Starting phenix.real_space_refine on Tue Sep 15 00:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446.map" model { file = "/net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5w_3446/09_2026/5m5w_3446_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.013 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 43 5.49 5 S 172 5.16 5 C 21849 2.51 5 N 6036 2.21 5 O 6673 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34780 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1493, 11760 Classifications: {'peptide': 1493} Link IDs: {'PCIS': 5, 'PTRANS': 56, 'TRANS': 1431} Chain breaks: 6 Chain: "B" Number of atoms: 9389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9389 Classifications: {'peptide': 1183} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1123} Chain breaks: 2 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1624 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 869 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 109} Chain breaks: 1 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "N" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1164 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 136} Chain breaks: 3 Chain: "S" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 376 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 781 SG CYS A 102 75.111 102.030 28.646 1.00 88.95 S ATOM 806 SG CYS A 105 77.366 100.924 26.377 1.00 91.29 S ATOM 1624 SG CYS A 233 78.635 104.447 27.945 1.00 92.17 S ATOM 1646 SG CYS A 236 77.872 104.045 25.780 1.00104.79 S ATOM 461 SG CYS A 62 68.170 56.309 49.759 1.00 74.92 S ATOM 480 SG CYS A 65 71.296 54.770 50.767 1.00 72.34 S ATOM 535 SG CYS A 72 71.773 56.631 52.033 1.00 72.92 S ATOM 20429 SG CYS B1104 84.953 61.677 41.638 1.00 61.64 S ATOM 20455 SG CYS B1107 83.596 64.229 42.215 1.00 68.74 S ATOM 20602 SG CYS B1128 81.245 61.556 41.235 1.00 64.61 S ATOM 20630 SG CYS B1131 83.032 63.888 38.611 1.00 68.47 S ATOM 29392 SG CYS I 13 44.989 142.991 86.113 1.00141.37 S ATOM 29512 SG CYS I 30 45.554 143.205 82.082 1.00174.69 S ATOM 29962 SG CYS I 89 119.365 97.643 98.285 1.00169.58 S ATOM 30230 SG CYS J 7 82.009 62.074 122.929 1.00 81.98 S ATOM 30253 SG CYS J 10 83.987 59.970 124.958 1.00 77.69 S ATOM 30533 SG CYS J 45 85.747 62.694 125.416 1.00 81.16 S ATOM 30539 SG CYS J 46 83.207 60.579 126.183 1.00 81.59 S ATOM 31565 SG CYS L 31 41.240 60.992 106.439 1.00105.00 S ATOM 31585 SG CYS L 34 39.622 59.758 108.635 1.00107.07 S ATOM 31689 SG CYS L 48 38.029 60.686 104.447 1.00119.22 S ATOM 31712 SG CYS L 51 37.657 62.003 107.019 1.00115.61 S Time building chain proxies: 8.41, per 1000 atoms: 0.24 Number of scatterers: 34780 At special positions: 0 Unit cell: (162, 174.15, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 172 16.00 P 43 15.00 O 6673 8.00 N 6036 7.00 C 21849 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: 3.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" NE2 GLN I 88 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 27 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8026 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 49 sheets defined 33.4% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.843A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.531A pdb=" N LEU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 126 removed outlier: 3.531A pdb=" N CYS A 120 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.850A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 197 removed outlier: 3.581A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 257 through 265 removed outlier: 3.876A pdb=" N ASN A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.917A pdb=" N PHE A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.420A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 381 through 400 removed outlier: 4.006A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.549A pdb=" N LYS A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.738A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 500 through 505 removed outlier: 3.525A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.083A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 560 removed outlier: 3.756A pdb=" N ARG A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.702A pdb=" N MET A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.762A pdb=" N GLY A 622 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 671 through 681 removed outlier: 3.702A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.690A pdb=" N TYR A 695 " --> pdb=" O GLN A 691 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.707A pdb=" N VAL A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.758A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 836 through 848 Processing helix chain 'A' and resid 852 through 863 removed outlier: 3.676A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 3.784A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.538A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 Processing helix chain 'A' and resid 936 through 945 removed outlier: 4.011A pdb=" N GLN A 942 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.993A pdb=" N GLY A 980 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1008 removed outlier: 4.379A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.913A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1072 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 3.860A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.730A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A1127 " --> pdb=" O VAL A1123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1127' Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.714A pdb=" N GLN A1141 " --> pdb=" O SER A1137 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.683A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1200 Proline residue: A1196 - end of helix Processing helix chain 'A' and resid 1218 through 1227 Processing helix chain 'A' and resid 1247 through 1254 removed outlier: 3.636A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1257 No H-bonds generated for 'chain 'A' and resid 1255 through 1257' Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.088A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.586A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A1318 " --> pdb=" O GLN A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1337 removed outlier: 3.746A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1452 Processing helix chain 'A' and resid 1485 through 1493 Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.586A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1554 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.874A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 4.022A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A1587 " --> pdb=" O ASP A1583 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A1590 " --> pdb=" O ALA A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1605 removed outlier: 4.102A pdb=" N THR A1605 " --> pdb=" O GLY A1602 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.617A pdb=" N TYR A1615 " --> pdb=" O MET A1611 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 3.514A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A1625 " --> pdb=" O PHE A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 4.456A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1653 Processing helix chain 'B' and resid 20 through 27 removed outlier: 3.529A pdb=" N ARG B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 42 through 54 removed outlier: 4.015A pdb=" N THR B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.591A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 3.540A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.546A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.956A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.698A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.801A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.715A pdb=" N LEU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.603A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.795A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 4.170A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 406 through 435 removed outlier: 3.752A pdb=" N ASP B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.540A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.684A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 579 through 583 removed outlier: 4.096A pdb=" N SER B 582 " --> pdb=" O ALA B 579 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 583 " --> pdb=" O GLY B 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 579 through 583' Processing helix chain 'B' and resid 597 through 612 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.564A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 697' Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.745A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 953 through 958 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.618A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.932A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1080 removed outlier: 3.868A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1083 No H-bonds generated for 'chain 'B' and resid 1081 through 1083' Processing helix chain 'B' and resid 1084 through 1093 removed outlier: 3.953A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B1090 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1193 removed outlier: 3.866A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 38 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.598A pdb=" N SER C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 176 through 180 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 251 removed outlier: 4.026A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.927A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 44 removed outlier: 3.872A pdb=" N VAL D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.695A pdb=" N ILE D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.538A pdb=" N ARG E 17 " --> pdb=" O TRP E 13 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.715A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.846A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.571A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.519A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.684A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.048A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.556A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.570A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.524A pdb=" N LEU G 54 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.518A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 3.599A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 60 through 65' Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.796A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.540A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.694A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 141 removed outlier: 3.989A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.664A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 5.225A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.646A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476 Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 486 removed outlier: 7.823A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 634 " --> pdb=" O ASN A 590 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 633 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.363A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA8, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.729A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB1, first strand: chain 'A' and resid 1237 through 1238 Processing sheet with id=AB2, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.089A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 7.019A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A1461 " --> pdb=" O GLU A1471 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB5, first strand: chain 'B' and resid 97 through 106 removed outlier: 4.224A pdb=" N GLU B 100 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS B 106 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ARG B 134 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 194 through 195 removed outlier: 3.633A pdb=" N LYS B 201 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.601A pdb=" N LEU B 206 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 234 through 239 removed outlier: 5.893A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 502 through 503 Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 571 through 572 removed outlier: 4.096A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 596 " --> pdb=" O CYS B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.158A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.158A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS L 58 " --> pdb=" O VAL B 885 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 787 through 789 removed outlier: 3.778A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 918 " --> pdb=" O GLN B1034 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 787 through 789 removed outlier: 3.778A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B 771 " --> pdb=" O VAL B1031 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 825 removed outlier: 4.125A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 872 " --> pdb=" O CYS B 859 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 861 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 870 " --> pdb=" O TYR B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD1, first strand: chain 'B' and resid 1099 through 1104 removed outlier: 3.553A pdb=" N THR B1174 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD3, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD4, first strand: chain 'C' and resid 42 through 46 removed outlier: 5.094A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.807A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.602A pdb=" N THR C 141 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.622A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AD9, first strand: chain 'D' and resid 22 through 24 Processing sheet with id=AE1, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.923A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.229A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE4, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'G' and resid 131 through 140 removed outlier: 6.331A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE G 145 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE G 157 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU G 147 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 149 " --> pdb=" O PHE G 153 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP G 131 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.949A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP H 41 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU H 125 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 102 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR H 95 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE8, first strand: chain 'I' and resid 110 through 113 removed outlier: 3.642A pdb=" N VAL I 110 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'M' and resid 87 through 88 removed outlier: 8.634A pdb=" N ILE M 88 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU M 11 " --> pdb=" O ILE M 88 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 54 through 56 removed outlier: 6.931A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 80 through 81 removed outlier: 4.173A pdb=" N ILE N 56 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE N 58 " --> pdb=" O GLN M 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 80 through 81 removed outlier: 6.299A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL N 136 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET N 80 " --> pdb=" O TYR N 87 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3078 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: 8.06 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10661 1.34 - 1.45: 4977 1.45 - 1.57: 19541 1.57 - 1.69: 88 1.69 - 1.81: 271 Bond restraints: 35538 Sorted by residual: bond pdb=" N ASP K 57 " pdb=" CA ASP K 57 " ideal model delta sigma weight residual 1.458 1.663 -0.205 1.27e-02 6.20e+03 2.61e+02 bond pdb=" CA LYS A 250 " pdb=" C LYS A 250 " ideal model delta sigma weight residual 1.523 1.370 0.153 1.34e-02 5.57e+03 1.31e+02 bond pdb=" N LYS B1064 " pdb=" CA LYS B1064 " ideal model delta sigma weight residual 1.458 1.556 -0.098 1.30e-02 5.92e+03 5.71e+01 bond pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 1.532 1.650 -0.119 1.62e-02 3.81e+03 5.36e+01 bond pdb=" CA GLY K 58 " pdb=" C GLY K 58 " ideal model delta sigma weight residual 1.514 1.430 0.084 1.41e-02 5.03e+03 3.55e+01 ... (remaining 35533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 48173 7.78 - 15.57: 16 15.57 - 23.35: 2 23.35 - 31.14: 1 31.14 - 38.92: 2 Bond angle restraints: 48194 Sorted by residual: angle pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" C LYS B1064 " ideal model delta sigma weight residual 113.55 79.37 34.18 1.26e+00 6.30e-01 7.36e+02 angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" C ASP K 57 " ideal model delta sigma weight residual 112.04 73.12 38.92 1.44e+00 4.82e-01 7.31e+02 angle pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.56 86.70 23.86 1.83e+00 2.99e-01 1.70e+02 angle pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta sigma weight residual 110.19 95.87 14.32 1.55e+00 4.16e-01 8.53e+01 angle pdb=" C LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta sigma weight residual 109.34 95.81 13.53 1.55e+00 4.16e-01 7.62e+01 ... (remaining 48189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 19961 17.17 - 34.35: 1182 34.35 - 51.52: 327 51.52 - 68.70: 81 68.70 - 85.87: 12 Dihedral angle restraints: 21563 sinusoidal: 9143 harmonic: 12420 Sorted by residual: dihedral pdb=" C ASP K 57 " pdb=" N ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual -122.60 -84.74 -37.86 0 2.50e+00 1.60e-01 2.29e+02 dihedral pdb=" C LYS B1064 " pdb=" N LYS B1064 " pdb=" CA LYS B1064 " pdb=" CB LYS B1064 " ideal model delta harmonic sigma weight residual -122.60 -93.68 -28.92 0 2.50e+00 1.60e-01 1.34e+02 dihedral pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CA ASP K 57 " pdb=" CB ASP K 57 " ideal model delta harmonic sigma weight residual 122.80 97.16 25.64 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 21560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 5374 0.291 - 0.582: 4 0.582 - 0.873: 0 0.873 - 1.164: 1 1.164 - 1.455: 1 Chirality restraints: 5380 Sorted by residual: chirality pdb=" CA ASP K 57 " pdb=" N ASP K 57 " pdb=" C ASP K 57 " pdb=" CB ASP K 57 " both_signs ideal model delta sigma weight residual False 2.51 3.97 -1.46 2.00e-01 2.50e+01 5.29e+01 chirality pdb=" CA LYS B1064 " pdb=" N LYS B1064 " pdb=" C LYS B1064 " pdb=" CB LYS B1064 " both_signs ideal model delta sigma weight residual False 2.51 3.63 -1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA LYS A 250 " pdb=" N LYS A 250 " pdb=" C LYS A 250 " pdb=" CB LYS A 250 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 5377 not shown) Planarity restraints: 6085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 58 " 0.028 2.00e-02 2.50e+03 5.42e-02 2.94e+01 pdb=" C GLY K 58 " -0.094 2.00e-02 2.50e+03 pdb=" O GLY K 58 " 0.032 2.00e-02 2.50e+03 pdb=" N THR K 59 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 246 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.96e+00 pdb=" C ASP A 246 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP A 246 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 247 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 342 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.029 5.00e-02 4.00e+02 ... (remaining 6082 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 6 2.10 - 2.80: 9457 2.80 - 3.50: 46755 3.50 - 4.20: 81841 4.20 - 4.90: 137250 Nonbonded interactions: 275309 Sorted by model distance: nonbonded pdb=" O LYS B1061 " pdb=" NH2 ARG B1065 " model vdw 1.405 3.120 nonbonded pdb=" OH TYR H 98 " pdb=" OD1 ASN H 139 " model vdw 1.424 3.040 nonbonded pdb=" O SER A 764 " pdb=" N GLU A 766 " model vdw 1.934 3.120 nonbonded pdb=" N ASP K 57 " pdb=" N GLY K 58 " model vdw 1.984 2.560 nonbonded pdb=" CE1 PHE A 248 " pdb=" NZ LYS A 442 " model vdw 2.035 3.420 ... (remaining 275304 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.080 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.004 0.337 35562 Z= 0.207 Angle : 0.936 69.637 48221 Z= 0.405 Chirality : 0.049 1.455 5380 Planarity : 0.004 0.057 6085 Dihedral : 12.280 85.873 13537 Min Nonbonded Distance : 1.405 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer: Outliers : 1.35 % Allowed : 11.39 % Favored : 87.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.15 (0.11), residues: 4211 helix: -3.31 (0.10), residues: 1186 sheet: -2.26 (0.20), residues: 545 loop : -2.66 (0.11), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 130 TYR 0.010 0.001 TYR B 655 PHE 0.009 0.001 PHE M 81 TRP 0.008 0.001 TRP B 264 HIS 0.004 0.000 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.19 (35538) covalent geometry : angle 0.62590 / 0.38 (48194) hydrogen bonds : bond 0.21263 / 14.05 ( 1083) hydrogen bonds : angle 10.19379 / 6.92 ( 3078) metal coordination : bond 0.08488 / 4.49 ( 24) metal coordination : angle 29.42756 / 17.63 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 1084 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7952 (pttt) cc_final: 0.7257 (pttm) REVERT: A 182 LYS cc_start: 0.6842 (tppt) cc_final: 0.6569 (ttpt) REVERT: A 191 MET cc_start: 0.7450 (ppp) cc_final: 0.7172 (ppp) REVERT: A 199 ASP cc_start: 0.6566 (p0) cc_final: 0.6248 (p0) REVERT: A 446 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.3899 (mmp-170) REVERT: A 540 ASP cc_start: 0.8410 (t70) cc_final: 0.8146 (t0) REVERT: A 914 ASP cc_start: 0.8268 (m-30) cc_final: 0.8021 (m-30) REVERT: A 1078 LYS cc_start: 0.8588 (tmtm) cc_final: 0.7933 (mtpp) REVERT: A 1124 LEU cc_start: 0.8119 (tp) cc_final: 0.7782 (tp) REVERT: A 1128 ASN cc_start: 0.8830 (t0) cc_final: 0.8333 (t0) REVERT: A 1175 MET cc_start: 0.8624 (tmm) cc_final: 0.8099 (tmm) REVERT: A 1269 LYS cc_start: 0.8218 (mttt) cc_final: 0.7935 (mtmp) REVERT: A 1308 VAL cc_start: 0.7768 (t) cc_final: 0.7161 (p) REVERT: A 1331 LYS cc_start: 0.6814 (tptm) cc_final: 0.6482 (ttmt) REVERT: A 1439 MET cc_start: 0.6583 (ppp) cc_final: 0.5811 (ptp) REVERT: A 1469 TRP cc_start: 0.6517 (p-90) cc_final: 0.6026 (p-90) REVERT: A 1475 GLU cc_start: 0.6861 (tt0) cc_final: 0.6171 (mt-10) REVERT: A 1483 LEU cc_start: 0.7386 (tt) cc_final: 0.6995 (tt) REVERT: A 1485 MET cc_start: 0.6360 (mmm) cc_final: 0.5413 (mmm) REVERT: A 1508 VAL cc_start: 0.7903 (t) cc_final: 0.7546 (m) REVERT: A 1634 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6719 (pp) REVERT: B 37 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8412 (tm) REVERT: B 54 GLU cc_start: 0.6899 (tt0) cc_final: 0.6561 (tp30) REVERT: B 90 TYR cc_start: 0.4939 (t80) cc_final: 0.4633 (t80) REVERT: B 188 ASP cc_start: 0.7610 (t70) cc_final: 0.7348 (t0) REVERT: B 243 GLN cc_start: 0.8612 (mp-120) cc_final: 0.8261 (mm-40) REVERT: B 311 ARG cc_start: 0.7113 (mpp80) cc_final: 0.6604 (mmm160) REVERT: B 317 TYR cc_start: 0.4913 (p90) cc_final: 0.4435 (p90) REVERT: B 336 VAL cc_start: 0.8682 (m) cc_final: 0.8457 (p) REVERT: B 389 CYS cc_start: 0.7751 (m) cc_final: 0.7465 (m) REVERT: B 420 TYR cc_start: 0.7254 (t80) cc_final: 0.6859 (t80) REVERT: B 434 ARG cc_start: 0.8498 (mmt90) cc_final: 0.7460 (ttt90) REVERT: B 446 MET cc_start: 0.6594 (tpp) cc_final: 0.6304 (tmm) REVERT: B 477 ASP cc_start: 0.6495 (t0) cc_final: 0.6230 (t0) REVERT: B 497 ILE cc_start: 0.8867 (tp) cc_final: 0.8583 (tp) REVERT: B 755 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (m-40) REVERT: B 759 ASP cc_start: 0.8427 (t0) cc_final: 0.8036 (t0) REVERT: B 878 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 915 ASP cc_start: 0.7219 (p0) cc_final: 0.7005 (p0) REVERT: B 946 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8620 (p0) REVERT: B 998 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8115 (pp20) REVERT: B 1020 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8009 (mm-30) REVERT: B 1039 MET cc_start: 0.6206 (pmt) cc_final: 0.5948 (pmm) REVERT: B 1089 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8243 (tm-30) REVERT: B 1201 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7939 (tt0) REVERT: C 53 ASN cc_start: 0.7030 (t0) cc_final: 0.6742 (t0) REVERT: C 107 LYS cc_start: 0.7314 (mttt) cc_final: 0.6731 (tmmt) REVERT: C 237 GLN cc_start: 0.7825 (mt0) cc_final: 0.7404 (mm-40) REVERT: C 246 ARG cc_start: 0.6258 (ptp90) cc_final: 0.5893 (ptt180) REVERT: C 315 PHE cc_start: 0.7320 (t80) cc_final: 0.6895 (t80) REVERT: D 37 LEU cc_start: 0.6942 (mm) cc_final: 0.6466 (mp) REVERT: E 39 LEU cc_start: 0.6466 (tm) cc_final: 0.6034 (tm) REVERT: E 54 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7255 (mp10) REVERT: E 58 MET cc_start: 0.8619 (mtp) cc_final: 0.7776 (mtp) REVERT: E 132 ILE cc_start: 0.8097 (pt) cc_final: 0.7883 (tt) REVERT: E 142 VAL cc_start: 0.9203 (t) cc_final: 0.8758 (p) REVERT: E 143 ASN cc_start: 0.7934 (t160) cc_final: 0.7672 (t0) REVERT: E 145 THR cc_start: 0.8135 (m) cc_final: 0.7362 (p) REVERT: F 61 HIS cc_start: 0.7140 (m90) cc_final: 0.6926 (m-70) REVERT: F 67 LYS cc_start: 0.9027 (mtmp) cc_final: 0.8701 (mmmt) REVERT: F 99 LEU cc_start: 0.8826 (mt) cc_final: 0.8624 (mt) REVERT: F 144 GLU cc_start: 0.8570 (pp20) cc_final: 0.8080 (pp20) REVERT: G 62 MET cc_start: 0.8618 (mtm) cc_final: 0.8219 (mtp) REVERT: G 80 VAL cc_start: 0.8033 (t) cc_final: 0.7755 (p) REVERT: G 84 TYR cc_start: 0.6983 (p90) cc_final: 0.6760 (p90) REVERT: H 8 ASP cc_start: 0.7587 (t0) cc_final: 0.7307 (t70) REVERT: H 52 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7777 (pt0) REVERT: H 58 THR cc_start: 0.7925 (m) cc_final: 0.7121 (m) REVERT: H 87 ARG cc_start: 0.7182 (tmt170) cc_final: 0.6909 (mmt-90) REVERT: I 19 ASN cc_start: 0.4846 (OUTLIER) cc_final: 0.4105 (m110) REVERT: J 27 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8141 (mt-10) REVERT: J 55 ASP cc_start: 0.8994 (t70) cc_final: 0.8575 (t0) REVERT: K 44 ARG cc_start: 0.5787 (mmp-170) cc_final: 0.4923 (mpp-170) REVERT: K 55 SER cc_start: 0.7523 (t) cc_final: 0.6436 (p) REVERT: K 98 GLU cc_start: 0.7116 (pp20) cc_final: 0.6662 (pp20) REVERT: L 30 ILE cc_start: 0.8475 (pp) cc_final: 0.7905 (mm) REVERT: L 68 GLU cc_start: 0.7969 (tp30) cc_final: 0.6851 (mt-10) REVERT: N 33 LYS cc_start: 0.6448 (pmmt) cc_final: 0.5682 (mmtt) REVERT: N 88 LYS cc_start: 0.6147 (tttp) cc_final: 0.5727 (tppt) outliers start: 51 outliers final: 4 residues processed: 1116 average time/residue: 0.2450 time to fit residues: 433.8045 Evaluate side-chains 655 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 645 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain I residue 19 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 GLN A 425 ASN ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 571 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN A1141 GLN A1250 GLN ** A1453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 248 ASN B 282 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 683 ASN B 688 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 867 ASN B 886 ASN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN B 944 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN C 53 ASN C 207 HIS C 216 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 49 ASN D 88 GLN E 143 ASN E 146 HIS G 144 HIS G 161 ASN H 33 GLN H 43 ASN I 19 ASN J 53 HIS ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN M 16 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN N 34 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153008 restraints weight = 53427.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152559 restraints weight = 35256.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153031 restraints weight = 28709.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153546 restraints weight = 25719.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.153691 restraints weight = 24668.715| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35562 Z= 0.212 Angle : 0.796 39.652 48221 Z= 0.378 Chirality : 0.047 0.196 5380 Planarity : 0.006 0.081 6085 Dihedral : 10.837 84.558 5121 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 4.91 % Allowed : 14.90 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.11), residues: 4211 helix: -1.87 (0.12), residues: 1200 sheet: -1.98 (0.19), residues: 598 loop : -2.19 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 261 TYR 0.023 0.002 TYR B 494 PHE 0.022 0.002 PHE B 262 TRP 0.015 0.002 TRP B1159 HIS 0.010 0.002 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (35538) covalent geometry : angle 0.72700 / 0.37 (48194) hydrogen bonds : bond 0.04699 / 3.14 ( 1083) hydrogen bonds : angle 6.78945 / 4.68 ( 3078) metal coordination : bond 0.01387 / 0.96 ( 24) metal coordination : angle 13.70489 / 8.39 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 693 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7110 (ppp) cc_final: 0.6802 (ppp) REVERT: A 199 ASP cc_start: 0.6088 (p0) cc_final: 0.5764 (p0) REVERT: A 342 ARG cc_start: 0.8685 (mtp85) cc_final: 0.8430 (mtt90) REVERT: A 442 LYS cc_start: 0.6594 (ttmt) cc_final: 0.6383 (ttmt) REVERT: A 446 ARG cc_start: 0.4894 (OUTLIER) cc_final: 0.3538 (mtp85) REVERT: A 799 GLU cc_start: 0.8023 (tp30) cc_final: 0.7701 (tp30) REVERT: A 816 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8771 (tp) REVERT: A 1020 GLN cc_start: 0.7943 (mt0) cc_final: 0.7433 (tt0) REVERT: A 1073 TYR cc_start: 0.8658 (t80) cc_final: 0.8446 (t80) REVERT: A 1124 LEU cc_start: 0.8568 (tp) cc_final: 0.8274 (tp) REVERT: A 1128 ASN cc_start: 0.8796 (t0) cc_final: 0.8429 (t0) REVERT: A 1175 MET cc_start: 0.8483 (tmm) cc_final: 0.8034 (tmm) REVERT: A 1235 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8094 (t) REVERT: A 1308 VAL cc_start: 0.7753 (t) cc_final: 0.7273 (p) REVERT: A 1331 LYS cc_start: 0.7232 (tptm) cc_final: 0.6993 (ttmt) REVERT: A 1439 MET cc_start: 0.6482 (ppp) cc_final: 0.5700 (ptm) REVERT: A 1469 TRP cc_start: 0.6498 (p-90) cc_final: 0.5984 (p-90) REVERT: A 1485 MET cc_start: 0.6518 (mmm) cc_final: 0.5576 (mmm) REVERT: A 1616 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: A 1634 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 37 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8514 (tm) REVERT: B 302 LEU cc_start: 0.8234 (mp) cc_final: 0.8025 (mt) REVERT: B 311 ARG cc_start: 0.7315 (mpp80) cc_final: 0.7097 (mmm160) REVERT: B 335 ARG cc_start: 0.6538 (tpt170) cc_final: 0.6273 (tpp80) REVERT: B 373 MET cc_start: 0.7937 (tpp) cc_final: 0.7707 (tpt) REVERT: B 446 MET cc_start: 0.6210 (tpp) cc_final: 0.5838 (tmm) REVERT: B 450 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 497 ILE cc_start: 0.9171 (tp) cc_final: 0.8782 (tp) REVERT: B 576 THR cc_start: 0.5473 (OUTLIER) cc_final: 0.5234 (p) REVERT: B 609 ARG cc_start: 0.7990 (mtp85) cc_final: 0.7701 (mtp85) REVERT: B 742 TYR cc_start: 0.8514 (m-80) cc_final: 0.8184 (m-80) REVERT: B 746 THR cc_start: 0.7434 (OUTLIER) cc_final: 0.6991 (p) REVERT: B 760 TYR cc_start: 0.8324 (m-80) cc_final: 0.8090 (m-80) REVERT: B 803 MET cc_start: 0.7311 (ttm) cc_final: 0.6940 (ttm) REVERT: B 851 TYR cc_start: 0.7118 (t80) cc_final: 0.6848 (t80) REVERT: B 1110 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7395 (mp) REVERT: C 45 SER cc_start: 0.8274 (p) cc_final: 0.7799 (p) REVERT: C 53 ASN cc_start: 0.8158 (t0) cc_final: 0.7891 (t0) REVERT: C 107 LYS cc_start: 0.7428 (mttt) cc_final: 0.7010 (tmmt) REVERT: C 315 PHE cc_start: 0.6836 (t80) cc_final: 0.6514 (t80) REVERT: D 88 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6558 (tp40) REVERT: E 54 GLN cc_start: 0.7512 (tp-100) cc_final: 0.6968 (mp10) REVERT: E 172 GLU cc_start: 0.8513 (mp0) cc_final: 0.8303 (mp0) REVERT: F 60 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8402 (mt0) REVERT: F 61 HIS cc_start: 0.7078 (m90) cc_final: 0.6759 (m-70) REVERT: F 110 ASP cc_start: 0.6943 (t0) cc_final: 0.6739 (t0) REVERT: G 72 LYS cc_start: 0.7864 (mttm) cc_final: 0.7507 (mtpp) REVERT: G 80 VAL cc_start: 0.8046 (t) cc_final: 0.7713 (p) REVERT: G 97 LYS cc_start: 0.7138 (pptt) cc_final: 0.6804 (ptmm) REVERT: G 125 TRP cc_start: 0.7566 (t60) cc_final: 0.7245 (t60) REVERT: H 62 SER cc_start: 0.8456 (t) cc_final: 0.8178 (m) REVERT: H 89 LEU cc_start: 0.8387 (mt) cc_final: 0.7872 (tt) REVERT: I 32 GLN cc_start: 0.6606 (mp-120) cc_final: 0.6375 (mp10) REVERT: I 46 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8029 (tptp) REVERT: I 54 ASP cc_start: 0.6367 (t0) cc_final: 0.6141 (t0) REVERT: I 76 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.4218 (pt) REVERT: K 98 GLU cc_start: 0.6295 (pp20) cc_final: 0.5822 (pp20) REVERT: L 29 TYR cc_start: 0.7592 (m-80) cc_final: 0.7391 (m-80) REVERT: L 40 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6341 (pp) REVERT: M 43 LYS cc_start: 0.6493 (tptp) cc_final: 0.5900 (tppt) REVERT: N 33 LYS cc_start: 0.6784 (pmmt) cc_final: 0.5992 (mmtt) outliers start: 186 outliers final: 85 residues processed: 840 average time/residue: 0.2243 time to fit residues: 307.4759 Evaluate side-chains 674 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 576 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1616 GLU Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 157 TYR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 142 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 351 optimal weight: 10.0000 chunk 386 optimal weight: 5.9990 chunk 400 optimal weight: 7.9990 chunk 411 optimal weight: 8.9990 chunk 27 optimal weight: 0.0670 chunk 290 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1453 HIS B 209 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 710 ASN B 767 ASN B 921 HIS ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN B1157 GLN C 88 ASN C 161 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.181503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150846 restraints weight = 53247.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150324 restraints weight = 41369.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151058 restraints weight = 37731.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151627 restraints weight = 30562.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.151882 restraints weight = 25978.185| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35562 Z= 0.157 Angle : 0.710 30.653 48221 Z= 0.338 Chirality : 0.045 0.191 5380 Planarity : 0.005 0.105 6085 Dihedral : 10.833 85.273 5113 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 4.57 % Allowed : 16.35 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.12), residues: 4211 helix: -1.14 (0.14), residues: 1205 sheet: -1.83 (0.20), residues: 595 loop : -2.01 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1572 TYR 0.029 0.002 TYR A 95 PHE 0.019 0.002 PHE A 223 TRP 0.020 0.001 TRP B 595 HIS 0.016 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (35538) covalent geometry : angle 0.65954 / 0.33 (48194) hydrogen bonds : bond 0.04306 / 2.90 ( 1083) hydrogen bonds : angle 6.21430 / 4.28 ( 3078) metal coordination : bond 0.01144 / 0.80 ( 24) metal coordination : angle 11.08733 / 7.10 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 620 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7373 (pttp) cc_final: 0.6646 (pttm) REVERT: A 182 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8368 (ttmt) REVERT: A 191 MET cc_start: 0.6851 (ppp) cc_final: 0.6575 (ppp) REVERT: A 201 ARG cc_start: 0.6783 (ttm110) cc_final: 0.6366 (mmm160) REVERT: A 225 LYS cc_start: 0.8127 (tptm) cc_final: 0.7645 (tmmt) REVERT: A 238 MET cc_start: 0.5170 (ptt) cc_final: 0.4902 (ptt) REVERT: A 244 ARG cc_start: 0.6899 (ttp-110) cc_final: 0.6428 (ttp-110) REVERT: A 446 ARG cc_start: 0.4165 (OUTLIER) cc_final: 0.3619 (mmp-170) REVERT: A 816 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 925 MET cc_start: 0.8248 (tmm) cc_final: 0.7974 (tmm) REVERT: A 1020 GLN cc_start: 0.7966 (mt0) cc_final: 0.7417 (tt0) REVERT: A 1064 THR cc_start: 0.6712 (OUTLIER) cc_final: 0.6485 (m) REVERT: A 1073 TYR cc_start: 0.8675 (t80) cc_final: 0.8438 (t80) REVERT: A 1085 LEU cc_start: 0.8372 (mt) cc_final: 0.7615 (tt) REVERT: A 1124 LEU cc_start: 0.8496 (tp) cc_final: 0.8232 (tp) REVERT: A 1175 MET cc_start: 0.8318 (tmm) cc_final: 0.8022 (tmm) REVERT: A 1275 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7083 (p) REVERT: A 1439 MET cc_start: 0.6332 (ppp) cc_final: 0.5652 (ptm) REVERT: A 1469 TRP cc_start: 0.6612 (p-90) cc_final: 0.6042 (p-90) REVERT: A 1573 TYR cc_start: 0.4716 (OUTLIER) cc_final: 0.4233 (t80) REVERT: A 1634 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7779 (pp) REVERT: B 37 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8454 (tm) REVERT: B 308 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7181 (mm) REVERT: B 346 ASP cc_start: 0.6740 (p0) cc_final: 0.6245 (p0) REVERT: B 373 MET cc_start: 0.8015 (tpp) cc_final: 0.7742 (tpt) REVERT: B 440 PHE cc_start: 0.5761 (m-10) cc_final: 0.5495 (m-10) REVERT: B 446 MET cc_start: 0.6346 (tpp) cc_final: 0.5940 (tmm) REVERT: B 447 SER cc_start: 0.8374 (m) cc_final: 0.8068 (p) REVERT: B 450 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 497 ILE cc_start: 0.9246 (tp) cc_final: 0.8903 (tp) REVERT: B 576 THR cc_start: 0.5594 (OUTLIER) cc_final: 0.5217 (p) REVERT: B 677 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 726 MET cc_start: 0.8253 (ttm) cc_final: 0.7996 (ttm) REVERT: B 746 THR cc_start: 0.7357 (OUTLIER) cc_final: 0.6968 (p) REVERT: B 930 LYS cc_start: 0.8825 (mttt) cc_final: 0.8601 (mtpp) REVERT: B 1013 MET cc_start: 0.8425 (mtp) cc_final: 0.8039 (mtp) REVERT: C 45 SER cc_start: 0.8410 (p) cc_final: 0.8062 (p) REVERT: C 246 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6518 (ptp90) REVERT: C 271 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7703 (mtp85) REVERT: C 315 PHE cc_start: 0.6734 (t80) cc_final: 0.6428 (t80) REVERT: E 54 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6985 (mp10) REVERT: E 146 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7913 (m90) REVERT: E 164 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8533 (tp) REVERT: E 172 GLU cc_start: 0.8553 (mp0) cc_final: 0.8270 (mp0) REVERT: F 60 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8520 (mt0) REVERT: F 61 HIS cc_start: 0.7188 (m90) cc_final: 0.6840 (m-70) REVERT: F 150 GLU cc_start: 0.7958 (pt0) cc_final: 0.7501 (pt0) REVERT: G 80 VAL cc_start: 0.8220 (t) cc_final: 0.7925 (p) REVERT: G 97 LYS cc_start: 0.7128 (pptt) cc_final: 0.6847 (ptmm) REVERT: G 125 TRP cc_start: 0.7283 (t60) cc_final: 0.6795 (t60) REVERT: H 9 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7391 (mt) REVERT: H 52 GLN cc_start: 0.8071 (mp-120) cc_final: 0.7176 (pm20) REVERT: H 62 SER cc_start: 0.8380 (t) cc_final: 0.8100 (m) REVERT: H 89 LEU cc_start: 0.8290 (mt) cc_final: 0.7857 (tt) REVERT: H 139 ASN cc_start: 0.7061 (m-40) cc_final: 0.6844 (m-40) REVERT: I 32 GLN cc_start: 0.6526 (mp-120) cc_final: 0.6319 (mp10) REVERT: I 54 ASP cc_start: 0.6174 (t0) cc_final: 0.5878 (t0) REVERT: I 76 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5245 (tt) REVERT: K 98 GLU cc_start: 0.6040 (pp20) cc_final: 0.5632 (pp20) REVERT: K 140 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7849 (tptt) REVERT: L 29 TYR cc_start: 0.7710 (m-80) cc_final: 0.7431 (m-80) REVERT: L 68 GLU cc_start: 0.7599 (mm-30) cc_final: 0.6757 (mt-10) REVERT: M 90 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6565 (mm) REVERT: N 33 LYS cc_start: 0.6912 (pmmt) cc_final: 0.6116 (mmtt) outliers start: 173 outliers final: 83 residues processed: 761 average time/residue: 0.2271 time to fit residues: 283.2029 Evaluate side-chains 656 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 555 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 146 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 36 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 70 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 423 optimal weight: 50.0000 chunk 100 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 284 optimal weight: 1.9990 chunk 192 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN L 53 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147482 restraints weight = 53244.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146177 restraints weight = 44051.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147328 restraints weight = 39486.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147813 restraints weight = 33404.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148043 restraints weight = 27772.049| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 35562 Z= 0.175 Angle : 0.693 22.983 48221 Z= 0.338 Chirality : 0.045 0.201 5380 Planarity : 0.005 0.081 6085 Dihedral : 10.888 84.645 5113 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 4.76 % Allowed : 17.01 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.12), residues: 4211 helix: -0.92 (0.14), residues: 1232 sheet: -1.63 (0.20), residues: 581 loop : -1.95 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 481 TYR 0.026 0.002 TYR A 981 PHE 0.022 0.002 PHE A 223 TRP 0.021 0.001 TRP B 595 HIS 0.011 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (35538) covalent geometry : angle 0.66276 / 0.34 (48194) hydrogen bonds : bond 0.03959 / 2.66 ( 1083) hydrogen bonds : angle 5.95076 / 4.10 ( 3078) metal coordination : bond 0.00987 / 0.69 ( 24) metal coordination : angle 8.62853 / 5.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 590 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7590 (pttp) cc_final: 0.6859 (pttm) REVERT: A 182 LYS cc_start: 0.8751 (ttpt) cc_final: 0.8477 (ttmt) REVERT: A 191 MET cc_start: 0.6909 (ppp) cc_final: 0.6626 (ppp) REVERT: A 201 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6162 (mmm160) REVERT: A 225 LYS cc_start: 0.8138 (tptm) cc_final: 0.7681 (tmmt) REVERT: A 446 ARG cc_start: 0.3774 (OUTLIER) cc_final: 0.3449 (mmm160) REVERT: A 472 MET cc_start: 0.8507 (mmp) cc_final: 0.8275 (mmp) REVERT: A 925 MET cc_start: 0.8285 (tmm) cc_final: 0.7922 (tmm) REVERT: A 977 MET cc_start: 0.7915 (tmm) cc_final: 0.7644 (tmm) REVERT: A 1020 GLN cc_start: 0.8065 (mt0) cc_final: 0.7500 (tt0) REVERT: A 1064 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6516 (m) REVERT: A 1073 TYR cc_start: 0.8741 (t80) cc_final: 0.8506 (t80) REVERT: A 1085 LEU cc_start: 0.8404 (mt) cc_final: 0.7703 (tt) REVERT: A 1124 LEU cc_start: 0.8662 (tp) cc_final: 0.8448 (tp) REVERT: A 1175 MET cc_start: 0.8412 (tmm) cc_final: 0.8099 (tmm) REVERT: A 1275 THR cc_start: 0.7532 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 1439 MET cc_start: 0.6283 (ppp) cc_final: 0.5975 (ptm) REVERT: A 1573 TYR cc_start: 0.4907 (OUTLIER) cc_final: 0.4384 (t80) REVERT: A 1634 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 37 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8560 (tm) REVERT: B 302 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7780 (mt) REVERT: B 308 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7215 (mm) REVERT: B 446 MET cc_start: 0.6288 (tpp) cc_final: 0.5920 (tmm) REVERT: B 447 SER cc_start: 0.8329 (m) cc_final: 0.8052 (p) REVERT: B 497 ILE cc_start: 0.9297 (tp) cc_final: 0.8989 (tp) REVERT: B 677 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 742 TYR cc_start: 0.8636 (m-80) cc_final: 0.8371 (m-10) REVERT: B 746 THR cc_start: 0.7450 (OUTLIER) cc_final: 0.7100 (p) REVERT: B 930 LYS cc_start: 0.8821 (mttt) cc_final: 0.8579 (mtpp) REVERT: B 1013 MET cc_start: 0.8699 (mtp) cc_final: 0.8254 (mtp) REVERT: C 82 TYR cc_start: 0.8263 (m-80) cc_final: 0.7997 (m-80) REVERT: C 107 LYS cc_start: 0.7580 (mttt) cc_final: 0.7160 (tmmt) REVERT: C 246 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6426 (ptp90) REVERT: C 271 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7522 (mtp85) REVERT: C 315 PHE cc_start: 0.6808 (t80) cc_final: 0.6493 (t80) REVERT: E 54 GLN cc_start: 0.7410 (tp-100) cc_final: 0.7010 (mp10) REVERT: E 164 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8582 (tp) REVERT: E 172 GLU cc_start: 0.8577 (mp0) cc_final: 0.8218 (mp0) REVERT: E 174 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: F 61 HIS cc_start: 0.7248 (m90) cc_final: 0.6884 (m-70) REVERT: F 79 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6822 (ptt90) REVERT: F 150 GLU cc_start: 0.7989 (pt0) cc_final: 0.7599 (pt0) REVERT: G 80 VAL cc_start: 0.8231 (t) cc_final: 0.7949 (p) REVERT: G 125 TRP cc_start: 0.7362 (t60) cc_final: 0.6842 (t60) REVERT: H 62 SER cc_start: 0.8463 (t) cc_final: 0.8196 (m) REVERT: H 89 LEU cc_start: 0.8259 (mt) cc_final: 0.7879 (tt) REVERT: H 139 ASN cc_start: 0.7293 (m-40) cc_final: 0.7059 (m-40) REVERT: I 32 GLN cc_start: 0.6401 (mp-120) cc_final: 0.6158 (mp10) REVERT: I 46 LYS cc_start: 0.8450 (tptp) cc_final: 0.7414 (tptm) REVERT: I 54 ASP cc_start: 0.6227 (t0) cc_final: 0.5856 (t0) REVERT: I 76 LEU cc_start: 0.5619 (OUTLIER) cc_final: 0.5341 (tt) REVERT: K 44 ARG cc_start: 0.5564 (mmp-170) cc_final: 0.4641 (mpp-170) REVERT: K 98 GLU cc_start: 0.6161 (pp20) cc_final: 0.5706 (pp20) REVERT: K 125 MET cc_start: 0.7833 (mmt) cc_final: 0.7513 (mmp) REVERT: K 140 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7742 (tptt) REVERT: L 29 TYR cc_start: 0.7825 (m-80) cc_final: 0.7508 (m-80) REVERT: L 40 LEU cc_start: 0.6278 (OUTLIER) cc_final: 0.5939 (pp) REVERT: L 68 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6787 (mt-10) REVERT: M 90 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6614 (mm) REVERT: N 33 LYS cc_start: 0.6946 (pmmt) cc_final: 0.6138 (mmtt) outliers start: 180 outliers final: 112 residues processed: 726 average time/residue: 0.2238 time to fit residues: 266.3625 Evaluate side-chains 687 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 558 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1660 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 283 optimal weight: 0.0570 chunk 402 optimal weight: 0.1980 chunk 173 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 313 optimal weight: 10.0000 chunk 282 optimal weight: 0.9990 chunk 226 optimal weight: 0.0870 chunk 218 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 390 optimal weight: 5.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS A 785 GLN A 795 HIS A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 HIS A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 147 HIS H 52 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149542 restraints weight = 52913.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150604 restraints weight = 40803.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150969 restraints weight = 31900.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151708 restraints weight = 28260.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152192 restraints weight = 24868.801| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 35562 Z= 0.119 Angle : 0.644 17.116 48221 Z= 0.316 Chirality : 0.044 0.275 5380 Planarity : 0.005 0.156 6085 Dihedral : 10.833 85.680 5113 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 4.17 % Allowed : 18.20 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.12), residues: 4211 helix: -0.64 (0.14), residues: 1215 sheet: -1.42 (0.21), residues: 574 loop : -1.80 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 119 TYR 0.027 0.001 TYR H 93 PHE 0.023 0.001 PHE B1135 TRP 0.029 0.002 TRP B 832 HIS 0.024 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (35538) covalent geometry : angle 0.62324 / 0.31 (48194) hydrogen bonds : bond 0.03617 / 2.43 ( 1083) hydrogen bonds : angle 5.67945 / 3.92 ( 3078) metal coordination : bond 0.00686 / 0.46 ( 24) metal coordination : angle 6.95066 / 4.09 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 616 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7498 (pttp) cc_final: 0.6816 (pttm) REVERT: A 182 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8353 (ttmt) REVERT: A 191 MET cc_start: 0.6742 (ppp) cc_final: 0.6495 (ppp) REVERT: A 201 ARG cc_start: 0.6672 (ttm110) cc_final: 0.6140 (mmm160) REVERT: A 225 LYS cc_start: 0.7990 (tptm) cc_final: 0.7633 (tmmt) REVERT: A 378 HIS cc_start: 0.6872 (m-70) cc_final: 0.6639 (m170) REVERT: A 446 ARG cc_start: 0.3768 (OUTLIER) cc_final: 0.3434 (mmm160) REVERT: A 471 MET cc_start: 0.7729 (mmt) cc_final: 0.7499 (mmt) REVERT: A 642 ASN cc_start: 0.8078 (t0) cc_final: 0.7789 (t0) REVERT: A 925 MET cc_start: 0.8145 (tmm) cc_final: 0.7836 (tmm) REVERT: A 1020 GLN cc_start: 0.8029 (mt0) cc_final: 0.7350 (tt0) REVERT: A 1040 ASP cc_start: 0.8921 (m-30) cc_final: 0.8707 (m-30) REVERT: A 1073 TYR cc_start: 0.8651 (t80) cc_final: 0.8413 (t80) REVERT: A 1085 LEU cc_start: 0.8302 (mt) cc_final: 0.7742 (tt) REVERT: A 1124 LEU cc_start: 0.8650 (tp) cc_final: 0.8448 (tp) REVERT: A 1175 MET cc_start: 0.8385 (tmm) cc_final: 0.8050 (tmm) REVERT: A 1227 MET cc_start: 0.7211 (mmm) cc_final: 0.6152 (mmm) REVERT: A 1275 THR cc_start: 0.7472 (OUTLIER) cc_final: 0.7229 (m) REVERT: A 1439 MET cc_start: 0.6231 (ppp) cc_final: 0.5968 (ptm) REVERT: A 1573 TYR cc_start: 0.4692 (OUTLIER) cc_final: 0.4230 (t80) REVERT: A 1588 MET cc_start: 0.8829 (mmm) cc_final: 0.8414 (tpt) REVERT: A 1634 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7854 (pp) REVERT: B 37 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8399 (tm) REVERT: B 71 LYS cc_start: 0.7150 (mtpp) cc_final: 0.6730 (mmtt) REVERT: B 205 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6691 (ttp) REVERT: B 302 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 305 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6872 (tpt90) REVERT: B 308 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7158 (mm) REVERT: B 335 ARG cc_start: 0.6268 (tpt170) cc_final: 0.5869 (tpp-160) REVERT: B 346 ASP cc_start: 0.7149 (p0) cc_final: 0.6877 (p0) REVERT: B 447 SER cc_start: 0.8195 (m) cc_final: 0.7721 (p) REVERT: B 576 THR cc_start: 0.5576 (OUTLIER) cc_final: 0.5336 (p) REVERT: B 667 PHE cc_start: 0.7648 (t80) cc_final: 0.7258 (t80) REVERT: B 677 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7663 (p) REVERT: B 725 THR cc_start: 0.9253 (p) cc_final: 0.8848 (t) REVERT: B 760 TYR cc_start: 0.8380 (m-80) cc_final: 0.7871 (m-80) REVERT: B 795 GLU cc_start: 0.7141 (pt0) cc_final: 0.6594 (pt0) REVERT: B 917 PHE cc_start: 0.8228 (m-80) cc_final: 0.8027 (m-80) REVERT: B 1013 MET cc_start: 0.8647 (mtp) cc_final: 0.8186 (mtp) REVERT: B 1088 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8294 (tt) REVERT: C 82 TYR cc_start: 0.8281 (m-80) cc_final: 0.8057 (m-80) REVERT: C 107 LYS cc_start: 0.7554 (mttt) cc_final: 0.7119 (tmmt) REVERT: C 246 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6393 (ptp90) REVERT: C 271 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7254 (mtp85) REVERT: E 54 GLN cc_start: 0.7325 (tp-100) cc_final: 0.6977 (mp10) REVERT: E 174 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: F 61 HIS cc_start: 0.7246 (m90) cc_final: 0.6851 (m-70) REVERT: F 62 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: F 150 GLU cc_start: 0.7912 (pt0) cc_final: 0.7630 (pt0) REVERT: G 43 ILE cc_start: 0.7586 (pt) cc_final: 0.7362 (pt) REVERT: G 52 MET cc_start: 0.8068 (ptm) cc_final: 0.7800 (ptp) REVERT: G 80 VAL cc_start: 0.8032 (t) cc_final: 0.7733 (p) REVERT: G 97 LYS cc_start: 0.7083 (pptt) cc_final: 0.6783 (ptmm) REVERT: G 125 TRP cc_start: 0.7335 (t60) cc_final: 0.7079 (t60) REVERT: H 9 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7440 (mt) REVERT: H 41 ASP cc_start: 0.7191 (m-30) cc_final: 0.6984 (m-30) REVERT: H 62 SER cc_start: 0.8507 (t) cc_final: 0.8179 (m) REVERT: H 89 LEU cc_start: 0.8280 (mt) cc_final: 0.7922 (tt) REVERT: H 94 ASP cc_start: 0.7598 (m-30) cc_final: 0.7333 (m-30) REVERT: I 7 LEU cc_start: 0.7354 (mt) cc_final: 0.6994 (mt) REVERT: I 32 GLN cc_start: 0.6405 (mp-120) cc_final: 0.6139 (mp10) REVERT: I 46 LYS cc_start: 0.8389 (tptp) cc_final: 0.7423 (tptm) REVERT: I 54 ASP cc_start: 0.6080 (t0) cc_final: 0.5707 (t0) REVERT: I 76 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4008 (pt) REVERT: J 25 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8978 (tt) REVERT: K 44 ARG cc_start: 0.5495 (mmp-170) cc_final: 0.4792 (mpp-170) REVERT: K 98 GLU cc_start: 0.5843 (pp20) cc_final: 0.5614 (pp20) REVERT: K 125 MET cc_start: 0.7674 (mmt) cc_final: 0.7374 (mmp) REVERT: K 140 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7690 (tptt) REVERT: L 29 TYR cc_start: 0.7705 (m-80) cc_final: 0.7428 (m-80) REVERT: L 40 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5906 (pp) REVERT: L 68 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6716 (mt-10) REVERT: M 90 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.6688 (mm) REVERT: N 33 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6112 (mmtt) outliers start: 158 outliers final: 88 residues processed: 732 average time/residue: 0.2258 time to fit residues: 272.4402 Evaluate side-chains 665 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 556 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 80 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 125 optimal weight: 0.7980 chunk 318 optimal weight: 0.7980 chunk 269 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 378 optimal weight: 0.8980 chunk 332 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS B 251 HIS ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN F 60 GLN G 237 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.180244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148294 restraints weight = 52737.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148862 restraints weight = 40697.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149525 restraints weight = 33098.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150212 restraints weight = 26927.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150291 restraints weight = 23042.985| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35562 Z= 0.132 Angle : 0.642 16.990 48221 Z= 0.318 Chirality : 0.044 0.222 5380 Planarity : 0.004 0.057 6085 Dihedral : 10.816 85.347 5113 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.28 % Rotamer: Outliers : 4.20 % Allowed : 18.89 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4211 helix: -0.50 (0.15), residues: 1215 sheet: -1.37 (0.21), residues: 575 loop : -1.76 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.030 0.002 TYR A 618 PHE 0.019 0.001 PHE B1135 TRP 0.042 0.002 TRP B 832 HIS 0.014 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (35538) covalent geometry : angle 0.62492 / 0.32 (48194) hydrogen bonds : bond 0.03569 / 2.39 ( 1083) hydrogen bonds : angle 5.56282 / 3.84 ( 3078) metal coordination : bond 0.00592 / 0.38 ( 24) metal coordination : angle 6.31080 / 3.63 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 567 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7471 (pttp) cc_final: 0.6648 (pttm) REVERT: A 182 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8387 (ttmt) REVERT: A 191 MET cc_start: 0.6890 (ppp) cc_final: 0.6620 (ppp) REVERT: A 201 ARG cc_start: 0.6705 (ttm110) cc_final: 0.6226 (mmm160) REVERT: A 225 LYS cc_start: 0.7956 (tptm) cc_final: 0.7642 (tmmt) REVERT: A 378 HIS cc_start: 0.6876 (m-70) cc_final: 0.6630 (m170) REVERT: A 471 MET cc_start: 0.7764 (mmt) cc_final: 0.7545 (mmt) REVERT: A 925 MET cc_start: 0.8189 (tmm) cc_final: 0.7900 (tmm) REVERT: A 928 MET cc_start: 0.8086 (ttp) cc_final: 0.7626 (tmm) REVERT: A 1020 GLN cc_start: 0.8034 (mt0) cc_final: 0.7320 (tt0) REVERT: A 1040 ASP cc_start: 0.8940 (m-30) cc_final: 0.8726 (m-30) REVERT: A 1073 TYR cc_start: 0.8676 (t80) cc_final: 0.8445 (t80) REVERT: A 1085 LEU cc_start: 0.8327 (mt) cc_final: 0.7788 (tt) REVERT: A 1175 MET cc_start: 0.8403 (tmm) cc_final: 0.8098 (tmm) REVERT: A 1227 MET cc_start: 0.7286 (mmm) cc_final: 0.6267 (mmm) REVERT: A 1275 THR cc_start: 0.7566 (OUTLIER) cc_final: 0.7324 (p) REVERT: A 1439 MET cc_start: 0.6190 (ppp) cc_final: 0.5864 (ptm) REVERT: A 1573 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.4317 (t80) REVERT: A 1588 MET cc_start: 0.8844 (mmm) cc_final: 0.8440 (tpt) REVERT: A 1634 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7944 (pp) REVERT: B 37 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8575 (tm) REVERT: B 71 LYS cc_start: 0.7169 (mtpp) cc_final: 0.6771 (mmtt) REVERT: B 205 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6791 (ttp) REVERT: B 219 ARG cc_start: 0.8390 (mtp180) cc_final: 0.8071 (ttm110) REVERT: B 302 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 305 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6933 (tpt90) REVERT: B 308 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7186 (mm) REVERT: B 346 ASP cc_start: 0.6893 (p0) cc_final: 0.6192 (m-30) REVERT: B 359 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6351 (mt) REVERT: B 447 SER cc_start: 0.8126 (m) cc_final: 0.6970 (p) REVERT: B 502 MET cc_start: 0.8505 (tmm) cc_final: 0.8269 (tmm) REVERT: B 576 THR cc_start: 0.5640 (OUTLIER) cc_final: 0.5321 (p) REVERT: B 667 PHE cc_start: 0.7802 (t80) cc_final: 0.7254 (t80) REVERT: B 668 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 725 THR cc_start: 0.9260 (p) cc_final: 0.8914 (t) REVERT: B 1013 MET cc_start: 0.8582 (mtp) cc_final: 0.8153 (mtp) REVERT: C 82 TYR cc_start: 0.8268 (m-80) cc_final: 0.8043 (m-80) REVERT: C 107 LYS cc_start: 0.7583 (mttt) cc_final: 0.7150 (tmmt) REVERT: C 246 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6428 (ptp90) REVERT: E 54 GLN cc_start: 0.7309 (tp-100) cc_final: 0.6983 (mp10) REVERT: E 149 LEU cc_start: 0.8828 (pt) cc_final: 0.8370 (pp) REVERT: E 164 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8462 (tp) REVERT: F 57 ASP cc_start: 0.6604 (p0) cc_final: 0.6322 (p0) REVERT: F 61 HIS cc_start: 0.7255 (m90) cc_final: 0.6866 (m-70) REVERT: F 79 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6942 (ptt90) REVERT: G 80 VAL cc_start: 0.8060 (t) cc_final: 0.7667 (p) REVERT: G 97 LYS cc_start: 0.7147 (pptt) cc_final: 0.6915 (ptmm) REVERT: G 125 TRP cc_start: 0.7323 (t60) cc_final: 0.6864 (t60) REVERT: H 9 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7442 (mt) REVERT: H 62 SER cc_start: 0.8563 (t) cc_final: 0.8251 (m) REVERT: H 89 LEU cc_start: 0.8109 (mt) cc_final: 0.7820 (tt) REVERT: I 7 LEU cc_start: 0.7390 (mt) cc_final: 0.7034 (mt) REVERT: I 32 GLN cc_start: 0.6375 (mp-120) cc_final: 0.6144 (mp10) REVERT: I 46 LYS cc_start: 0.8417 (tptp) cc_final: 0.7379 (tptm) REVERT: I 54 ASP cc_start: 0.6126 (t0) cc_final: 0.5683 (t0) REVERT: I 76 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5128 (tt) REVERT: J 25 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9047 (tt) REVERT: K 98 GLU cc_start: 0.5940 (pp20) cc_final: 0.5634 (pp20) REVERT: K 125 MET cc_start: 0.7541 (mmt) cc_final: 0.7089 (mmp) REVERT: K 140 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7704 (tptt) REVERT: L 29 TYR cc_start: 0.7743 (m-80) cc_final: 0.7524 (m-80) REVERT: L 33 GLU cc_start: 0.6791 (pm20) cc_final: 0.5604 (pm20) REVERT: L 40 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5944 (pp) REVERT: L 68 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6793 (mt-10) REVERT: M 90 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6680 (mm) REVERT: N 33 LYS cc_start: 0.6937 (pmmt) cc_final: 0.6150 (mmtt) outliers start: 159 outliers final: 101 residues processed: 679 average time/residue: 0.2172 time to fit residues: 243.6079 Evaluate side-chains 665 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 546 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 52 GLN Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 106 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 99 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 285 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 2 optimal weight: 0.0000 chunk 9 optimal weight: 3.9990 chunk 370 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS B1041 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN G 56 ASN G 237 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148792 restraints weight = 52942.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148479 restraints weight = 41741.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.149952 restraints weight = 33498.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150286 restraints weight = 29062.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150634 restraints weight = 25923.219| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35562 Z= 0.126 Angle : 0.641 17.325 48221 Z= 0.318 Chirality : 0.044 0.257 5380 Planarity : 0.004 0.052 6085 Dihedral : 10.797 85.763 5109 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 4.23 % Allowed : 19.10 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.12), residues: 4211 helix: -0.39 (0.15), residues: 1203 sheet: -1.31 (0.21), residues: 590 loop : -1.69 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 609 TYR 0.022 0.001 TYR A 618 PHE 0.026 0.001 PHE L 67 TRP 0.026 0.001 TRP B 832 HIS 0.036 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (35538) covalent geometry : angle 0.62648 / 0.32 (48194) hydrogen bonds : bond 0.03476 / 2.33 ( 1083) hydrogen bonds : angle 5.47905 / 3.78 ( 3078) metal coordination : bond 0.00609 / 0.35 ( 24) metal coordination : angle 5.78140 / 3.24 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 565 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7517 (pttp) cc_final: 0.6724 (pttm) REVERT: A 182 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8365 (ttmt) REVERT: A 191 MET cc_start: 0.6896 (ppp) cc_final: 0.6657 (ppp) REVERT: A 201 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6130 (mmm160) REVERT: A 225 LYS cc_start: 0.7947 (tptm) cc_final: 0.7626 (tmmt) REVERT: A 378 HIS cc_start: 0.6928 (m-70) cc_final: 0.6675 (m170) REVERT: A 574 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7104 (m-40) REVERT: A 925 MET cc_start: 0.8158 (tmm) cc_final: 0.7891 (tmm) REVERT: A 1020 GLN cc_start: 0.8044 (mt0) cc_final: 0.7244 (tt0) REVERT: A 1073 TYR cc_start: 0.8666 (t80) cc_final: 0.8453 (t80) REVERT: A 1085 LEU cc_start: 0.8274 (mt) cc_final: 0.7740 (tt) REVERT: A 1108 HIS cc_start: 0.6426 (t-90) cc_final: 0.6216 (t-90) REVERT: A 1175 MET cc_start: 0.8360 (tmm) cc_final: 0.8044 (tmm) REVERT: A 1227 MET cc_start: 0.7265 (mmm) cc_final: 0.6158 (mmm) REVERT: A 1275 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7443 (p) REVERT: A 1439 MET cc_start: 0.6224 (ppp) cc_final: 0.5803 (ptt) REVERT: A 1573 TYR cc_start: 0.4964 (OUTLIER) cc_final: 0.4411 (t80) REVERT: A 1588 MET cc_start: 0.8863 (mmm) cc_final: 0.8487 (tpt) REVERT: A 1611 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7591 (tmm) REVERT: A 1634 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7994 (pp) REVERT: B 37 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8551 (tm) REVERT: B 60 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 71 LYS cc_start: 0.7197 (mtpp) cc_final: 0.6808 (mmtt) REVERT: B 205 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6846 (ttp) REVERT: B 219 ARG cc_start: 0.8338 (mtp180) cc_final: 0.8051 (ttm110) REVERT: B 302 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 305 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7010 (tpt90) REVERT: B 308 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 346 ASP cc_start: 0.6817 (p0) cc_final: 0.6294 (m-30) REVERT: B 359 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6399 (mt) REVERT: B 447 SER cc_start: 0.8129 (m) cc_final: 0.7537 (p) REVERT: B 502 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: B 576 THR cc_start: 0.5667 (OUTLIER) cc_final: 0.5339 (p) REVERT: B 667 PHE cc_start: 0.7769 (t80) cc_final: 0.7178 (t80) REVERT: B 668 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6370 (tp30) REVERT: B 725 THR cc_start: 0.9294 (p) cc_final: 0.8923 (t) REVERT: B 1013 MET cc_start: 0.8573 (mtp) cc_final: 0.8094 (mtp) REVERT: C 107 LYS cc_start: 0.7549 (mttt) cc_final: 0.7144 (tmmt) REVERT: C 246 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6721 (ptp90) REVERT: E 54 GLN cc_start: 0.7363 (tp-100) cc_final: 0.7088 (mp10) REVERT: E 164 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8487 (tp) REVERT: E 174 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: F 57 ASP cc_start: 0.7331 (p0) cc_final: 0.7120 (p0) REVERT: F 61 HIS cc_start: 0.7280 (m90) cc_final: 0.6878 (m-70) REVERT: G 76 LYS cc_start: 0.8053 (mmtm) cc_final: 0.7317 (mmmt) REVERT: G 80 VAL cc_start: 0.8010 (t) cc_final: 0.7781 (p) REVERT: G 97 LYS cc_start: 0.7087 (pptt) cc_final: 0.6880 (ptmm) REVERT: G 125 TRP cc_start: 0.7427 (t60) cc_final: 0.6934 (t60) REVERT: H 9 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7456 (mt) REVERT: H 62 SER cc_start: 0.8537 (t) cc_final: 0.8228 (m) REVERT: H 89 LEU cc_start: 0.8247 (mt) cc_final: 0.7933 (tt) REVERT: I 7 LEU cc_start: 0.7393 (mt) cc_final: 0.7048 (mt) REVERT: I 32 GLN cc_start: 0.6425 (mp-120) cc_final: 0.5791 (mm110) REVERT: I 46 LYS cc_start: 0.8397 (tptp) cc_final: 0.7370 (tptm) REVERT: I 54 ASP cc_start: 0.6218 (t0) cc_final: 0.5742 (t0) REVERT: I 76 LEU cc_start: 0.5239 (OUTLIER) cc_final: 0.4959 (tt) REVERT: J 25 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9055 (tt) REVERT: K 52 GLN cc_start: 0.7722 (mp10) cc_final: 0.7094 (mt0) REVERT: K 125 MET cc_start: 0.7487 (mmt) cc_final: 0.7002 (mmp) REVERT: K 140 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7640 (tppt) REVERT: L 40 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5885 (pp) REVERT: L 68 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6785 (mt-10) REVERT: M 60 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.6091 (tm) REVERT: M 90 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.6694 (mm) REVERT: N 33 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6218 (mmtt) outliers start: 160 outliers final: 96 residues processed: 682 average time/residue: 0.2061 time to fit residues: 234.0071 Evaluate side-chains 664 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 544 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1138 GLU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 654 ARG Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 103 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 383 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 225 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 393 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 431 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E 104 ASN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS H 134 ASN J 23 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.169213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137263 restraints weight = 53380.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136490 restraints weight = 43160.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137474 restraints weight = 37744.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138083 restraints weight = 29660.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.138130 restraints weight = 27027.469| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 35562 Z= 0.324 Angle : 0.863 17.645 48221 Z= 0.437 Chirality : 0.052 0.218 5380 Planarity : 0.006 0.073 6085 Dihedral : 11.179 83.173 5109 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.03 % Favored : 91.90 % Rotamer: Outliers : 5.02 % Allowed : 19.13 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.12), residues: 4211 helix: -0.89 (0.14), residues: 1225 sheet: -1.53 (0.21), residues: 564 loop : -1.94 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 63 TYR 0.038 0.003 TYR A 618 PHE 0.024 0.003 PHE C 300 TRP 0.021 0.003 TRP B 595 HIS 0.046 0.003 HIS A 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.32 (35538) covalent geometry : angle 0.84812 / 0.44 (48194) hydrogen bonds : bond 0.04889 / 3.27 ( 1083) hydrogen bonds : angle 5.95791 / 4.12 ( 3078) metal coordination : bond 0.01486 / 0.85 ( 24) metal coordination : angle 6.69639 / 4.03 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 563 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7951 (pttp) cc_final: 0.7277 (pttm) REVERT: A 182 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8451 (mmtt) REVERT: A 378 HIS cc_start: 0.6970 (m-70) cc_final: 0.6733 (m170) REVERT: A 574 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7498 (m-40) REVERT: A 585 ASP cc_start: 0.8024 (m-30) cc_final: 0.7814 (m-30) REVERT: A 925 MET cc_start: 0.8426 (tmm) cc_final: 0.8028 (tmm) REVERT: A 1020 GLN cc_start: 0.8160 (mt0) cc_final: 0.7539 (tt0) REVERT: A 1072 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8955 (m-40) REVERT: A 1073 TYR cc_start: 0.8873 (t80) cc_final: 0.8616 (t80) REVERT: A 1175 MET cc_start: 0.8334 (tmm) cc_final: 0.8110 (tmm) REVERT: A 1227 MET cc_start: 0.7215 (mmm) cc_final: 0.6046 (mmm) REVERT: A 1439 MET cc_start: 0.6389 (ppp) cc_final: 0.5869 (ptt) REVERT: A 1440 ASN cc_start: 0.5673 (t0) cc_final: 0.5366 (t0) REVERT: A 1464 ASP cc_start: 0.5972 (p0) cc_final: 0.5706 (m-30) REVERT: A 1571 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.8064 (t) REVERT: A 1573 TYR cc_start: 0.5345 (OUTLIER) cc_final: 0.4630 (t80) REVERT: A 1588 MET cc_start: 0.8960 (mmm) cc_final: 0.8719 (tpt) REVERT: A 1599 ASN cc_start: 0.7274 (p0) cc_final: 0.6375 (p0) REVERT: A 1634 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8070 (pp) REVERT: B 37 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8771 (tm) REVERT: B 205 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6994 (mtt) REVERT: B 219 ARG cc_start: 0.8509 (mtp180) cc_final: 0.8175 (ttm110) REVERT: B 308 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7361 (mm) REVERT: B 373 MET cc_start: 0.8001 (tpp) cc_final: 0.7684 (tpp) REVERT: B 525 TRP cc_start: 0.8615 (t-100) cc_final: 0.8184 (t-100) REVERT: B 909 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7894 (mmm-85) REVERT: B 912 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.6302 (pm20) REVERT: B 946 ASP cc_start: 0.8954 (p0) cc_final: 0.8744 (p0) REVERT: B 1013 MET cc_start: 0.8592 (mtp) cc_final: 0.7876 (mtp) REVERT: B 1077 ASP cc_start: 0.7672 (p0) cc_final: 0.7389 (p0) REVERT: B 1089 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7681 (tm-30) REVERT: B 1158 ILE cc_start: 0.7481 (tt) cc_final: 0.7238 (tt) REVERT: C 60 ASP cc_start: 0.8246 (t70) cc_final: 0.8042 (t0) REVERT: C 246 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6669 (ttp80) REVERT: E 54 GLN cc_start: 0.7536 (tp-100) cc_final: 0.6768 (mp10) REVERT: E 164 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 174 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: F 57 ASP cc_start: 0.7628 (p0) cc_final: 0.7396 (p0) REVERT: F 61 HIS cc_start: 0.7309 (m90) cc_final: 0.6919 (m-70) REVERT: G 80 VAL cc_start: 0.8260 (t) cc_final: 0.7944 (p) REVERT: G 125 TRP cc_start: 0.7708 (t60) cc_final: 0.7240 (t60) REVERT: H 62 SER cc_start: 0.8726 (t) cc_final: 0.8461 (m) REVERT: H 89 LEU cc_start: 0.8483 (mt) cc_final: 0.8026 (tt) REVERT: H 130 ARG cc_start: 0.6750 (ptp90) cc_final: 0.6517 (ptp90) REVERT: I 32 GLN cc_start: 0.6656 (mp-120) cc_final: 0.6101 (mm110) REVERT: I 46 LYS cc_start: 0.8527 (tptp) cc_final: 0.7593 (tptm) REVERT: I 54 ASP cc_start: 0.6482 (t0) cc_final: 0.6080 (t0) REVERT: K 98 GLU cc_start: 0.6127 (pp20) cc_final: 0.5831 (pp20) REVERT: K 125 MET cc_start: 0.7773 (mmt) cc_final: 0.7271 (mmp) REVERT: K 140 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7865 (tppt) REVERT: L 30 ILE cc_start: 0.8853 (mp) cc_final: 0.8525 (mm) REVERT: L 40 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6046 (pp) REVERT: M 60 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6559 (tm) REVERT: M 90 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.6792 (mm) REVERT: N 33 LYS cc_start: 0.6924 (pmmt) cc_final: 0.6134 (mmtt) outliers start: 190 outliers final: 129 residues processed: 696 average time/residue: 0.2256 time to fit residues: 259.3185 Evaluate side-chains 665 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 521 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 314 TYR Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 945 CYS Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1114 TYR Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1571 SER Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 183 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 417 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 311 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 422 optimal weight: 40.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS E 104 ASN E 114 ASN E 146 HIS H 134 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.175912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143616 restraints weight = 52568.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144801 restraints weight = 39537.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145748 restraints weight = 31707.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145896 restraints weight = 24998.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145986 restraints weight = 22527.383| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35562 Z= 0.136 Angle : 0.706 17.042 48221 Z= 0.351 Chirality : 0.045 0.195 5380 Planarity : 0.005 0.052 6085 Dihedral : 10.988 85.883 5109 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 3.51 % Allowed : 20.95 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.12), residues: 4211 helix: -0.45 (0.15), residues: 1218 sheet: -1.40 (0.21), residues: 571 loop : -1.74 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 609 TYR 0.022 0.002 TYR A 618 PHE 0.035 0.002 PHE A 223 TRP 0.025 0.002 TRP B 525 HIS 0.012 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (35538) covalent geometry : angle 0.69192 / 0.35 (48194) hydrogen bonds : bond 0.03759 / 2.53 ( 1083) hydrogen bonds : angle 5.49269 / 3.80 ( 3078) metal coordination : bond 0.00896 / 0.56 ( 24) metal coordination : angle 6.00083 / 3.69 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 578 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7645 (pttp) cc_final: 0.6957 (pttm) REVERT: A 182 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8169 (mmtt) REVERT: A 191 MET cc_start: 0.6544 (ppp) cc_final: 0.6295 (ppp) REVERT: A 225 LYS cc_start: 0.8172 (tptm) cc_final: 0.7852 (tmmt) REVERT: A 357 MET cc_start: 0.7796 (mpp) cc_final: 0.7268 (mtm) REVERT: A 378 HIS cc_start: 0.6980 (m-70) cc_final: 0.6753 (m170) REVERT: A 507 TYR cc_start: 0.8745 (t80) cc_final: 0.8512 (t80) REVERT: A 585 ASP cc_start: 0.7882 (m-30) cc_final: 0.7604 (m-30) REVERT: A 925 MET cc_start: 0.8190 (tmm) cc_final: 0.7974 (tmm) REVERT: A 1020 GLN cc_start: 0.7988 (mt0) cc_final: 0.7445 (tt0) REVERT: A 1072 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8732 (m-40) REVERT: A 1073 TYR cc_start: 0.8770 (t80) cc_final: 0.8516 (t80) REVERT: A 1085 LEU cc_start: 0.8455 (mt) cc_final: 0.7852 (tt) REVERT: A 1227 MET cc_start: 0.7299 (mmm) cc_final: 0.6149 (mmm) REVERT: A 1334 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7717 (tttm) REVERT: A 1439 MET cc_start: 0.6177 (ppp) cc_final: 0.5824 (ptt) REVERT: A 1573 TYR cc_start: 0.4728 (OUTLIER) cc_final: 0.4154 (t80) REVERT: A 1588 MET cc_start: 0.9055 (mmm) cc_final: 0.8555 (tpt) REVERT: A 1599 ASN cc_start: 0.7117 (p0) cc_final: 0.6333 (p0) REVERT: A 1634 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8113 (pp) REVERT: B 37 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8424 (tm) REVERT: B 205 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6835 (mtt) REVERT: B 286 ARG cc_start: 0.6125 (tpm170) cc_final: 0.5758 (tpm170) REVERT: B 302 LEU cc_start: 0.8291 (mp) cc_final: 0.7949 (mt) REVERT: B 346 ASP cc_start: 0.7280 (p0) cc_final: 0.7066 (p0) REVERT: B 373 MET cc_start: 0.7807 (tpp) cc_final: 0.7402 (tpp) REVERT: B 760 TYR cc_start: 0.8486 (m-80) cc_final: 0.8192 (m-80) REVERT: B 1013 MET cc_start: 0.8513 (mtp) cc_final: 0.7827 (mtp) REVERT: B 1037 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7519 (ttp-170) REVERT: B 1089 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7945 (tt0) REVERT: C 107 LYS cc_start: 0.7730 (mttt) cc_final: 0.7344 (tmmt) REVERT: C 246 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6522 (ttp80) REVERT: E 54 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6976 (mp10) REVERT: E 164 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8283 (tp) REVERT: F 61 HIS cc_start: 0.7628 (m90) cc_final: 0.7273 (m-70) REVERT: G 80 VAL cc_start: 0.8103 (t) cc_final: 0.7863 (p) REVERT: G 125 TRP cc_start: 0.7616 (t60) cc_final: 0.7147 (t60) REVERT: H 62 SER cc_start: 0.8598 (t) cc_final: 0.8239 (m) REVERT: H 89 LEU cc_start: 0.8405 (mt) cc_final: 0.8046 (tt) REVERT: H 130 ARG cc_start: 0.5932 (ptp90) cc_final: 0.5677 (ptp90) REVERT: I 32 GLN cc_start: 0.6592 (mp-120) cc_final: 0.6052 (mm110) REVERT: I 46 LYS cc_start: 0.8498 (tptp) cc_final: 0.7579 (tptm) REVERT: I 54 ASP cc_start: 0.6435 (t0) cc_final: 0.6031 (t0) REVERT: J 10 CYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7281 (p) REVERT: K 52 GLN cc_start: 0.7841 (mp10) cc_final: 0.7214 (mt0) REVERT: K 81 MET cc_start: 0.8858 (mmm) cc_final: 0.8379 (mmt) REVERT: K 140 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7835 (tppt) REVERT: L 29 TYR cc_start: 0.7508 (m-80) cc_final: 0.7197 (m-10) REVERT: L 40 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5914 (pp) REVERT: M 60 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6234 (tm) REVERT: M 90 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.6676 (mm) REVERT: N 33 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6280 (mmtt) outliers start: 133 outliers final: 101 residues processed: 668 average time/residue: 0.2088 time to fit residues: 230.6032 Evaluate side-chains 659 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 546 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 420 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 319 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 403 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143571 restraints weight = 53120.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144892 restraints weight = 41677.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145886 restraints weight = 33298.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145895 restraints weight = 25959.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146064 restraints weight = 22671.584| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 35562 Z= 0.216 Angle : 0.819 59.199 48221 Z= 0.430 Chirality : 0.047 0.462 5380 Planarity : 0.005 0.063 6085 Dihedral : 10.985 85.887 5109 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 3.33 % Allowed : 21.69 % Favored : 74.98 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4211 helix: -0.45 (0.15), residues: 1217 sheet: -1.39 (0.21), residues: 571 loop : -1.73 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 609 TYR 0.068 0.002 TYR B 317 PHE 0.030 0.002 PHE A 223 TRP 0.022 0.002 TRP B 525 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (35538) covalent geometry : angle 0.80693 / 0.43 (48194) hydrogen bonds : bond 0.03834 / 2.59 ( 1083) hydrogen bonds : angle 5.49785 / 3.81 ( 3078) metal coordination : bond 0.00951 / 0.59 ( 24) metal coordination : angle 5.95469 / 3.64 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8422 Ramachandran restraints generated. 4211 Oldfield, 0 Emsley, 4211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 545 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7624 (pttp) cc_final: 0.6930 (pttm) REVERT: A 182 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8200 (mmtt) REVERT: A 191 MET cc_start: 0.6509 (ppp) cc_final: 0.6254 (ppp) REVERT: A 225 LYS cc_start: 0.8182 (tptm) cc_final: 0.7872 (tmmt) REVERT: A 357 MET cc_start: 0.7780 (mpp) cc_final: 0.7242 (mtm) REVERT: A 378 HIS cc_start: 0.6975 (m-70) cc_final: 0.6735 (m170) REVERT: A 433 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6353 (t0) REVERT: A 585 ASP cc_start: 0.7897 (m-30) cc_final: 0.7634 (m-30) REVERT: A 925 MET cc_start: 0.8163 (tmm) cc_final: 0.7960 (tmm) REVERT: A 1020 GLN cc_start: 0.7970 (mt0) cc_final: 0.7433 (tt0) REVERT: A 1072 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8721 (m-40) REVERT: A 1073 TYR cc_start: 0.8773 (t80) cc_final: 0.8528 (t80) REVERT: A 1085 LEU cc_start: 0.8479 (mt) cc_final: 0.7847 (tt) REVERT: A 1227 MET cc_start: 0.7323 (mmm) cc_final: 0.6138 (mmm) REVERT: A 1334 LYS cc_start: 0.8532 (mmtt) cc_final: 0.7724 (tttm) REVERT: A 1439 MET cc_start: 0.6155 (ppp) cc_final: 0.5821 (ptt) REVERT: A 1573 TYR cc_start: 0.4724 (OUTLIER) cc_final: 0.4161 (t80) REVERT: A 1588 MET cc_start: 0.9071 (mmm) cc_final: 0.8562 (tpt) REVERT: A 1599 ASN cc_start: 0.7110 (p0) cc_final: 0.6324 (p0) REVERT: A 1634 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8134 (pp) REVERT: B 37 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8429 (tm) REVERT: B 71 LYS cc_start: 0.7191 (mtpp) cc_final: 0.6602 (mmtt) REVERT: B 205 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: B 286 ARG cc_start: 0.6085 (tpm170) cc_final: 0.5725 (tpm170) REVERT: B 302 LEU cc_start: 0.8285 (mp) cc_final: 0.7963 (mt) REVERT: B 373 MET cc_start: 0.7797 (tpp) cc_final: 0.7390 (tpp) REVERT: B 760 TYR cc_start: 0.8528 (m-80) cc_final: 0.8207 (m-80) REVERT: B 1013 MET cc_start: 0.8521 (mtp) cc_final: 0.7814 (mtp) REVERT: B 1037 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7493 (ttp-170) REVERT: B 1089 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7962 (tt0) REVERT: C 107 LYS cc_start: 0.7728 (mttt) cc_final: 0.7351 (tmmt) REVERT: C 224 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6111 (p) REVERT: C 246 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6535 (ttp80) REVERT: E 54 GLN cc_start: 0.7402 (tp-100) cc_final: 0.6971 (mp10) REVERT: E 164 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8297 (tp) REVERT: F 61 HIS cc_start: 0.7650 (m90) cc_final: 0.7274 (m-70) REVERT: G 80 VAL cc_start: 0.8117 (t) cc_final: 0.7904 (p) REVERT: G 125 TRP cc_start: 0.7552 (t60) cc_final: 0.7114 (t60) REVERT: H 62 SER cc_start: 0.8570 (t) cc_final: 0.8245 (m) REVERT: H 89 LEU cc_start: 0.8404 (mt) cc_final: 0.8059 (tt) REVERT: I 32 GLN cc_start: 0.6625 (mp-120) cc_final: 0.6089 (mm110) REVERT: I 46 LYS cc_start: 0.8494 (tptp) cc_final: 0.7574 (tptm) REVERT: I 54 ASP cc_start: 0.6447 (t0) cc_final: 0.6064 (t0) REVERT: J 10 CYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7380 (p) REVERT: K 52 GLN cc_start: 0.7852 (mp10) cc_final: 0.7214 (mt0) REVERT: K 81 MET cc_start: 0.8845 (mmm) cc_final: 0.8384 (mmt) REVERT: K 125 MET cc_start: 0.7509 (mmt) cc_final: 0.6838 (mmp) REVERT: K 140 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7842 (tppt) REVERT: L 29 TYR cc_start: 0.7529 (m-80) cc_final: 0.7205 (m-10) REVERT: L 40 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5924 (pp) REVERT: M 60 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6252 (tm) REVERT: M 90 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.6682 (mm) REVERT: N 33 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6304 (mmtt) outliers start: 126 outliers final: 105 residues processed: 631 average time/residue: 0.2129 time to fit residues: 224.3427 Evaluate side-chains 656 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 537 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1072 ASN Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1187 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1441 LYS Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1508 VAL Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1627 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 305 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 66 LYS Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 382 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 118 optimal weight: 0.0170 chunk 115 optimal weight: 0.2980 chunk 326 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 293 optimal weight: 5.9990 chunk 353 optimal weight: 0.8980 chunk 365 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 GLN ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144240 restraints weight = 52706.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143190 restraints weight = 39563.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144090 restraints weight = 33654.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144543 restraints weight = 29200.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144709 restraints weight = 26648.159| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 35562 Z= 0.216 Angle : 0.819 59.199 48221 Z= 0.430 Chirality : 0.047 0.462 5380 Planarity : 0.005 0.063 6085 Dihedral : 10.985 85.887 5109 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 3.14 % Allowed : 21.72 % Favored : 75.14 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4211 helix: -0.45 (0.15), residues: 1217 sheet: -1.39 (0.21), residues: 571 loop : -1.73 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 609 TYR 0.068 0.002 TYR B 317 PHE 0.030 0.002 PHE A 223 TRP 0.022 0.002 TRP B 525 HIS 0.009 0.001 HIS J 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (35538) covalent geometry : angle 0.80693 / 0.43 (48194) hydrogen bonds : bond 0.03834 / 2.59 ( 1083) hydrogen bonds : angle 5.49785 / 3.81 ( 3078) metal coordination : bond 0.00951 / 0.59 ( 24) metal coordination : angle 5.95469 / 3.64 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6312.78 seconds wall clock time: 110 minutes 15.77 seconds (6615.77 seconds total)