Starting phenix.real_space_refine on Sat Sep 28 15:37:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7evn_31330/09_2024/7evn_31330.cif" } resolution = 2.6 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= 0.007 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 Zn 3 6.06 5 S 105 5.16 5 C 12414 2.51 5 N 3431 2.21 5 O 3715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19668 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 646 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6487 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 780} Chain: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "A" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9227 Classifications: {'peptide': 1177} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1116} Chain breaks: 5 Chain: "E" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 2605 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'CIS': 3, 'PTRANS': 21, 'TRANS': 461} Chain breaks: 5 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1340 Unresolved non-hydrogen angles: 1709 Unresolved non-hydrogen dihedrals: 1114 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 21, 'ARG:plan': 27, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 5, 'HIS:plan': 14, 'PHE:plan': 18, 'GLU:plan': 26, 'ASP:plan': 26} Unresolved non-hydrogen planarities: 731 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7319 SG CYS D 30 58.922 85.880 76.427 1.00 19.46 S ATOM 7340 SG CYS D 33 56.017 84.874 74.168 1.00 21.93 S ATOM 7635 SG CYS D 72 58.670 82.608 74.913 1.00 18.16 S ATOM 7659 SG CYS D 75 59.864 85.440 72.822 1.00 17.46 S ATOM 7268 SG CYS D 23 53.801 93.245 88.762 1.00 29.17 S ATOM 7292 SG CYS D 26 53.348 92.295 85.340 1.00 33.37 S ATOM 7539 SG CYS D 58 56.697 94.038 86.219 1.00 27.69 S ATOM 7560 SG CYS D 61 53.726 96.297 86.896 1.00 29.63 S ATOM 7181 SG CYS D 11 66.385 101.049 77.365 1.00 21.15 S ATOM 7444 SG CYS D 46 69.231 100.497 80.129 1.00 21.46 S ATOM 7467 SG CYS D 49 65.623 101.088 81.190 1.00 27.61 S ATOM 7738 SG CYS D 85 66.306 97.609 79.305 1.00 20.01 S Time building chain proxies: 11.06, per 1000 atoms: 0.56 Number of scatterers: 19668 At special positions: 0 Unit cell: (144.571, 150.006, 142.397, 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) Zn 3 29.99 S 105 16.00 O 3715 8.00 N 3431 7.00 C 12414 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: 5.51 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 30 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 26 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 11 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 49 " Number of angles added : 18 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 30 sheets defined 43.9% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 27 through 46 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.532A pdb=" N LEU B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'C' and resid 491 through 498 removed outlier: 4.121A pdb=" N ARG C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C 496 " --> pdb=" O GLN C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 Processing helix chain 'C' and resid 508 through 527 removed outlier: 5.545A pdb=" N ARG C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C 525 " --> pdb=" O ASP C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 540 removed outlier: 3.541A pdb=" N LEU C 531 " --> pdb=" O GLY C 527 " (cutoff:3.500A) Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 545 through 563 removed outlier: 3.606A pdb=" N LYS C 562 " --> pdb=" O ARG C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 579 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.787A pdb=" N ARG C 590 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 614 Processing helix chain 'C' and resid 615 through 618 removed outlier: 4.005A pdb=" N ASP C 618 " --> pdb=" O PRO C 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 621 through 640 Processing helix chain 'C' and resid 640 through 652 removed outlier: 3.932A pdb=" N LEU C 644 " --> pdb=" O GLY C 640 " (cutoff:3.500A) Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 657 through 676 Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.568A pdb=" N LEU C 680 " --> pdb=" O CYS C 677 " (cutoff:3.500A) Proline residue: C 681 - end of helix No H-bonds generated for 'chain 'C' and resid 677 through 681' Processing helix chain 'C' and resid 682 through 691 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.808A pdb=" N VAL C 695 " --> pdb=" O HIS C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 717 Processing helix chain 'C' and resid 727 through 738 removed outlier: 3.573A pdb=" N TRP C 732 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 778 Processing helix chain 'C' and resid 781 through 796 removed outlier: 3.591A pdb=" N LYS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 810 Processing helix chain 'C' and resid 810 through 819 removed outlier: 4.048A pdb=" N TRP C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 removed outlier: 3.548A pdb=" N ASP C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 845 removed outlier: 3.649A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 854 removed outlier: 3.897A pdb=" N ILE C 849 " --> pdb=" O GLY C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 858 removed outlier: 3.702A pdb=" N LYS C 858 " --> pdb=" O ASP C 855 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 855 through 858' Processing helix chain 'C' and resid 861 through 879 Processing helix chain 'C' and resid 888 through 902 Processing helix chain 'C' and resid 907 through 922 removed outlier: 4.299A pdb=" N LEU C 911 " --> pdb=" O ASP C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 925 No H-bonds generated for 'chain 'C' and resid 923 through 925' Processing helix chain 'C' and resid 928 through 942 removed outlier: 4.100A pdb=" N ASN C 942 " --> pdb=" O TRP C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 5.202A pdb=" N VAL C 960 " --> pdb=" O SER C 956 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL C 961 " --> pdb=" O ARG C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 981 Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.561A pdb=" N VAL C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1021 Proline residue: C1018 - end of helix Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1028 through 1046 Processing helix chain 'C' and resid 1047 through 1050 Processing helix chain 'C' and resid 1051 through 1063 Processing helix chain 'C' and resid 1064 through 1068 removed outlier: 3.788A pdb=" N LYS C1067 " --> pdb=" O GLU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1089 Processing helix chain 'C' and resid 1090 through 1104 removed outlier: 3.696A pdb=" N ALA C1095 " --> pdb=" O HIS C1091 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C1096 " --> pdb=" O ASP C1092 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C1102 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C1103 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 4.671A pdb=" N CYS C1111 " --> pdb=" O GLN C1107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1127 Processing helix chain 'C' and resid 1128 through 1137 removed outlier: 3.555A pdb=" N TYR C1136 " --> pdb=" O LEU C1132 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1159 Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.506A pdb=" N LYS C1163 " --> pdb=" O GLU C1160 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C1164 " --> pdb=" O MET C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1165 through 1178 removed outlier: 3.714A pdb=" N VAL C1169 " --> pdb=" O TYR C1165 " (cutoff:3.500A) Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.588A pdb=" N ARG C1185 " --> pdb=" O ASP C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1204 through 1216 removed outlier: 3.774A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1220 removed outlier: 4.190A pdb=" N PHE C1220 " --> pdb=" O PRO C1217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1217 through 1220' Processing helix chain 'C' and resid 1223 through 1242 Processing helix chain 'C' and resid 1242 through 1251 removed outlier: 3.726A pdb=" N MET C1246 " --> pdb=" O GLY C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1275 Processing helix chain 'C' and resid 1277 through 1283 removed outlier: 3.558A pdb=" N ILE C1281 " --> pdb=" O ASP C1278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1282 " --> pdb=" O ALA C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1298 through 1302 Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.061A pdb=" N ASP D 83 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 Processing helix chain 'A' and resid 808 through 825 Processing helix chain 'A' and resid 838 through 845 removed outlier: 3.518A pdb=" N GLU A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 4.056A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1165 Processing helix chain 'A' and resid 1176 through 1180 Processing helix chain 'A' and resid 1181 through 1185 Processing helix chain 'A' and resid 1186 through 1197 Processing helix chain 'A' and resid 1200 through 1216 removed outlier: 3.812A pdb=" N TYR A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 77 Processing helix chain 'E' and resid 115 through 132 removed outlier: 4.244A pdb=" N GLU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 155 through 167 Processing helix chain 'E' and resid 221 through 226 Processing helix chain 'E' and resid 228 through 239 Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.636A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 271 Processing helix chain 'E' and resid 277 through 289 Proline residue: E 285 - end of helix Processing helix chain 'E' and resid 302 through 317 Proline residue: E 310 - end of helix Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 365 through 376 removed outlier: 3.554A pdb=" N GLY E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 417 through 428 Processing helix chain 'E' and resid 442 through 453 Processing helix chain 'E' and resid 463 through 465 No H-bonds generated for 'chain 'E' and resid 463 through 465' Processing helix chain 'E' and resid 480 through 482 No H-bonds generated for 'chain 'E' and resid 480 through 482' Processing helix chain 'E' and resid 483 through 497 removed outlier: 3.546A pdb=" N ARG E 491 " --> pdb=" O TRP E 487 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL E 493 " --> pdb=" O THR E 489 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU E 494 " --> pdb=" O ARG E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 521 Processing helix chain 'E' and resid 533 through 546 Processing helix chain 'E' and resid 557 through 559 No H-bonds generated for 'chain 'E' and resid 557 through 559' Processing helix chain 'E' and resid 578 through 587 Processing helix chain 'E' and resid 603 through 605 No H-bonds generated for 'chain 'E' and resid 603 through 605' Processing helix chain 'E' and resid 606 through 620 Processing helix chain 'E' and resid 625 through 633 Processing helix chain 'E' and resid 635 through 640 Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 19 removed outlier: 4.101A pdb=" N ALA D 18 " --> pdb=" O ILE D 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.056A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1101 through 1108 removed outlier: 3.905A pdb=" N SER A1103 " --> pdb=" O THR A1120 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLU A1115 " --> pdb=" O PRO A1131 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.673A pdb=" N PHE A 16 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU A 38 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 55 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 40 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.726A pdb=" N VAL A 88 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER A 82 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 87 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN A 104 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 89 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AA9, first strand: chain 'A' and resid 120 through 123 Processing sheet with id=AB1, first strand: chain 'A' and resid 165 through 173 removed outlier: 5.640A pdb=" N VAL A 167 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET A 187 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS A 169 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N MET A 181 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 208 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 225 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE A 210 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS A 219 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 237 removed outlier: 4.394A pdb=" N PHE A 234 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 255 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.320A pdb=" N ARG A 273 " --> pdb=" O PHE A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 287 through 294 removed outlier: 6.940A pdb=" N GLN A 304 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER A 290 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 302 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 292 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE A 300 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE A 299 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU A 315 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE A 310 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A 329 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 312 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 327 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 314 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE A 325 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU A 316 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 336 through 342 removed outlier: 7.127A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N HIS A 356 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 400 " --> pdb=" O HIS A 356 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 358 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.629A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 434 " --> pdb=" O CYS A 427 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 448 through 450 Processing sheet with id=AB8, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.584A pdb=" N ALA A 458 " --> pdb=" O SER A 477 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 507 through 510 removed outlier: 4.102A pdb=" N HIS A 526 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 534 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 544 through 549 removed outlier: 3.647A pdb=" N VAL A 545 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ALA A 557 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 547 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 555 " --> pdb=" O CYS A 547 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 556 " --> pdb=" O VAL A 564 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 587 through 592 removed outlier: 3.627A pdb=" N CYS A 589 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 629 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER A 618 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 637 through 643 removed outlier: 6.994A pdb=" N GLY A 668 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 640 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 666 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE A 642 " --> pdb=" O TYR A 664 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR A 664 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 703 through 706 Processing sheet with id=AC5, first strand: chain 'A' and resid 720 through 724 Processing sheet with id=AC6, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.147A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 886 through 894 removed outlier: 6.492A pdb=" N GLY A 908 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 891 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 906 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 893 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR A 904 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A 922 " --> pdb=" O LYS A 911 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 923 " --> pdb=" O PRO A 944 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 925 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS A 942 " --> pdb=" O VAL A 925 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR A 927 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 953 through 955 removed outlier: 6.829A pdb=" N LEU A 967 " --> pdb=" O GLU A 982 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 982 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 969 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 990 through 996 removed outlier: 3.830A pdb=" N GLY A 992 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP A1011 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1033 through 1040 removed outlier: 3.863A pdb=" N THR A1035 " --> pdb=" O ALA A1047 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR A1043 " --> pdb=" O LEU A1039 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ASN A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A1053 " --> pdb=" O ASN A1094 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1094 " --> pdb=" O ILE A1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A1055 " --> pdb=" O ILE A1092 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 241 through 244 removed outlier: 6.343A pdb=" N ILE E 294 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN E 461 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE E 296 " --> pdb=" O GLN E 461 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 329 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS E 382 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 331 " --> pdb=" O CYS E 382 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 472 through 477 removed outlier: 6.487A pdb=" N THR E 472 " --> pdb=" O ALA E 598 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 600 " --> pdb=" O THR E 472 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 474 " --> pdb=" O THR E 600 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU E 602 " --> pdb=" O ILE E 474 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU E 476 " --> pdb=" O LEU E 602 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N SER E 500 " --> pdb=" O ILE E 567 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2808 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: 8.22 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4677 1.33 - 1.45: 3802 1.45 - 1.57: 11363 1.57 - 1.69: 0 1.69 - 1.81: 163 Bond restraints: 20005 Sorted by residual: bond pdb=" C HIS A 804 " pdb=" O HIS A 804 " ideal model delta sigma weight residual 1.234 1.318 -0.083 1.27e-02 6.20e+03 4.29e+01 bond pdb=" N GLU E 80 " pdb=" CA GLU E 80 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.25e-02 6.40e+03 1.52e+01 bond pdb=" N ILE E 151 " pdb=" CA ILE E 151 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.36e+00 bond pdb=" N GLU E 153 " pdb=" CA GLU E 153 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.23e-02 6.61e+03 8.25e+00 bond pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.19e+00 ... (remaining 20000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 26650 2.51 - 5.03: 472 5.03 - 7.54: 32 7.54 - 10.06: 9 10.06 - 12.57: 2 Bond angle restraints: 27165 Sorted by residual: angle pdb=" C GLN E 275 " pdb=" N PRO E 276 " pdb=" CA PRO E 276 " ideal model delta sigma weight residual 119.85 111.73 8.12 1.01e+00 9.80e-01 6.47e+01 angle pdb=" C SER E 271 " pdb=" N GLU E 272 " pdb=" CA GLU E 272 " ideal model delta sigma weight residual 121.70 134.27 -12.57 1.80e+00 3.09e-01 4.88e+01 angle pdb=" CA SER E 271 " pdb=" C SER E 271 " pdb=" N GLU E 272 " ideal model delta sigma weight residual 115.30 124.13 -8.83 1.33e+00 5.65e-01 4.41e+01 angle pdb=" N ASP C 565 " pdb=" CA ASP C 565 " pdb=" C ASP C 565 " ideal model delta sigma weight residual 113.61 104.74 8.87 1.50e+00 4.44e-01 3.50e+01 angle pdb=" O ASP C 564 " pdb=" C ASP C 564 " pdb=" N ASP C 565 " ideal model delta sigma weight residual 122.30 114.49 7.81 1.35e+00 5.49e-01 3.35e+01 ... (remaining 27160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 10565 17.98 - 35.97: 1072 35.97 - 53.95: 341 53.95 - 71.94: 81 71.94 - 89.92: 30 Dihedral angle restraints: 12089 sinusoidal: 4410 harmonic: 7679 Sorted by residual: dihedral pdb=" CA THR A 490 " pdb=" C THR A 490 " pdb=" N VAL A 491 " pdb=" CA VAL A 491 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR E 273 " pdb=" C TYR E 273 " pdb=" N THR E 274 " pdb=" CA THR E 274 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LYS C 943 " pdb=" C LYS C 943 " pdb=" N SER C 944 " pdb=" CA SER C 944 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 12086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2645 0.073 - 0.147: 465 0.147 - 0.220: 26 0.220 - 0.293: 1 0.293 - 0.366: 1 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CA HIS A 804 " pdb=" N HIS A 804 " pdb=" C HIS A 804 " pdb=" CB HIS A 804 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA ILE E 147 " pdb=" N ILE E 147 " pdb=" C ILE E 147 " pdb=" CB ILE E 147 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA MET E 131 " pdb=" N MET E 131 " pdb=" C MET E 131 " pdb=" CB MET E 131 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3135 not shown) Planarity restraints: 3565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 564 " -0.024 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C ASP C 564 " 0.079 2.00e-02 2.50e+03 pdb=" O ASP C 564 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP C 565 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 945 " -0.013 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C ALA C 945 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA C 945 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 946 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 680 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO C 681 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " -0.029 5.00e-02 4.00e+02 ... (remaining 3562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 858 2.71 - 3.26: 18649 3.26 - 3.81: 31065 3.81 - 4.35: 38964 4.35 - 4.90: 65300 Nonbonded interactions: 154836 Sorted by model distance: nonbonded pdb=" O LYS A 343 " pdb=" OG1 THR A 344 " model vdw 2.168 3.040 nonbonded pdb=" N ASP E 149 " pdb=" OD1 ASP E 149 " model vdw 2.203 3.120 nonbonded pdb=" O ALA C 762 " pdb=" OG1 THR C 766 " model vdw 2.205 3.040 nonbonded pdb=" O GLY E 300 " pdb=" N GLY E 302 " model vdw 2.206 3.120 nonbonded pdb=" O ALA A 200 " pdb=" OG1 THR A 204 " model vdw 2.219 3.040 ... (remaining 154831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic 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: 0.950 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 51.210 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.006 0.083 20005 Z= 0.416 Angle : 0.858 12.570 27165 Z= 0.543 Chirality : 0.052 0.366 3138 Planarity : 0.005 0.052 3565 Dihedral : 17.469 89.923 7129 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.70 % Favored : 95.15 % Rotamer: Outliers : 6.98 % Allowed : 18.90 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -2.09 (0.15), residues: 2619 helix: -0.74 (0.14), residues: 1023 sheet: -0.76 (0.21), residues: 548 loop : -2.32 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1011 HIS 0.008 0.001 HIS A 804 PHE 0.024 0.002 PHE C 724 TYR 0.018 0.002 TYR A 424 ARG 0.010 0.001 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 246 time to evaluate : 2.238 Fit side-chains REVERT: C 497 ILE cc_start: 0.7398 (mt) cc_final: 0.7001 (mp) REVERT: C 543 THR cc_start: 0.8337 (m) cc_final: 0.8081 (t) REVERT: C 894 ASP cc_start: 0.7380 (m-30) cc_final: 0.7163 (m-30) REVERT: C 910 MET cc_start: 0.7385 (mmt) cc_final: 0.6978 (mmt) REVERT: C 1070 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7398 (ttmm) REVERT: D 34 ASP cc_start: 0.8113 (m-30) cc_final: 0.7837 (m-30) REVERT: A 39 GLU cc_start: 0.7800 (tt0) cc_final: 0.7573 (mt-10) REVERT: A 377 MET cc_start: 0.8626 (mtt) cc_final: 0.8322 (mtp) REVERT: A 520 TYR cc_start: 0.3231 (OUTLIER) cc_final: 0.2824 (p90) REVERT: A 734 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 873 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6683 (pt0) REVERT: A 984 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: A 986 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 1191 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8283 (tppt) REVERT: E 120 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6290 (mmm) outliers start: 134 outliers final: 74 residues processed: 366 average time/residue: 1.3204 time to fit residues: 543.3094 Evaluate side-chains 283 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 202 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 754 ILE Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain C residue 779 SER Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 905 THR Chi-restraints excluded: chain C residue 956 SER Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 520 TYR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 994 GLN Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 145 LYS Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 133 optimal weight: 0.0000 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B 35 GLN C 547 GLN C 662 HIS C 737 GLN C 804 ASN C 829 ASN C 903 GLN C 941 ASN C1184 HIS C1256 HIS C1289 ASN C1293 ASN D 55 GLN D 90 ASN A 104 GLN A 138 GLN A 219 HIS A 264 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN A 776 GLN A 796 ASN A 844 ASN A 870 ASN A 875 ASN A 916 ASN A1052 ASN A1147 HIS E 126 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20005 Z= 0.182 Angle : 0.599 13.688 27165 Z= 0.321 Chirality : 0.044 0.168 3138 Planarity : 0.005 0.056 3565 Dihedral : 8.210 59.951 2983 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.16 % Allowed : 21.92 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.77 (0.16), residues: 2619 helix: 0.73 (0.16), residues: 1030 sheet: -0.41 (0.22), residues: 543 loop : -1.81 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1011 HIS 0.004 0.001 HIS C1184 PHE 0.019 0.001 PHE C1126 TYR 0.016 0.001 TYR C 830 ARG 0.006 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 214 time to evaluate : 2.166 Fit side-chains REVERT: C 497 ILE cc_start: 0.7319 (mt) cc_final: 0.6938 (mp) REVERT: C 543 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8152 (t) REVERT: C 822 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5061 (pmt-80) REVERT: C 894 ASP cc_start: 0.7278 (m-30) cc_final: 0.7039 (m-30) REVERT: C 910 MET cc_start: 0.7329 (mmt) cc_final: 0.6844 (mmt) REVERT: C 1137 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7044 (mtt90) REVERT: A 274 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8619 (mtt180) REVERT: A 377 MET cc_start: 0.8582 (mtt) cc_final: 0.8289 (mtp) REVERT: A 679 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5262 (tp) REVERT: A 715 MET cc_start: 0.6408 (mtp) cc_final: 0.6098 (ttm) REVERT: A 873 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6635 (pt0) REVERT: A 1191 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8180 (tppt) REVERT: E 120 MET cc_start: 0.7044 (mmp) cc_final: 0.6445 (mmm) outliers start: 80 outliers final: 39 residues processed: 276 average time/residue: 1.3346 time to fit residues: 415.2573 Evaluate side-chains 242 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 238 optimal weight: 0.0870 chunk 257 optimal weight: 30.0000 chunk 212 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN A 203 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A 994 GLN A1061 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20005 Z= 0.247 Angle : 0.608 15.668 27165 Z= 0.322 Chirality : 0.045 0.157 3138 Planarity : 0.005 0.054 3565 Dihedral : 6.673 58.280 2881 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.89 % Allowed : 21.29 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.46 (0.16), residues: 2619 helix: 1.04 (0.16), residues: 1045 sheet: -0.35 (0.22), residues: 557 loop : -1.70 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1011 HIS 0.005 0.001 HIS C1007 PHE 0.021 0.002 PHE C1126 TYR 0.016 0.002 TYR C 623 ARG 0.004 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 205 time to evaluate : 2.242 Fit side-chains REVERT: C 543 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (t) REVERT: C 750 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (mt) REVERT: C 822 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5485 (pmt-80) REVERT: C 890 GLU cc_start: 0.7031 (tp30) cc_final: 0.6803 (mm-30) REVERT: C 910 MET cc_start: 0.7420 (mmt) cc_final: 0.6887 (mmt) REVERT: C 1137 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7107 (mtt90) REVERT: A 274 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8630 (mtt180) REVERT: A 321 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7951 (mtm) REVERT: A 377 MET cc_start: 0.8573 (mtt) cc_final: 0.8272 (mtp) REVERT: A 645 MET cc_start: 0.5584 (mpt) cc_final: 0.5192 (mpm) REVERT: A 706 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6159 (tpt) REVERT: A 734 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7303 (mp) REVERT: A 873 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: A 984 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8140 (ptmm) REVERT: E 120 MET cc_start: 0.7239 (mmp) cc_final: 0.6586 (mmm) outliers start: 94 outliers final: 45 residues processed: 274 average time/residue: 1.3640 time to fit residues: 420.0989 Evaluate side-chains 251 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 197 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 902 GLU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1160 GLU Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 5.9990 chunk 179 optimal weight: 0.0040 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 239 optimal weight: 50.0000 chunk 253 optimal weight: 50.0000 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 50.0000 chunk 68 optimal weight: 3.9990 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1061 ASN E 167 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20005 Z= 0.210 Angle : 0.581 16.509 27165 Z= 0.306 Chirality : 0.044 0.150 3138 Planarity : 0.004 0.053 3565 Dihedral : 6.361 58.911 2876 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.05 % Allowed : 21.08 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.28 (0.16), residues: 2619 helix: 1.23 (0.17), residues: 1047 sheet: -0.31 (0.22), residues: 564 loop : -1.62 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1011 HIS 0.005 0.001 HIS A 526 PHE 0.019 0.001 PHE C1126 TYR 0.015 0.001 TYR C 830 ARG 0.004 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 200 time to evaluate : 2.261 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8177 (t) REVERT: C 750 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 822 ARG cc_start: 0.5815 (OUTLIER) cc_final: 0.5189 (pmt-80) REVERT: C 910 MET cc_start: 0.7467 (mmt) cc_final: 0.6983 (mmt) REVERT: C 1053 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6393 (mtm110) REVERT: C 1137 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7100 (mtt90) REVERT: A 42 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7696 (ttm-80) REVERT: A 274 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8645 (mtt180) REVERT: A 321 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8037 (mtt) REVERT: A 377 MET cc_start: 0.8570 (mtt) cc_final: 0.8271 (mtp) REVERT: A 503 THR cc_start: 0.2697 (OUTLIER) cc_final: 0.2120 (t) REVERT: A 510 LEU cc_start: 0.3037 (OUTLIER) cc_final: 0.2626 (tp) REVERT: A 631 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5383 (tm-30) REVERT: A 645 MET cc_start: 0.5470 (mpt) cc_final: 0.5184 (mpm) REVERT: A 679 LEU cc_start: 0.5698 (OUTLIER) cc_final: 0.5364 (tp) REVERT: A 706 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.5968 (tpt) REVERT: A 873 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6739 (pt0) REVERT: A 984 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8071 (ptmm) REVERT: E 120 MET cc_start: 0.7243 (mmp) cc_final: 0.6784 (mmm) REVERT: E 129 ARG cc_start: 0.4457 (ttp80) cc_final: 0.3641 (mtm-85) outliers start: 97 outliers final: 54 residues processed: 276 average time/residue: 1.3684 time to fit residues: 425.1253 Evaluate side-chains 260 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 192 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1006 MET Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1053 ARG Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 227 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20005 Z= 0.241 Angle : 0.593 16.666 27165 Z= 0.313 Chirality : 0.045 0.150 3138 Planarity : 0.004 0.053 3565 Dihedral : 6.360 58.246 2876 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.00 % Allowed : 20.93 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.18 (0.16), residues: 2619 helix: 1.33 (0.17), residues: 1035 sheet: -0.31 (0.22), residues: 569 loop : -1.53 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1011 HIS 0.007 0.001 HIS C1007 PHE 0.017 0.002 PHE C1126 TYR 0.017 0.002 TYR C 623 ARG 0.005 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 200 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8186 (t) REVERT: C 560 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7803 (mp) REVERT: C 750 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8900 (mt) REVERT: C 822 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.5208 (pmt-80) REVERT: C 910 MET cc_start: 0.7447 (mmt) cc_final: 0.6954 (mmt) REVERT: C 1006 MET cc_start: 0.6548 (tpp) cc_final: 0.5993 (tpt) REVERT: C 1137 ARG cc_start: 0.7642 (ttm-80) cc_final: 0.7076 (mtt90) REVERT: A 42 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7701 (ttm-80) REVERT: A 274 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8642 (mtt180) REVERT: A 321 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: A 377 MET cc_start: 0.8566 (mtt) cc_final: 0.8265 (mtp) REVERT: A 503 THR cc_start: 0.2727 (OUTLIER) cc_final: 0.2150 (t) REVERT: A 510 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2563 (tp) REVERT: A 631 GLN cc_start: 0.5799 (OUTLIER) cc_final: 0.5348 (tm-30) REVERT: A 645 MET cc_start: 0.5543 (mpt) cc_final: 0.5180 (mpm) REVERT: A 706 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5957 (tpt) REVERT: A 734 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 984 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8092 (ptmm) REVERT: E 120 MET cc_start: 0.7202 (mmp) cc_final: 0.6649 (mmm) outliers start: 96 outliers final: 60 residues processed: 278 average time/residue: 1.3837 time to fit residues: 432.6654 Evaluate side-chains 268 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 195 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1160 GLU Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 920 VAL Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 253 optimal weight: 50.0000 chunk 210 optimal weight: 0.0870 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20005 Z= 0.200 Angle : 0.567 16.620 27165 Z= 0.298 Chirality : 0.044 0.207 3138 Planarity : 0.004 0.050 3565 Dihedral : 6.084 59.490 2872 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.21 % Allowed : 20.98 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.04 (0.17), residues: 2619 helix: 1.46 (0.17), residues: 1035 sheet: -0.24 (0.22), residues: 563 loop : -1.45 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1011 HIS 0.004 0.001 HIS A1152 PHE 0.016 0.001 PHE C1126 TYR 0.016 0.001 TYR C 830 ARG 0.005 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 195 time to evaluate : 2.392 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (t) REVERT: C 560 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7904 (mp) REVERT: C 750 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8875 (mt) REVERT: C 822 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5258 (pmt-80) REVERT: C 910 MET cc_start: 0.7481 (mmt) cc_final: 0.6968 (mmt) REVERT: C 1006 MET cc_start: 0.6653 (tpp) cc_final: 0.6242 (tpt) REVERT: C 1070 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7730 (ttmm) REVERT: C 1137 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7079 (mtt90) REVERT: A 42 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7714 (ttm-80) REVERT: A 274 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8638 (mtt180) REVERT: A 321 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7887 (mtm) REVERT: A 377 MET cc_start: 0.8563 (mtt) cc_final: 0.8264 (mtp) REVERT: A 510 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2391 (tp) REVERT: A 631 GLN cc_start: 0.5798 (OUTLIER) cc_final: 0.5452 (tm-30) REVERT: A 645 MET cc_start: 0.5519 (mpt) cc_final: 0.5177 (mpm) REVERT: A 706 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6612 (mpm) REVERT: A 734 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 984 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8068 (ptmm) REVERT: E 120 MET cc_start: 0.7265 (mmp) cc_final: 0.6740 (mmm) outliers start: 100 outliers final: 68 residues processed: 276 average time/residue: 1.3963 time to fit residues: 433.3737 Evaluate side-chains 275 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 194 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 chunk 213 optimal weight: 1.9990 chunk 141 optimal weight: 0.0570 chunk 252 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 116 optimal weight: 0.0870 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20005 Z= 0.215 Angle : 0.577 16.495 27165 Z= 0.302 Chirality : 0.044 0.199 3138 Planarity : 0.004 0.054 3565 Dihedral : 6.017 58.995 2871 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.15 % Allowed : 20.98 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: -0.00 (0.17), residues: 2619 helix: 1.49 (0.17), residues: 1042 sheet: -0.21 (0.22), residues: 561 loop : -1.46 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1011 HIS 0.004 0.001 HIS C1194 PHE 0.026 0.002 PHE C1126 TYR 0.014 0.001 TYR C 830 ARG 0.006 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 198 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8216 (t) REVERT: C 560 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.7856 (mp) REVERT: C 750 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8896 (mt) REVERT: C 822 ARG cc_start: 0.5775 (OUTLIER) cc_final: 0.5257 (pmt-80) REVERT: C 910 MET cc_start: 0.7472 (mmt) cc_final: 0.6995 (mmt) REVERT: C 1006 MET cc_start: 0.6659 (tpp) cc_final: 0.6170 (tpt) REVERT: C 1070 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7736 (ttmm) REVERT: C 1137 ARG cc_start: 0.7635 (ttm-80) cc_final: 0.7089 (mtt90) REVERT: A 42 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7712 (ttm-80) REVERT: A 274 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8639 (mtt180) REVERT: A 321 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: A 377 MET cc_start: 0.8562 (mtt) cc_final: 0.8341 (mtp) REVERT: A 503 THR cc_start: 0.2665 (OUTLIER) cc_final: 0.2151 (t) REVERT: A 510 LEU cc_start: 0.2754 (OUTLIER) cc_final: 0.2309 (tp) REVERT: A 631 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5397 (tm-30) REVERT: A 645 MET cc_start: 0.5535 (mpt) cc_final: 0.5189 (mpm) REVERT: A 734 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7262 (mp) REVERT: A 984 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8153 (ptmm) REVERT: E 120 MET cc_start: 0.7282 (mmp) cc_final: 0.6729 (mmm) outliers start: 99 outliers final: 69 residues processed: 278 average time/residue: 1.3272 time to fit residues: 415.7283 Evaluate side-chains 273 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 191 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 760 GLU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 778 GLN Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 903 GLN Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1009 MET Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1160 GLU Chi-restraints excluded: chain C residue 1271 SER Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 782 GLN Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1217 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 198 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 966 GLN A 553 GLN A 844 ASN A1061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20005 Z= 0.141 Angle : 0.531 16.466 27165 Z= 0.276 Chirality : 0.043 0.173 3138 Planarity : 0.004 0.056 3565 Dihedral : 5.685 56.416 2871 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.64 % Allowed : 22.38 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: 0.18 (0.17), residues: 2619 helix: 1.62 (0.17), residues: 1049 sheet: -0.13 (0.22), residues: 560 loop : -1.34 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 732 HIS 0.003 0.001 HIS A 526 PHE 0.027 0.001 PHE C1126 TYR 0.015 0.001 TYR C 830 ARG 0.006 0.000 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 195 time to evaluate : 2.235 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8198 (t) REVERT: C 822 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.5310 (pmt-80) REVERT: C 910 MET cc_start: 0.7441 (mmt) cc_final: 0.6918 (mmt) REVERT: C 1006 MET cc_start: 0.6631 (tpp) cc_final: 0.6211 (tpt) REVERT: C 1070 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7686 (ttmm) REVERT: C 1137 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7016 (mtt90) REVERT: A 321 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7784 (mtm) REVERT: A 377 MET cc_start: 0.8559 (mtt) cc_final: 0.8264 (mtp) REVERT: A 503 THR cc_start: 0.2668 (OUTLIER) cc_final: 0.2185 (t) REVERT: A 631 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5379 (tm-30) REVERT: A 645 MET cc_start: 0.5443 (mpt) cc_final: 0.5118 (mpm) REVERT: A 986 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7945 (mm) REVERT: E 120 MET cc_start: 0.7255 (mmp) cc_final: 0.6698 (mmm) REVERT: E 129 ARG cc_start: 0.4266 (ttp80) cc_final: 0.3974 (mtm-85) outliers start: 70 outliers final: 41 residues processed: 253 average time/residue: 1.3660 time to fit residues: 389.2214 Evaluate side-chains 233 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 220 optimal weight: 50.0000 chunk 235 optimal weight: 40.0000 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 903 GLN C 966 GLN A 844 ASN A1061 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20005 Z= 0.327 Angle : 0.644 16.336 27165 Z= 0.335 Chirality : 0.047 0.230 3138 Planarity : 0.005 0.056 3565 Dihedral : 5.922 57.963 2863 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 3.80 % Allowed : 22.70 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: 0.03 (0.16), residues: 2619 helix: 1.49 (0.16), residues: 1035 sheet: -0.17 (0.23), residues: 561 loop : -1.40 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1011 HIS 0.006 0.001 HIS C1194 PHE 0.025 0.002 PHE C1126 TYR 0.015 0.002 TYR A 926 ARG 0.006 0.001 ARG C1057 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 199 time to evaluate : 2.394 Fit side-chains revert: symmetry clash REVERT: C 543 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8269 (t) REVERT: C 822 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5308 (pmt-80) REVERT: C 910 MET cc_start: 0.7492 (mmt) cc_final: 0.7021 (mmt) REVERT: C 1070 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (ttmm) REVERT: C 1137 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7117 (mtt90) REVERT: A 42 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7688 (ttm-80) REVERT: A 214 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 274 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8634 (mtt180) REVERT: A 321 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7876 (mtm) REVERT: A 377 MET cc_start: 0.8564 (mtt) cc_final: 0.8255 (mtp) REVERT: A 503 THR cc_start: 0.2697 (OUTLIER) cc_final: 0.2176 (t) REVERT: A 631 GLN cc_start: 0.5995 (OUTLIER) cc_final: 0.5689 (tm-30) REVERT: A 645 MET cc_start: 0.5568 (mpt) cc_final: 0.5225 (mpm) REVERT: A 984 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8187 (ptmm) REVERT: A 986 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8006 (mm) REVERT: E 120 MET cc_start: 0.7397 (mmp) cc_final: 0.6945 (mmm) outliers start: 73 outliers final: 52 residues processed: 257 average time/residue: 1.4036 time to fit residues: 405.0487 Evaluate side-chains 256 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 193 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 585 GLU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 870 GLU Chi-restraints excluded: chain C residue 904 THR Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 274 ARG Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 984 LYS Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 30.0000 chunk 248 optimal weight: 40.0000 chunk 151 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 172 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 160 optimal weight: 0.3980 chunk 127 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 966 GLN A 844 ASN A1061 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20005 Z= 0.165 Angle : 0.556 16.350 27165 Z= 0.287 Chirality : 0.043 0.169 3138 Planarity : 0.004 0.056 3565 Dihedral : 5.544 57.217 2863 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.81 % Allowed : 23.74 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: 0.19 (0.17), residues: 2619 helix: 1.62 (0.17), residues: 1045 sheet: -0.14 (0.23), residues: 561 loop : -1.30 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 732 HIS 0.003 0.001 HIS A1152 PHE 0.029 0.001 PHE C1126 TYR 0.016 0.001 TYR E 75 ARG 0.006 0.000 ARG C1057 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5238 Ramachandran restraints generated. 2619 Oldfield, 0 Emsley, 2619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 2.203 Fit side-chains revert: symmetry clash REVERT: C 822 ARG cc_start: 0.5681 (OUTLIER) cc_final: 0.5309 (pmt-80) REVERT: C 910 MET cc_start: 0.7460 (mmt) cc_final: 0.6979 (mmt) REVERT: C 1070 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7666 (ttmm) REVERT: C 1137 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7033 (mtt90) REVERT: A 321 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: A 377 MET cc_start: 0.8570 (mtt) cc_final: 0.8259 (mtp) REVERT: A 503 THR cc_start: 0.2636 (OUTLIER) cc_final: 0.2135 (t) REVERT: A 631 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: A 645 MET cc_start: 0.5426 (mpt) cc_final: 0.5116 (mpm) REVERT: A 986 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7987 (mm) REVERT: E 120 MET cc_start: 0.7384 (mmp) cc_final: 0.7003 (mmm) outliers start: 54 outliers final: 40 residues processed: 236 average time/residue: 1.4120 time to fit residues: 374.8271 Evaluate side-chains 238 residues out of total 2287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 792 VAL Chi-restraints excluded: chain C residue 822 ARG Chi-restraints excluded: chain C residue 965 CYS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1070 LYS Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain D residue 26 CYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 296 LYS Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 578 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 624 CYS Chi-restraints excluded: chain A residue 631 GLN Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 805 ASN Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 873 GLN Chi-restraints excluded: chain A residue 890 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 162 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.5980 chunk 221 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 966 GLN A 844 ASN A1061 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.115156 restraints weight = 22434.967| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.81 r_work: 0.3018 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20005 Z= 0.210 Angle : 0.581 16.085 27165 Z= 0.300 Chirality : 0.044 0.169 3138 Planarity : 0.004 0.055 3565 Dihedral : 5.598 56.972 2863 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.92 % Allowed : 23.84 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.12 % 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: 0.19 (0.17), residues: 2619 helix: 1.62 (0.17), residues: 1045 sheet: -0.14 (0.23), residues: 562 loop : -1.29 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1011 HIS 0.004 0.001 HIS C1194 PHE 0.027 0.002 PHE C1126 TYR 0.014 0.001 TYR C 830 ARG 0.006 0.000 ARG C1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.69 seconds wall clock time: 135 minutes 29.90 seconds (8129.90 seconds total)