Appendix E: Test output from CCP4 REFMAC
data_phosphate_binding_protein[A197C_chromophore]
_entry.id phosphate_binding_protein
_diffrn.id A197C_chromophore
_audit.creation_date 1997-10-30T14:02:24+00:00
_software.classification refinement
_software.contact_author 'Garib N. Murshudov'
_software.contact_author_email garib@yorvic.york.ac.uk
_software.description '(un)restrained refinement or idealisation of macromolecular structure'
_software.name refmac
_software.version 'CCP4 1.0.1 16/7/97'
_Symmetry.Int_Tables_number 19
_Symmetry.space_group_name_H-M 'P 21 21 21'
loop_
_Symmetry_equiv.id
_Symmetry_equiv.pos_as_xyz
1 X,Y,Z
2 1/2-X,-Y,1/2+Z
3 -X,1/2+Y,1/2-Z
4 1/2+X,1/2-Y,-Z
_cell.length_a 41.498
_cell.length_b 62.651
_cell.length_c 122.608
_cell.angle_alpha 90.000
_cell.angle_beta 90.000
_cell.angle_gamma 90.000
_refine.ls_matrix_type ' Method of minimisation : Conjugate Direction'
_refine.ls_d_res_low 10.000
_refine.ls_d_res_high 1.600
_refine.details
;
Refinement type : Restrained
Residual : Maximum Likelihood for Fs
Experimental sigmas used for weighting
Refinement of individual isotropic Bfactors
Scaling type: FoKBFc
Scaling type: Tronrud bulk solvent Using 2 Gaussians
using working set of reflns but not experimental sigmas
Estimation of SigmaA Using 2 Gaussians:
using free set of reflns with experimental sigmas
;
_refine.ls_number_reflns_R_work 2049
_refine.ls_number_reflns_R_free 38759
_refine.ls_R_factor_R_work 0.175
_refine.ls_R_factor_R_free 0.206
_refine.ls_wR_factor_R_work 0.170
_refine.ls_percent_reflns_R_free 100.000
_refine.ebi_ls_Correlation_coeff_Fo_to_Fc 0.948289
_refine.ebi_ls_Correlation_coeff_Fo_to_Fc_Free 0.937064
_refine.ebi_ls_goodness_of_fit_work 3130.583252
_refine.ebi_ls_goodness_of_fit_FreeR 2789.774414
_refine.ebi_ls_Overall_ESU_R_Cruickshanks_DPI 0.091250
_refine.ebi_ls_Overall_ESU_Rfree 0.090438
_refine.ebi_ls_Overall_ESU_ML 0.057872
_refine.ebi_ls_Overall_ESU_B 1.647772
_refine.ebi_ls_overall_FOM_free_Rset 0.872775
_refine.ebi_ls_overall_FOM_work_Rset 0.873170
loop_
_atom_type.symbol
_atom_type.scat_Cromer_Mann_a1
_atom_type.scat_Cromer_Mann_a2
_atom_type.scat_Cromer_Mann_a3
_atom_type.scat_Cromer_Mann_a4
_atom_type.scat_Cromer_Mann_b1
_atom_type.scat_Cromer_Mann_b2
_atom_type.scat_Cromer_Mann_b3
_atom_type.scat_Cromer_Mann_b4
_atom_type.scat_Cromer_Mann_c
C 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156
N 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290
O 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508
H 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7997 0.0030
S 6.9053 1.4679 5.2034 22.2151 1.4379 0.2536 1.5863 56.1720 0.8669
P 6.4345 1.9067 4.1791 27.1570 1.7800 0.5260 1.4908 68.1645 1.1149
loop_
_refine_ls_shell.d_res_high
_refine_ls_shell.d_res_low
_refine_ls_shell.number_reflns_all
_refine_ls_shell.number_reflns_R_work
_refine_ls_shell.R_factor_R_work
_refine_ls_shell.number_reflns_R_free
_refine_ls_shell.R_factor_R_free
_refine_ls_shell.wR_factor_R_work
_refine_ls_shell.ebi_weight_used
_refine_ls_shell.ebi_weight_exp
7.92 10.00 203 193 0.287 10 0.230 0.333 51.315 8.060
6.56 7.92 296 281 0.286 15 0.314 0.301 46.462 7.298
5.59 6.56 418 393 0.261 25 0.264 0.275 46.486 7.302
4.88 5.59 539 516 0.226 23 0.257 0.241 50.127 7.874
4.32 4.88 691 648 0.188 43 0.169 0.209 54.404 8.545
3.88 4.32 859 831 0.175 28 0.159 0.192 56.278 8.840
3.52 3.88 1041 991 0.171 50 0.169 0.178 58.200 9.142
3.23 3.52 1239 1173 0.174 66 0.233 0.180 58.990 9.266
2.97 3.23 1428 1346 0.180 82 0.207 0.181 58.449 9.181
2.76 2.97 1666 1574 0.170 92 0.199 0.167 54.990 8.637
2.57 2.76 1920 1835 0.165 85 0.173 0.159 54.596 8.575
2.41 2.57 2178 2070 0.165 108 0.205 0.155 55.694 8.748
2.27 2.41 2453 2324 0.161 129 0.200 0.148 60.207 9.457
2.14 2.27 2726 2597 0.162 129 0.182 0.149 63.368 9.953
2.03 2.14 3014 2867 0.166 147 0.212 0.152 65.767 10.330
1.92 2.03 3328 3163 0.161 165 0.213 0.142 68.539 10.766
1.83 1.92 3645 3458 0.163 187 0.227 0.141 70.861 11.130
1.75 1.83 4007 3832 0.166 175 0.207 0.141 76.325 11.988
1.67 1.75 4421 4206 0.168 215 0.207 0.143 83.412 13.102
1.60 1.67 4736 4461 0.194 275 0.235 0.166 89.772 14.101
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
' Bond distances (1-2 neibours)' 2545 0.009 0.020
' Angle distances(1-3 neibours)' 3457 0.027 0.040
' Planar 1-4 distances' 910 0.038 0.050
' Bond distances (1-2 neibours)' 2545 0.009 0.020
' Angle distances(1-3 neibours)' 3457 0.027 0.040
' Planar 1-4 distances' 910 0.038 0.050
' Planarity restraints' 2200 0.021 0.015
' Chirality restraints' 377 0.105 0.150
' VDW: Single-Torsion contact' 547 0.205 0.300
' VDW: Multiple-Torsion contact' 1082 0.250 0.300
' VDW: H-bonds' 402 0.146 0.300
' Sym_VDW: Single-Torsion contact' 29 0.195 0.300
' Sym_VDW: Multiple-Torsion contact' 19 0.229 0.300
' Planar angles (0,180)' 324 4.726 7.000
' Staggered angles (+/-60,180)' 420 15.441 15.000
' Orthonormal (+/-90)' 33 30.959 20.000
' B restraints: Main chain bond' 1452 1.513 3.000
' B restraints: Main chain angle' 1730 2.037 5.000
' B restraints: Side chain bond' 1093 3.248 6.000
' B restraints: Side chain angle' 1727 4.432 8.000
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