Starting phenix.real_space_refine on Mon Sep 23 23:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xum_33474/09_2024/7xum_33474.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 1 5.60 5 S 39 5.16 5 C 3948 2.51 5 N 1045 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6155 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6154 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 33, 'TRANS': 782} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.73 Number of scatterers: 6155 At special positions: 0 Unit cell: (142.974, 91.26, 78.078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 1 28.99 S 39 16.00 O 1122 8.00 N 1045 7.00 C 3948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 956.9 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1510 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 53.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.514A pdb=" N THR A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 Processing helix chain 'A' and resid 637 through 642 removed outlier: 4.167A pdb=" N LEU A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 removed outlier: 3.965A pdb=" N VAL A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 673 removed outlier: 3.576A pdb=" N ILE A 673 " --> pdb=" O ILE A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 711 removed outlier: 3.565A pdb=" N GLY A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 Processing helix chain 'A' and resid 728 through 754 removed outlier: 4.066A pdb=" N LEU A 732 " --> pdb=" O ASN A 728 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 733 " --> pdb=" O MET A 729 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 787 removed outlier: 3.640A pdb=" N MET A 769 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 773 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 782 " --> pdb=" O ARG A 778 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 797 Processing helix chain 'A' and resid 894 through 907 removed outlier: 3.973A pdb=" N GLN A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 922 Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.811A pdb=" N PHE A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 952 removed outlier: 4.440A pdb=" N VAL A 950 " --> pdb=" O ASP A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 978 removed outlier: 3.565A pdb=" N VAL A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 967 " --> pdb=" O GLN A 963 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 989 removed outlier: 3.866A pdb=" N LEU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1004 removed outlier: 3.853A pdb=" N THR A 993 " --> pdb=" O LEU A 989 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1018 removed outlier: 3.997A pdb=" N GLU A1016 " --> pdb=" O GLY A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1065 Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.587A pdb=" N ALA A1074 " --> pdb=" O PRO A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1114 removed outlier: 3.547A pdb=" N LEU A1113 " --> pdb=" O VAL A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1157 removed outlier: 3.723A pdb=" N LEU A1154 " --> pdb=" O ASN A1150 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1155 " --> pdb=" O ARG A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1167 Processing helix chain 'A' and resid 1168 through 1175 removed outlier: 4.368A pdb=" N HIS A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1213 removed outlier: 4.094A pdb=" N VAL A1206 " --> pdb=" O ALA A1202 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS A1207 " --> pdb=" O ALA A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1235 removed outlier: 3.595A pdb=" N ALA A1227 " --> pdb=" O ASN A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1257 Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1271 through 1278 removed outlier: 3.531A pdb=" N GLN A1277 " --> pdb=" O PRO A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1340 removed outlier: 4.230A pdb=" N VAL A1308 " --> pdb=" O LEU A1304 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG A1320 " --> pdb=" O ARG A1316 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A1321 " --> pdb=" O THR A1317 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A1331 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Proline residue: A1337 - end of helix Processing helix chain 'A' and resid 1351 through 1372 removed outlier: 3.552A pdb=" N SER A1356 " --> pdb=" O PRO A1352 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1358 " --> pdb=" O MET A1354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A1361 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A1362 " --> pdb=" O ALA A1358 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1364 " --> pdb=" O ALA A1360 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A1365 " --> pdb=" O ALA A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1375 No H-bonds generated for 'chain 'A' and resid 1373 through 1375' Processing helix chain 'A' and resid 1380 through 1389 removed outlier: 3.961A pdb=" N GLN A1387 " --> pdb=" O ARG A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1400 Processing sheet with id=AA1, first strand: chain 'A' and resid 592 through 598 removed outlier: 4.648A pdb=" N TYR A 594 " --> pdb=" O LYS A 607 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 607 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 603 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS A 628 " --> pdb=" O THR A 571 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 689 removed outlier: 3.884A pdb=" N ILE A 689 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 814 through 821 removed outlier: 4.899A pdb=" N ARG A 816 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 807 " --> pdb=" O ARG A 816 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A 804 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 830 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU A 884 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 843 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 864 through 866 removed outlier: 3.937A pdb=" N ASP A 853 " --> pdb=" O ILE A 877 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 877 " --> pdb=" O ASP A 853 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1007 through 1009 removed outlier: 3.758A pdb=" N VAL A1298 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A1262 " --> pdb=" O MET A1280 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL A1282 " --> pdb=" O VAL A1262 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET A1264 " --> pdb=" O VAL A1282 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR A1023 " --> pdb=" O ALA A1263 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N VAL A1265 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET A1025 " --> pdb=" O VAL A1265 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N PHE A1240 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1218 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1038 through 1044 removed outlier: 7.224A pdb=" N ALA A1193 " --> pdb=" O MET A1040 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A1042 " --> pdb=" O MET A1191 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET A1191 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU A1044 " --> pdb=" O CYS A1189 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N CYS A1189 " --> pdb=" O LEU A1044 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU A1188 " --> pdb=" O ILE A1184 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A1184 " --> pdb=" O LEU A1188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A1190 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1182 " --> pdb=" O GLY A1190 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A1181 " --> pdb=" O GLY A1149 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A1149 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A1105 " --> pdb=" O ASP A1093 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASP A1093 " --> pdb=" O LYS A1105 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A1107 " --> pdb=" O CYS A1091 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N CYS A1091 " --> pdb=" O SER A1107 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1997 1.35 - 1.46: 1282 1.46 - 1.58: 2914 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 6260 Sorted by residual: bond pdb=" CG1 ILE A1021 " pdb=" CD1 ILE A1021 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CB ASP A1267 " pdb=" CG ASP A1267 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.51e-01 bond pdb=" C ASN A 635 " pdb=" N PRO A 636 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.77e-01 bond pdb=" CB MET A1040 " pdb=" CG MET A1040 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.97e-01 bond pdb=" C MET A1344 " pdb=" N PRO A1345 " ideal model delta sigma weight residual 1.334 1.345 -0.011 1.51e-02 4.39e+03 5.41e-01 ... (remaining 6255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8305 1.47 - 2.94: 143 2.94 - 4.42: 33 4.42 - 5.89: 13 5.89 - 7.36: 8 Bond angle restraints: 8502 Sorted by residual: angle pdb=" N VAL A1334 " pdb=" CA VAL A1334 " pdb=" C VAL A1334 " ideal model delta sigma weight residual 112.96 108.05 4.91 1.00e+00 1.00e+00 2.41e+01 angle pdb=" N VAL A1249 " pdb=" CA VAL A1249 " pdb=" C VAL A1249 " ideal model delta sigma weight residual 113.71 109.15 4.56 9.50e-01 1.11e+00 2.30e+01 angle pdb=" N GLY A 988 " pdb=" CA GLY A 988 " pdb=" C GLY A 988 " ideal model delta sigma weight residual 112.50 116.47 -3.97 1.16e+00 7.43e-01 1.17e+01 angle pdb=" CA MET A 671 " pdb=" CB MET A 671 " pdb=" CG MET A 671 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.31e+00 angle pdb=" CA VAL A1249 " pdb=" C VAL A1249 " pdb=" N ALA A1250 " ideal model delta sigma weight residual 119.87 116.50 3.37 1.34e+00 5.57e-01 6.34e+00 ... (remaining 8497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3390 17.29 - 34.59: 322 34.59 - 51.88: 61 51.88 - 69.18: 4 69.18 - 86.47: 5 Dihedral angle restraints: 3782 sinusoidal: 1444 harmonic: 2338 Sorted by residual: dihedral pdb=" CB GLU A 567 " pdb=" CG GLU A 567 " pdb=" CD GLU A 567 " pdb=" OE1 GLU A 567 " ideal model delta sinusoidal sigma weight residual 0.00 81.63 -81.63 1 3.00e+01 1.11e-03 9.11e+00 dihedral pdb=" CA HIS A1247 " pdb=" C HIS A1247 " pdb=" N LYS A1248 " pdb=" CA LYS A1248 " ideal model delta harmonic sigma weight residual 180.00 164.99 15.01 0 5.00e+00 4.00e-02 9.02e+00 dihedral pdb=" CB GLU A1293 " pdb=" CG GLU A1293 " pdb=" CD GLU A1293 " pdb=" OE1 GLU A1293 " ideal model delta sinusoidal sigma weight residual 0.00 -80.33 80.33 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 3779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 597 0.029 - 0.058: 278 0.058 - 0.087: 94 0.087 - 0.116: 69 0.116 - 0.146: 8 Chirality restraints: 1046 Sorted by residual: chirality pdb=" CA THR A 766 " pdb=" N THR A 766 " pdb=" C THR A 766 " pdb=" CB THR A 766 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ASP A1267 " pdb=" N ASP A1267 " pdb=" C ASP A1267 " pdb=" CB ASP A1267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE A1194 " pdb=" N ILE A1194 " pdb=" C ILE A1194 " pdb=" CB ILE A1194 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 1043 not shown) Planarity restraints: 1064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A1344 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A1345 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1345 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1345 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 911 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 912 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 912 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 912 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 820 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 821 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " 0.017 5.00e-02 4.00e+02 ... (remaining 1061 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 34 2.53 - 3.12: 4698 3.12 - 3.72: 9550 3.72 - 4.31: 12304 4.31 - 4.90: 20650 Nonbonded interactions: 47236 Sorted by model distance: nonbonded pdb=" CD1 ILE A 733 " pdb="CU CU A2000 " model vdw 1.938 2.660 nonbonded pdb=" OG1 THR A 804 " pdb=" O LYS A 832 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR A 858 " pdb=" OE1 GLU A 860 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG A1320 " pdb=" OE1 GLN A1372 " model vdw 2.249 3.120 nonbonded pdb=" OG SER A1398 " pdb=" OE1 GLN A1399 " model vdw 2.305 3.040 ... (remaining 47231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 6260 Z= 0.153 Angle : 0.565 7.359 8502 Z= 0.291 Chirality : 0.043 0.146 1046 Planarity : 0.003 0.041 1064 Dihedral : 13.816 86.471 2272 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 812 helix: 0.68 (0.27), residues: 380 sheet: 0.01 (0.48), residues: 117 loop : -1.02 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 779 HIS 0.002 0.000 HIS A 782 PHE 0.005 0.001 PHE A 972 TYR 0.006 0.001 TYR A 953 ARG 0.004 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.653 Fit side-chains REVERT: A 588 ARG cc_start: 0.5767 (ptm-80) cc_final: 0.5544 (ptm-80) REVERT: A 1293 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7206 (mm-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1597 time to fit residues: 24.9835 Evaluate side-chains 99 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6260 Z= 0.181 Angle : 0.561 8.481 8502 Z= 0.286 Chirality : 0.044 0.154 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.671 12.968 854 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.33 % Allowed : 11.09 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 812 helix: 0.80 (0.27), residues: 386 sheet: 0.03 (0.48), residues: 111 loop : -0.96 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1153 HIS 0.005 0.001 HIS A1312 PHE 0.008 0.001 PHE A 627 TYR 0.007 0.001 TYR A 719 ARG 0.002 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.680 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 119 average time/residue: 0.1584 time to fit residues: 26.0410 Evaluate side-chains 107 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1315 LYS Chi-restraints excluded: chain A residue 1330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6260 Z= 0.213 Angle : 0.553 6.384 8502 Z= 0.282 Chirality : 0.044 0.155 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.697 14.237 854 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.11 % Allowed : 14.50 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 812 helix: 0.77 (0.27), residues: 385 sheet: -0.07 (0.46), residues: 113 loop : -0.95 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1153 HIS 0.002 0.001 HIS A1034 PHE 0.006 0.001 PHE A 927 TYR 0.008 0.001 TYR A 953 ARG 0.002 0.000 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.700 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.1670 time to fit residues: 27.3190 Evaluate side-chains 113 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1315 LYS Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 20.0000 chunk 38 optimal weight: 0.0870 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6260 Z= 0.145 Angle : 0.534 11.061 8502 Z= 0.266 Chirality : 0.043 0.197 1046 Planarity : 0.004 0.040 1064 Dihedral : 3.654 15.142 854 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.33 % Allowed : 18.20 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.30), residues: 812 helix: 0.99 (0.27), residues: 384 sheet: 0.08 (0.47), residues: 111 loop : -0.97 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1353 HIS 0.007 0.001 HIS A1312 PHE 0.007 0.001 PHE A 627 TYR 0.005 0.001 TYR A 953 ARG 0.001 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.428 Fit side-chains REVERT: A 641 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5543 (pp) outliers start: 9 outliers final: 4 residues processed: 111 average time/residue: 0.1174 time to fit residues: 17.7964 Evaluate side-chains 102 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1330 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN A1312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6260 Z= 0.207 Angle : 0.553 9.958 8502 Z= 0.277 Chirality : 0.044 0.151 1046 Planarity : 0.004 0.039 1064 Dihedral : 3.692 14.638 854 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.25 % Allowed : 18.20 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 812 helix: 0.83 (0.27), residues: 388 sheet: -0.24 (0.45), residues: 116 loop : -0.91 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 712 HIS 0.007 0.001 HIS A1312 PHE 0.006 0.001 PHE A 927 TYR 0.007 0.001 TYR A 953 ARG 0.001 0.000 ARG A1320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.657 Fit side-chains REVERT: A 641 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5609 (pp) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.1534 time to fit residues: 24.3202 Evaluate side-chains 114 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1019 HIS Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 78 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 6260 Z= 0.155 Angle : 0.538 10.916 8502 Z= 0.264 Chirality : 0.043 0.146 1046 Planarity : 0.003 0.041 1064 Dihedral : 3.610 14.580 854 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.22 % Allowed : 19.23 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.30), residues: 812 helix: 1.11 (0.27), residues: 385 sheet: -0.26 (0.45), residues: 118 loop : -0.82 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1353 HIS 0.005 0.000 HIS A1312 PHE 0.006 0.001 PHE A 627 TYR 0.005 0.001 TYR A 953 ARG 0.001 0.000 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.671 Fit side-chains REVERT: A 641 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5573 (pp) outliers start: 15 outliers final: 8 residues processed: 116 average time/residue: 0.1561 time to fit residues: 24.7552 Evaluate side-chains 109 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1393 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 48 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1257 ASN A1312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6260 Z= 0.145 Angle : 0.536 10.939 8502 Z= 0.262 Chirality : 0.042 0.141 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.541 13.864 854 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.07 % Allowed : 19.67 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 812 helix: 1.24 (0.27), residues: 385 sheet: -0.22 (0.45), residues: 123 loop : -0.84 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1353 HIS 0.011 0.001 HIS A1312 PHE 0.006 0.001 PHE A 627 TYR 0.004 0.001 TYR A 713 ARG 0.001 0.000 ARG A 919 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.618 Fit side-chains REVERT: A 641 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5390 (pp) REVERT: A 743 TYR cc_start: 0.8195 (t80) cc_final: 0.7909 (t80) outliers start: 14 outliers final: 8 residues processed: 121 average time/residue: 0.1461 time to fit residues: 24.6482 Evaluate side-chains 109 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 GLN A1257 ASN A1312 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6260 Z= 0.175 Angle : 0.570 15.026 8502 Z= 0.276 Chirality : 0.043 0.146 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.524 13.262 854 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.37 % Allowed : 21.30 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 812 helix: 1.16 (0.27), residues: 386 sheet: -0.22 (0.45), residues: 123 loop : -0.89 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1353 HIS 0.012 0.001 HIS A1312 PHE 0.004 0.001 PHE A 927 TYR 0.005 0.001 TYR A 953 ARG 0.001 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.676 Fit side-chains REVERT: A 641 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5436 (pp) REVERT: A 916 LEU cc_start: 0.8457 (mp) cc_final: 0.8195 (pp) outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.1484 time to fit residues: 23.9388 Evaluate side-chains 111 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 GLN ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6260 Z= 0.175 Angle : 0.575 14.548 8502 Z= 0.278 Chirality : 0.043 0.147 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.520 12.701 854 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.51 % Allowed : 22.04 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 812 helix: 1.17 (0.27), residues: 385 sheet: -0.18 (0.45), residues: 123 loop : -0.89 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1353 HIS 0.013 0.001 HIS A1312 PHE 0.006 0.001 PHE A 970 TYR 0.006 0.001 TYR A 953 ARG 0.001 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.640 Fit side-chains REVERT: A 641 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5407 (pp) REVERT: A 779 TRP cc_start: 0.7445 (t60) cc_final: 0.6629 (t60) REVERT: A 916 LEU cc_start: 0.8450 (mp) cc_final: 0.8201 (pp) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.1559 time to fit residues: 23.8212 Evaluate side-chains 111 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1393 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6260 Z= 0.199 Angle : 0.621 14.485 8502 Z= 0.297 Chirality : 0.044 0.148 1046 Planarity : 0.004 0.041 1064 Dihedral : 3.617 14.810 854 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.37 % Allowed : 22.63 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.30), residues: 812 helix: 1.11 (0.27), residues: 384 sheet: -0.09 (0.45), residues: 121 loop : -0.94 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 939 HIS 0.013 0.001 HIS A1312 PHE 0.006 0.001 PHE A 970 TYR 0.007 0.001 TYR A 953 ARG 0.003 0.000 ARG A 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.666 Fit side-chains REVERT: A 641 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5394 (pp) REVERT: A 916 LEU cc_start: 0.8479 (mp) cc_final: 0.8233 (pp) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1457 time to fit residues: 22.2000 Evaluate side-chains 107 residues out of total 676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 CYS Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 1016 GLU Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1393 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 0.0970 chunk 73 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.194572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146607 restraints weight = 8317.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151148 restraints weight = 4363.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.153628 restraints weight = 3010.942| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6260 Z= 0.162 Angle : 0.592 14.210 8502 Z= 0.283 Chirality : 0.043 0.141 1046 Planarity : 0.004 0.042 1064 Dihedral : 3.547 13.940 854 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.63 % Allowed : 23.67 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.30), residues: 812 helix: 1.20 (0.27), residues: 384 sheet: -0.11 (0.45), residues: 122 loop : -0.87 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1353 HIS 0.012 0.001 HIS A1312 PHE 0.016 0.001 PHE A 764 TYR 0.008 0.001 TYR A1090 ARG 0.001 0.000 ARG A 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.14 seconds wall clock time: 33 minutes 47.37 seconds (2027.37 seconds total)