 
  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0049
  Refinement of individual isotropic Bfactors
  Refinement resln        :    46.9323  3.2002
  Estimated number of reflections :       3404
  Free R exclusion - flag equals:     0
  Weighting by comparison of trace of matrix
  Weighting parameters   :     0.1000
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian
  using working set of reflns and experimental sigmas
 
  Estimation of SigmaA Using 2 Gaussians:
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation
 
  Scaling and SigmaA resln:    46.9323  3.2002
 
  Damping factors:     1.0000  1.0000
 
 
    ****          Geometry restraints and weights           ****
 
 
                                              Sigma:
 Bonding distances
          Weight =  1.00
 
 Bond angles
          Weight =  1.00
 
 Planar groups
          WEIGHT= 1.00
 
 Chiral centers
          Weight= 1.00
 
 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)
 
 TORSION ANGLES
          Weight= 1.00
 
 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)         1.50A**2
     Main chain angle (1-3 neighbour)        2.00A**2
     Side chain bond                         3.00A**2
     Side chain angle                        4.50A**2
 
 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00
 
 RADIUS OF CONFIDENCE
     Positional parameters 0.30A
     Thermal parameters    0.03A**2
     Occupancy parameters  0.50
 
Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------
 
 Input file :/home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      4.12
 _lib_update       20/09/07
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          :  2436
                with complete description    :   454
  NUMBER OF MODIFICATIONS                    :    47
  NUMBER OF LINKS                            :    64
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/lib/data/atomsf.lib


  Number of atoms    :    1287
  Number of residues :     170
  Number of chains   :       2
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =     88.83
            ch:BB   res: 138  PRO      --> 139  VAL
  INFO:     link is found (not be used) dist=   1.616 ideal_dist=   1.457
            ch:AA   res: 117  LEU      at:CD1 .->ch:AA   res: 127  PHE      at:CZ  .
  INFO:     link is found (not be used) dist=   1.526 ideal_dist=   1.195
            ch:AA   res: 137  ASP      at:OD1 .->ch:BB   res: 138  PRO      at:N   .
  INFO:     link is found (not be used) dist=   1.473 ideal_dist=   1.337
            ch:AA   res: 137  ASP      at:OD1 .->ch:BB   res: 138  PRO      at:CG  .
  INFO:     link is found (not be used) dist=   1.426 ideal_dist=   1.337
            ch:AA   res: 137  ASP      at:OD1 .->ch:BB   res: 138  PRO      at:CD  .
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:O    ASP       137  AA   is missing in the structure
  ATTENTION: atom:O    UNK       180  BB   is missing in the structure
  Number of chains                  :       2
  Total number of monomers          :     170
  Number of atoms                   :    1289
  Number of missing atoms           :       2
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1313
  Number of angles restraints   :    1777
  Number of torsions restraints :     898
  Number of chiralities         :     207
  Number of planar groups       :     229
 
 
 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c
 
 
  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
 
 
 Number of reflections in file       2948
 Number of reflection read           2948
 
 
     CGMAT cycle number =      1
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A     27 GLY C   . - A     28 VAL N   . mod.= 0.972 id.= 1.329 dev=  0.357 sig.= 0.014
A     28 VAL C   . - A     29 ASP N   . mod.= 1.067 id.= 1.329 dev=  0.262 sig.= 0.014
A     29 ASP N   . - A     29 ASP CA  . mod.= 1.152 id.= 1.458 dev=  0.306 sig.= 0.021
A     30 HIS C   . - A     31 LYS N   . mod.= 1.043 id.= 1.329 dev=  0.286 sig.= 0.014
A     32 THR CA  . - A     32 THR C   . mod.= 1.295 id.= 1.525 dev=  0.230 sig.= 0.021
A     36 PRO CD  . - A     36 PRO N   . mod.= 2.226 id.= 1.473 dev= -0.753 sig.= 0.014
A     37 PRO CD  . - A     37 PRO N   . mod.= 2.082 id.= 1.473 dev= -0.609 sig.= 0.014
A     52 PRO CD  . - A     52 PRO N   . mod.= 1.990 id.= 1.473 dev= -0.517 sig.= 0.014
A    105 LEU C   . - A    106 GLY N   . mod.= 1.176 id.= 1.329 dev=  0.153 sig.= 0.014
A    109 PRO CD  . - A    109 PRO N   . mod.= 1.790 id.= 1.473 dev= -0.317 sig.= 0.014
B    138 PRO CD  . - B    138 PRO N   . mod.= 2.059 id.= 1.473 dev= -0.586 sig.= 0.014
B    138 PRO C   . - B    139 VAL N   . mod.= 1.103 id.= 1.329 dev=  0.226 sig.= 0.014
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A     30 HIS O     - A     31 LYS N     mod.=  91.04 id.= 123.00 dev= 31.965 sig.=  1.600
A     30 HIS CA    - A     31 LYS N     mod.= 148.06 id.= 116.20 dev=-31.864 sig.=  2.000
A     30 HIS C     - A     31 LYS CA    mod.= 151.13 id.= 121.70 dev=-29.426 sig.=  1.800
A     32 THR O     - A     33 LEU N     mod.= 105.57 id.= 123.00 dev= 17.428 sig.=  1.600
A     35 HIS O     - A     36 PRO N     mod.=  85.16 id.= 123.00 dev= 37.840 sig.=  1.600
A     35 HIS CA    - A     36 PRO N     mod.= 154.01 id.= 116.90 dev=-37.106 sig.=  1.500
A     36 PRO CA    - A     36 PRO CD    mod.=  80.63 id.= 112.00 dev= 31.373 sig.=  1.400
A     36 PRO N     - A     36 PRO CG    mod.=  79.49 id.= 103.20 dev= 23.713 sig.=  1.500
A     37 PRO CA    - A     37 PRO CD    mod.=  82.94 id.= 112.00 dev= 29.060 sig.=  1.400
A     37 PRO N     - A     37 PRO CG    mod.=  81.37 id.= 103.20 dev= 21.826 sig.=  1.500
A     52 PRO CA    - A     52 PRO CD    mod.=  88.49 id.= 112.00 dev= 23.509 sig.=  1.400
A     52 PRO N     - A     52 PRO CG    mod.=  80.85 id.= 103.20 dev= 22.348 sig.=  1.500
A    105 LEU O     - A    106 GLY N     mod.=  91.18 id.= 123.00 dev= 31.821 sig.=  1.600
A    105 LEU CA    - A    106 GLY N     mod.= 147.90 id.= 116.20 dev=-31.705 sig.=  2.000
A    106 GLY C     - A    107 VAL CA    mod.= 103.57 id.= 121.70 dev= 18.126 sig.=  1.800
A    107 VAL N     - A    107 VAL C     mod.= 142.13 id.= 111.20 dev=-30.925 sig.=  2.800
A    109 PRO N     - A    109 PRO CG    mod.=  80.41 id.= 103.20 dev= 22.793 sig.=  1.500
B    138 PRO CA    - B    138 PRO CD    mod.=  88.71 id.= 112.00 dev= 23.294 sig.=  1.400
B    138 PRO N     - B    138 PRO CG    mod.=  79.50 id.= 103.20 dev= 23.695 sig.=  1.500
B    138 PRO O     - B    139 VAL N     mod.=  64.86 id.= 123.00 dev= 58.135 sig.=  1.600
B    138 PRO CA    - B    139 VAL N     mod.= 174.26 id.= 116.20 dev=-58.064 sig.=  2.000
B    138 PRO C     - B    139 VAL CA    mod.= 168.43 id.= 121.70 dev=-46.729 sig.=  1.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A     52 PRO CA    - A     53 GLY CA    mod.=-123.55 id.= 180.00 per.= 1 dev= -56.45 sig.=   5.00
A     90 SER CA    - A     91 GLY CA    mod.= -93.24 id.= 180.00 per.= 1 dev= -86.76 sig.=   5.00
B    138 PRO CA    - B    139 VAL CA    mod.= -88.83 id.=   0.00 per.= 1 dev=  88.83 sig.=   5.00
 
    ****      Large deviation of atoms from planarity       ****
 
Deviations from the planarity >10.000Sigma will be monitored
Atom: A     37 PRO N     deviation=  -0.32 sigma.=   0.02
Atom: A     52 PRO N     deviation=  -0.33 sigma.=   0.02
Atom: A    109 PRO N     deviation=  -0.22 sigma.=   0.02
 
    ****                    VDW outliers                    ****
 
VDW deviations from the ideal >10.000Sigma or dist <  1.000 will be monitored
 
A     32 THR CG2 . - B    150 THR CG2 . mod.= 1.776 id.= 3.880 dev= -2.10 sig.= 0.20 sym.=  1  0  0  0
A    117 LEU CD1 . - A    127 PHE CZ  . mod.= 1.616 id.= 3.760 dev= -2.14 sig.= 0.20 sym.=  1  0  0  0
A    137 ASP OD1 . - B    138 PRO CD  . mod.= 1.426 id.= 3.440 dev= -2.01 sig.= 0.20 sym.=  1  0  0  0
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.047     0.022
Bond angles  : refined atoms                   1777     5.127     1.960
Torsion angles, period  1. refined              168    16.126     5.000
Torsion angles, period  2. refined               54    37.237    23.889
Torsion angles, period  3. refined              218     7.072    15.000
Torsion angles, period  4. refined                7     8.813    15.000
Chiral centres: refined atoms                   207     0.180     0.200
Planar groups: refined atoms                    976     0.020     0.020
VDW repulsions: refined atoms                   815     0.502     0.200
VDW; torsion: refined atoms                     903     0.363     0.200
HBOND: refined atoms                             52     0.359     0.200
VDW repulsions; symmetry: refined atoms          59     0.604     0.200
HBOND; symmetry: refined atoms                    4     0.441     0.200
M. chain bond B values: refined atoms           840     0.000     1.500
M. chain angle B values: refined atoms         1342     0.000     2.000
S. chain bond B values: refined atoms           473     0.000     3.000
S. chain angle B values: refined atoms          435     0.000     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.513, B  = -44.340
Partial structure    1: scale =    0.331, B  =  19.044
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   520.9   417.0  0.44  0.50       5   607.2   579.2  0.23  0.29
 0.008      70  98.63   775.2   606.5  0.33  0.35       2   454.9   238.8  0.47  0.42
 0.013      80 100.00   704.9   626.0  0.25  0.25       9   598.7   471.1  0.42  0.50
 0.017      93 100.00   501.7   511.8  0.35  0.34       6   539.4   493.8  0.36  0.40
 0.022     102 100.00   484.5   494.7  0.37  0.37       4   664.8   502.7  0.58  0.52
 0.027     129 100.00   503.9   482.5  0.39  0.39       2   778.9   488.3  0.40  0.37
 0.032     112  98.41   499.3   509.9  0.41  0.40      12   565.2   454.9  0.37  0.34
 0.037     125 100.00   639.2   624.2  0.37  0.38       9   680.4   696.5  0.44  0.44
 0.042     141 100.00   706.0   706.4  0.29  0.31       5   811.1   613.8  0.31  0.30
 0.047     148 100.00   684.6   635.8  0.33  0.34       3   624.0   371.4  0.52  0.44
 0.051     159 100.00   686.7   618.5  0.33  0.34       6   831.4   695.0  0.24  0.25
 0.056     159 100.00   775.3   677.8  0.31  0.32       4   608.0   516.7  0.50  0.48
 0.061     158 100.00   693.1   616.5  0.31  0.31       9   686.3   424.7  0.47  0.42
 0.066     167 100.00   614.6   570.8  0.34  0.35       6   670.9   343.4  0.61  0.58
 0.071     181 100.00   633.9   553.3  0.32  0.33       5   827.9   622.9  0.35  0.37
 0.076     180 100.00   642.7   592.8  0.37  0.36      11   656.6   557.5  0.37  0.37
 0.081     178 100.00   617.4   579.4  0.32  0.32      14   492.3   472.1  0.43  0.36
 0.085     185 100.00   555.1   521.2  0.36  0.34       8   443.2   294.6  0.41  0.38
 0.090     194 100.00   521.7   484.0  0.34  0.34      11   694.8   453.9  0.41  0.37
 0.095     192 100.00   547.9   516.6  0.40  0.40      12   397.5   362.9  0.48  0.45
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle    1. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.980    33   0.908    46   0.929  0.913
  0.0077    30   0.949    40   0.943    70   0.946  0.910
  0.0126    41   0.928    39   0.878    80   0.903  0.908
  0.0175    56   0.935    37   0.829    93   0.893  0.907
  0.0223    64   0.925    38   0.861   102   0.901  0.905
  0.0272    81   0.925    48   0.817   129   0.885  0.904
  0.0320    73   0.922    39   0.865   112   0.902  0.902
  0.0369    86   0.924    39   0.851   125   0.901  0.901
  0.0418   100   0.948    41   0.847   141   0.919  0.900
  0.0466   109   0.931    39   0.847   148   0.909  0.899
  0.0515   113   0.923    46   0.824   159   0.894  0.898
  0.0563   114   0.935    45   0.901   159   0.925  0.898
  0.0612   122   0.935    36   0.821   158   0.909  0.897
  0.0661   124   0.895    43   0.802   167   0.871  0.896
  0.0709   141   0.892    40   0.712   181   0.852  0.895
  0.0758   133   0.903    47   0.632   180   0.833  0.894
  0.0806   140   0.896    38   0.796   178   0.875  0.894
  0.0855   145   0.891    40   0.741   185   0.859  0.893
  0.0904   152   0.872    42   0.748   194   0.845  0.892
  0.0952   151   0.878    41   0.809   192   0.864  0.891
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.3414
Free R factor                        =     0.4106
Overall weighted R factor            =     0.3456
Free weighted R factor               =     0.3986
Overall correlation coefficient      =     0.7216
Free correlation coefficient         =     0.5801
DPI based on free R factor           =     0.9064
Overall figure of merit              =     0.8842
ML based su of positional parameters =     0.8066
ML based su of thermal parameters    =    44.9462
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      2
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.054     0.022
Bond angles  : refined atoms                   1777     4.728     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.519, B  =  -8.761
Partial structure    1: scale =    0.327, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2820
Free R factor                        =     0.3768
Overall figure of merit              =     0.8916
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      3
 
 weigth matrix   9.9999994E-02
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.053     0.022
Bond angles  : refined atoms                   1777     4.533     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.522, B  =  -8.257
Partial structure    1: scale =    0.327, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2626
Free R factor                        =     0.3852
Overall figure of merit              =     0.8902
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      4
 
 weigth matrix   9.9999994E-02
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.056     0.022
Bond angles  : refined atoms                   1777     4.445     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.527, B  =  -7.481
Partial structure    1: scale =    0.325, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2555
Free R factor                        =     0.3855
Overall figure of merit              =     0.8932
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      5
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.056     0.022
Bond angles  : refined atoms                   1777     4.208     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.526, B  =  -8.132
Partial structure    1: scale =    0.326, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2492
Free R factor                        =     0.3836
Overall figure of merit              =     0.8922
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      6
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.057     0.022
Bond angles  : refined atoms                   1777     4.263     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.530, B  =  -7.742
Partial structure    1: scale =    0.324, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2444
Free R factor                        =     0.3721
Overall figure of merit              =     0.8947
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      7
 
 weigth matrix   9.9999994E-02
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.057     0.022
Bond angles  : refined atoms                   1777     4.136     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.530, B  =  -7.880
Partial structure    1: scale =    0.326, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2413
Free R factor                        =     0.3740
Overall figure of merit              =     0.8937
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      8
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.056     0.022
Bond angles  : refined atoms                   1777     4.096     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.534, B  =  -7.419
Partial structure    1: scale =    0.326, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2382
Free R factor                        =     0.3597
Overall figure of merit              =     0.8966
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =      9
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.056     0.022
Bond angles  : refined atoms                   1777     4.084     1.960
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.535, B  =  -7.289
Partial structure    1: scale =    0.327, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall R factor                     =     0.2361
Free R factor                        =     0.3670
Overall figure of merit              =     0.8956
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
     CGMAT cycle number =     10
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A    127 PHE CE1 . - A    127 PHE CZ  . mod.= 1.775 id.= 1.382 dev= -0.393 sig.= 0.030
A    137 ASP CG  . - A    137 ASP OD2 . mod.= 1.574 id.= 1.249 dev= -0.325 sig.= 0.019
A    137 ASP CA  . - A    137 ASP C   . mod.= 1.797 id.= 1.525 dev= -0.272 sig.= 0.021
B    145 LYS CD  . - B    145 LYS CE  . mod.= 1.823 id.= 1.520 dev= -0.303 sig.= 0.030
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    106 GLY C     - A    107 VAL CA    mod.= 102.00 id.= 121.70 dev= 19.700 sig.=  1.800
A    107 VAL N     - A    107 VAL C     mod.= 141.34 id.= 111.20 dev=-30.136 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A     52 PRO CA    - A     53 GLY CA    mod.=-126.82 id.= 180.00 per.= 1 dev= -53.18 sig.=   5.00
A     90 SER CA    - A     91 GLY CA    mod.= -85.37 id.= 180.00 per.= 1 dev= -94.63 sig.=   5.00
B    138 PRO CA    - B    139 VAL CA    mod.=-117.43 id.=   0.00 per.= 1 dev= 117.43 sig.=   5.00
 
 weigth matrix   0.1000000    
 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.054     0.022
Bond angles  : refined atoms                   1777     3.980     1.960
Torsion angles, period  1. refined              168    16.818     5.000
Torsion angles, period  2. refined               54    39.210    23.889
Torsion angles, period  3. refined              218    23.373    15.000
Torsion angles, period  4. refined                7    24.130    15.000
Chiral centres: refined atoms                   207     0.227     0.200
Planar groups: refined atoms                    976     0.012     0.020
VDW repulsions: refined atoms                   657     0.341     0.200
VDW; torsion: refined atoms                     888     0.379     0.200
HBOND: refined atoms                             47     0.333     0.200
VDW repulsions; symmetry: refined atoms          38     0.387     0.200
HBOND; symmetry: refined atoms                    1     0.188     0.200
M. chain bond B values: refined atoms           870     0.466     1.500
M. chain angle B values: refined atoms         1342     0.601     2.000
S. chain bond B values: refined atoms           501     2.367     3.000
S. chain angle B values: refined atoms          435     3.326     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.537, B  =  -7.030
Partial structure    1: scale =    0.326, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10.  v. resln :N:1,6,7,11,12:
:Cycle   10.  and  v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   497.7   415.7  0.39  0.43       5   580.1   461.8  0.34  0.41
 0.008      70  98.63   740.7   656.9  0.22  0.24       2   434.6   232.5  0.46  0.40
 0.013      80 100.00   673.5   617.6  0.22  0.23       9   572.0   461.5  0.33  0.41
 0.017      93 100.00   479.4   488.9  0.31  0.31       6   515.4   524.3  0.37  0.36
 0.022     102 100.00   462.9   475.3  0.29  0.30       4   635.1   468.6  0.55  0.52
 0.027     129 100.00   481.4   475.1  0.33  0.33       2   744.1   609.6  0.18  0.24
 0.032     112  98.41   477.0   490.4  0.29  0.29      12   540.0   432.4  0.33  0.30
 0.037     125 100.00   610.7   624.6  0.26  0.27       9   650.1   657.4  0.38  0.35
 0.042     141 100.00   674.5   671.3  0.19  0.20       5   774.9   595.5  0.23  0.24
 0.047     148 100.00   654.0   632.2  0.22  0.23       3   596.1   447.6  0.25  0.18
 0.051     159 100.00   656.1   633.8  0.19  0.19       6   794.3   709.9  0.22  0.23
 0.056     159 100.00   740.8   694.8  0.20  0.20       4   580.9   603.9  0.39  0.38
 0.061     158 100.00   662.2   598.7  0.23  0.24       9   655.7   466.7  0.36  0.38
 0.066     167 100.00   587.2   543.2  0.24  0.24       6   641.0   462.7  0.33  0.35
 0.071     181 100.00   605.6   558.4  0.22  0.23       5   790.9   825.0  0.37  0.40
 0.076     180 100.00   614.0   594.8  0.24  0.24      11   627.3   640.0  0.32  0.29
 0.081     178 100.00   589.9   554.9  0.21  0.22      14   470.3   462.2  0.31  0.29
 0.085     185 100.00   530.3   520.1  0.23  0.23       8   423.4   406.9  0.58  0.47
 0.090     194 100.00   498.4   471.1  0.24  0.23      11   663.8   516.5  0.42  0.39
 0.095     192 100.00   523.4   504.1  0.23  0.23      12   379.7   285.4  0.45  0.41
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   10. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.981    33   0.945    46   0.955  0.939
  0.0077    30   0.953    40   0.960    70   0.957  0.934
  0.0126    41   0.931    39   0.898    80   0.915  0.931
  0.0175    56   0.942    37   0.829    93   0.897  0.929
  0.0223    64   0.926    38   0.863   102   0.902  0.927
  0.0272    81   0.937    48   0.823   129   0.895  0.925
  0.0320    73   0.935    39   0.872   112   0.913  0.923
  0.0369    86   0.930    39   0.854   125   0.907  0.921
  0.0418   100   0.953    41   0.852   141   0.923  0.920
  0.0466   109   0.938    39   0.860   148   0.918  0.918
  0.0515   113   0.929    46   0.839   159   0.903  0.917
  0.0563   114   0.951    45   0.918   159   0.941  0.915
  0.0612   122   0.942    36   0.836   158   0.918  0.914
  0.0661   124   0.911    43   0.808   167   0.885  0.913
  0.0709   141   0.909    40   0.739   181   0.872  0.912
  0.0758   133   0.920    47   0.633   180   0.845  0.911
  0.0806   140   0.905    38   0.845   178   0.892  0.910
  0.0855   145   0.904    40   0.790   185   0.879  0.908
  0.0904   152   0.890    42   0.795   194   0.869  0.907
  0.0952   151   0.897    41   0.828   192   0.882  0.906
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.2345
Free R factor                        =     0.3561
Overall weighted R factor            =     0.2409
Free weighted R factor               =     0.3519
Overall correlation coefficient      =     0.8691
Free correlation coefficient         =     0.6979
DPI based on free R factor           =     0.7862
Overall figure of merit              =     0.8974
ML based su of positional parameters =     0.6422
ML based su of thermal parameters    =    35.9339
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 
 
    ****               Bond distance outliers               ****
 
Bond distance deviations from the ideal >10.000Sigma will be monitored
 
A     90 SER CB  . - A     90 SER OG  . mod.= 1.630 id.= 1.417 dev= -0.213 sig.= 0.020
A    101 MET SD  . - A    101 MET CE  . mod.= 1.538 id.= 1.791 dev=  0.253 sig.= 0.025
A    127 PHE CE1 . - A    127 PHE CZ  . mod.= 1.914 id.= 1.382 dev= -0.532 sig.= 0.030
A    137 ASP CG  . - A    137 ASP OD2 . mod.= 1.447 id.= 1.249 dev= -0.198 sig.= 0.019
B    145 LYS CD  . - B    145 LYS CE  . mod.= 1.826 id.= 1.520 dev= -0.306 sig.= 0.030
 
    ****                Bond angle outliers                 ****
 
Bond angle deviations from the ideal >10.000Sigma will be monitored
 
A    106 GLY C     - A    107 VAL CA    mod.= 102.27 id.= 121.70 dev= 19.431 sig.=  1.800
A    107 VAL N     - A    107 VAL C     mod.= 140.82 id.= 111.20 dev=-29.618 sig.=  2.800
A    137 ASP N     - A    137 ASP C     mod.= 139.88 id.= 111.20 dev=-28.678 sig.=  2.800
 
    ****               Torsion angle outliers               ****
 
Torsion angle deviations from the ideal >10.000Sigma will be monitored
 
A     52 PRO CA    - A     53 GLY CA    mod.=-127.35 id.= 180.00 per.= 1 dev= -52.65 sig.=   5.00
A     53 GLY CA    - A     54 GLY CA    mod.=-127.44 id.= 180.00 per.= 1 dev= -52.56 sig.=   5.00
A     90 SER CA    - A     91 GLY CA    mod.= -92.61 id.= 180.00 per.= 1 dev= -87.39 sig.=   5.00
B    138 PRO CA    - B    139 VAL CA    mod.=-113.87 id.=   0.00 per.= 1 dev= 113.87 sig.=   5.00
 

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz 

 
 
 
-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1313     0.054     0.022
Bond angles  : refined atoms                   1777     3.918     1.960
Torsion angles, period  1. refined              168    16.352     5.000
Torsion angles, period  2. refined               54    39.244    23.889
Torsion angles, period  3. refined              218    23.553    15.000
Torsion angles, period  4. refined                7    24.443    15.000
Chiral centres: refined atoms                   207     0.228     0.200
Planar groups: refined atoms                    976     0.012     0.020
VDW repulsions: refined atoms                   649     0.338     0.200
VDW; torsion: refined atoms                     896     0.375     0.200
HBOND: refined atoms                             48     0.330     0.200
VDW repulsions; symmetry: refined atoms          38     0.312     0.200
M. chain bond B values: refined atoms           873     0.476     1.500
M. chain angle B values: refined atoms         1342     0.627     2.000
S. chain bond B values: refined atoms           501     2.370     3.000
S. chain angle B values: refined atoms          435     3.313     4.500
-------------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
Overall               : scale =    0.537, B  =  -7.199
Partial structure    1: scale =    0.329, B  = -10.000
Overall anisotropic scale factors
   B11 =  0.00 B22 =  0.00 B33 =  0.00 B12 =  0.00 B13 =  0.00 B23 =  0.00
-----------------------------------------------------------------------------
 
-----------------------------------------------------------------------------
 
    ****      Things for loggraph, R factor and others      ****
 
 
$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.003      46  96.23   497.4   404.9  0.39  0.44       5   579.7   461.5  0.34  0.41
 0.008      70  98.63   740.2   655.3  0.21  0.23       2   434.3   237.5  0.45  0.40
 0.013      80 100.00   673.1   619.6  0.21  0.22       9   571.6   453.9  0.33  0.41
 0.017      93 100.00   479.0   488.2  0.31  0.31       6   515.0   543.2  0.40  0.38
 0.022     102 100.00   462.6   474.1  0.29  0.30       4   634.7   463.8  0.54  0.51
 0.027     129 100.00   481.1   472.4  0.32  0.32       2   743.6   622.3  0.16  0.21
 0.032     112  98.41   476.7   490.4  0.29  0.29      12   539.6   430.8  0.33  0.31
 0.037     125 100.00   610.3   626.4  0.25  0.26       9   649.7   671.7  0.37  0.34
 0.042     141 100.00   674.1   672.2  0.19  0.20       5   774.4   595.9  0.23  0.24
 0.047     148 100.00   653.6   629.8  0.22  0.22       3   595.8   479.1  0.20  0.11
 0.051     159 100.00   655.7   635.3  0.19  0.19       6   793.8   710.7  0.22  0.22
 0.056     159 100.00   740.3   694.8  0.19  0.20       4   580.5   611.5  0.39  0.37
 0.061     158 100.00   661.8   601.3  0.23  0.23       9   655.3   464.5  0.35  0.36
 0.066     167 100.00   586.8   545.2  0.23  0.23       6   640.5   454.7  0.34  0.37
 0.071     181 100.00   605.2   562.4  0.22  0.22       5   790.4   812.9  0.37  0.40
 0.076     180 100.00   613.6   594.0  0.23  0.23      11   626.9   643.7  0.35  0.32
 0.081     178 100.00   589.5   560.3  0.21  0.22      14   470.0   463.6  0.28  0.26
 0.085     185 100.00   530.0   525.0  0.23  0.23       8   423.1   399.3  0.62  0.50
 0.090     194 100.00   498.1   470.1  0.23  0.22      11   663.4   513.3  0.43  0.40
 0.095     192 100.00   523.1   509.5  0.23  0.22      12   379.5   298.8  0.42  0.38
$$
 
    ****            Fom and SigmaA vs resolution            ****
 
 $TABLE: Cycle   11. Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 $$
 $$
  0.0029    13   0.982    33   0.944    46   0.954  0.939
  0.0077    30   0.954    40   0.959    70   0.957  0.935
  0.0126    41   0.931    39   0.896    80   0.914  0.931
  0.0175    56   0.942    37   0.829    93   0.897  0.928
  0.0223    64   0.926    38   0.864   102   0.903  0.926
  0.0272    81   0.938    48   0.820   129   0.894  0.924
  0.0320    73   0.934    39   0.871   112   0.912  0.922
  0.0369    86   0.930    39   0.853   125   0.906  0.920
  0.0418   100   0.953    41   0.849   141   0.922  0.918
  0.0466   109   0.938    39   0.856   148   0.916  0.917
  0.0515   113   0.930    46   0.840   159   0.904  0.915
  0.0563   114   0.950    45   0.916   159   0.940  0.913
  0.0612   122   0.943    36   0.838   158   0.919  0.912
  0.0661   124   0.911    43   0.808   167   0.885  0.911
  0.0709   141   0.909    40   0.732   181   0.870  0.909
  0.0758   133   0.919    47   0.640   180   0.846  0.908
  0.0806   140   0.904    38   0.849   178   0.892  0.907
  0.0855   145   0.904    40   0.785   185   0.878  0.906
  0.0904   152   0.888    42   0.792   194   0.867  0.905
  0.0952   151   0.896    41   0.829   192   0.882  0.903
 $$
Resolution limits                    =     46.932     3.200
Number of used reflections           =       2799
Percentage observed                  =    99.8303
Percentage of free reflections       =     4.8606
Overall R factor                     =     0.2317
Free R factor                        =     0.3549
Overall weighted R factor            =     0.2377
Free weighted R factor               =     0.3510
Overall correlation coefficient      =     0.8723
Free correlation coefficient         =     0.6974
DPI based on free R factor           =     0.7835
Overall figure of merit              =     0.8970
ML based su of positional parameters =     0.6422
ML based su of thermal parameters    =    35.9339
-----------------------------------------------------------------------------
  Time in seconds: CPU =         5.98
             Elapsed =           6.00
 
    **** Things for loggraph, R factor and others vs cycle  ****
 
 
$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LLG vs cycle :N:1,5:
:Geometry vs cycle:N:1,6,7,8:
$$
      Ncyc   Rfact   Rfree     FOM         LLG  rmsBOND  rmsANGLE rmsCHIRAL $$
$$
         0   0.341   0.411    0.884         282.3    0.047    5.127    0.180
         1   0.282   0.377    0.892        -418.1    0.054    4.728    0.201
         2   0.263   0.385    0.890        -521.1    0.053    4.533    0.221
         3   0.256   0.386    0.893        -696.1    0.056    4.445    0.239
         4   0.249   0.384    0.892        -690.9    0.056    4.208    0.238
         5   0.244   0.372    0.895        -805.9    0.057    4.263    0.240
         6   0.241   0.374    0.894        -792.9    0.057    4.136    0.238
         7   0.238   0.360    0.897        -934.5    0.056    4.096    0.233
         8   0.236   0.367    0.896        -924.5    0.056    4.084    0.232
         9   0.234   0.356    0.897       -1025.6    0.054    3.980    0.227
        10   0.232   0.355    0.897       -1031.4    0.054    3.918    0.228
 $$

 Refmac_5.3.0037:  End of Refmac_5.3.0037
Times: User:       8.9s System:    0.4s Elapsed:     0:09  
#CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 20 Nov 2007 15:15:16 #CCP4I TERMINATION OUTPUT_FILES /home/cowtan/work/ccp4/project/393_temporary_buccaneer.pdb PROJECT /home/cowtan/work/ccp4/project/393_temporary_refmac.pdb PROJECT /home/cowtan/work/ccp4/project/393_temporary_refmac.mtz PROJECT #CCP4I MESSAGE Task completed successfully