Starting phenix.real_space_refine on Thu Nov 20 13:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_3446_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_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 { model { file = "/net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_3446_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_3446_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_3446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m5w_3446/11_2025/5m5w_3446.map" } 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): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 8.29, 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: 2.79 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: 1.51 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: 9.28 Time building geometry restraints manager: 3.69 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.170 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 : 0.003 0.337 35562 Z= 0.177 Angle : 0.929 69.637 48221 Z= 0.383 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 covalent geometry : bond 0.00253 (35538) covalent geometry : angle 0.61542 (48194) hydrogen bonds : bond 0.21263 ( 1083) hydrogen bonds : angle 10.19379 ( 3078) metal coordination : bond 0.08488 ( 24) metal coordination : angle 29.42756 ( 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 : 1.327 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: 0.6172 (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: 0.7904 (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: 0.4912 (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: 0.6303 (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: 0.8010 (mm-30) REVERT: B 1039 MET cc_start: 0.6207 (pmt) cc_final: 0.5949 (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: 0.7031 (t0) cc_final: 0.6743 (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: 0.7319 (t80) cc_final: 0.6894 (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: 0.8620 (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: 0.7122 (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: 0.2292 time to fit residues: 402.0976 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 : 1.284 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 425 ASN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** 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 669 GLN B 683 ASN B 688 HIS ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN 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 99 HIS C 161 HIS C 207 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 49 ASN D 88 GLN E 101 GLN E 143 ASN E 146 HIS G 59 GLN G 144 HIS G 161 ASN H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.180792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149349 restraints weight = 53216.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149778 restraints weight = 43313.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150354 restraints weight = 36906.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150922 restraints weight = 29375.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151146 restraints weight = 24701.157| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 35562 Z= 0.206 Angle : 0.766 38.566 48221 Z= 0.360 Chirality : 0.046 0.217 5380 Planarity : 0.005 0.066 6085 Dihedral : 10.741 81.654 5121 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 4.65 % Allowed : 15.03 % Favored : 80.32 % 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: -3.05 (0.11), residues: 4211 helix: -1.80 (0.13), residues: 1202 sheet: -1.92 (0.20), residues: 573 loop : -2.22 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 52 TYR 0.024 0.002 TYR B 494 PHE 0.019 0.002 PHE B1135 TRP 0.014 0.002 TRP B1159 HIS 0.010 0.002 HIS B 532 Details of bonding type rmsd covalent geometry : bond 0.00478 (35538) covalent geometry : angle 0.69127 (48194) hydrogen bonds : bond 0.04936 ( 1083) hydrogen bonds : angle 6.72439 ( 3078) metal coordination : bond 0.01302 ( 24) metal coordination : angle 13.93448 ( 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 856 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 680 time to evaluate : 1.307 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: A 70 LYS cc_start: 0.8020 (pttt) cc_final: 0.7397 (pttm) REVERT: A 191 MET cc_start: 0.7003 (ppp) cc_final: 0.6732 (ppp) REVERT: A 201 ARG cc_start: 0.6858 (ttm110) cc_final: 0.6373 (mmm160) REVERT: A 225 LYS cc_start: 0.8323 (tptm) cc_final: 0.7848 (tmmt) REVERT: A 342 ARG cc_start: 0.8682 (mtp85) cc_final: 0.8443 (mtt90) REVERT: A 446 ARG cc_start: 0.4539 (OUTLIER) cc_final: 0.3360 (mtp85) REVERT: A 451 VAL cc_start: 0.5184 (OUTLIER) cc_final: 0.4976 (m) REVERT: A 540 ASP cc_start: 0.8035 (t70) cc_final: 0.7820 (t0) REVERT: A 799 GLU cc_start: 0.8024 (tp30) cc_final: 0.7615 (tp30) REVERT: A 816 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8803 (tp) REVERT: A 977 MET cc_start: 0.7966 (tmm) cc_final: 0.7745 (tmm) REVERT: A 1020 GLN cc_start: 0.7959 (mt0) cc_final: 0.7739 (tt0) REVERT: A 1073 TYR cc_start: 0.8672 (t80) cc_final: 0.8460 (t80) REVERT: A 1124 LEU cc_start: 0.8672 (tp) cc_final: 0.8389 (tp) REVERT: A 1175 MET cc_start: 0.8533 (tmm) cc_final: 0.8119 (tmm) REVERT: A 1235 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8147 (t) REVERT: A 1248 ASP cc_start: 0.7175 (t0) cc_final: 0.6481 (t70) REVERT: A 1439 MET cc_start: 0.6320 (ppp) cc_final: 0.5494 (ptm) REVERT: A 1469 TRP cc_start: 0.6650 (p-90) cc_final: 0.6062 (p-90) REVERT: A 1485 MET cc_start: 0.6606 (mmm) cc_final: 0.5382 (mmm) REVERT: A 1634 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7745 (pp) REVERT: B 37 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8673 (tm) REVERT: B 243 GLN cc_start: 0.8550 (mp-120) cc_final: 0.8155 (mm-40) REVERT: B 290 ASP cc_start: 0.8011 (t0) cc_final: 0.7762 (m-30) REVERT: B 335 ARG cc_start: 0.6517 (tpt170) cc_final: 0.6289 (tpp80) REVERT: B 373 MET cc_start: 0.7924 (tpp) cc_final: 0.7480 (tpt) REVERT: B 434 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7609 (tpt90) REVERT: B 446 MET cc_start: 0.6334 (tpp) cc_final: 0.6029 (tmm) REVERT: B 450 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7723 (tt) REVERT: B 497 ILE cc_start: 0.9218 (tp) cc_final: 0.8863 (tp) REVERT: B 742 TYR cc_start: 0.8486 (m-80) cc_final: 0.8170 (m-80) REVERT: B 746 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7072 (p) REVERT: B 803 MET cc_start: 0.7340 (ttm) cc_final: 0.7013 (ttm) REVERT: B 851 TYR cc_start: 0.7071 (t80) cc_final: 0.6859 (t80) REVERT: B 1013 MET cc_start: 0.8420 (mtp) cc_final: 0.8164 (mtp) REVERT: C 53 ASN cc_start: 0.8215 (t0) cc_final: 0.7959 (t0) REVERT: C 142 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7746 (tpp-160) REVERT: C 201 GLU cc_start: 0.8096 (mp0) cc_final: 0.7874 (mp0) REVERT: C 315 PHE cc_start: 0.6843 (t80) cc_final: 0.6533 (t80) REVERT: D 88 GLN cc_start: 0.7164 (mm-40) cc_final: 0.6697 (tp40) REVERT: E 54 GLN cc_start: 0.7452 (tp-100) cc_final: 0.6888 (mp10) REVERT: E 58 MET cc_start: 0.8238 (mtp) cc_final: 0.7971 (mtp) REVERT: F 60 GLN cc_start: 0.8715 (tp-100) cc_final: 0.8443 (mt0) REVERT: F 61 HIS cc_start: 0.7043 (m90) cc_final: 0.6755 (m-70) REVERT: G 80 VAL cc_start: 0.8218 (t) cc_final: 0.7913 (p) REVERT: G 97 LYS cc_start: 0.7085 (pptt) cc_final: 0.6720 (ptmm) REVERT: G 125 TRP cc_start: 0.7439 (t60) cc_final: 0.6917 (t60) REVERT: H 62 SER cc_start: 0.8366 (t) cc_final: 0.8106 (m) REVERT: H 89 LEU cc_start: 0.8234 (mt) cc_final: 0.7723 (tt) REVERT: I 32 GLN cc_start: 0.6555 (mp-120) cc_final: 0.6330 (mp10) REVERT: I 46 LYS cc_start: 0.8370 (tptp) cc_final: 0.7415 (tptm) REVERT: K 44 ARG cc_start: 0.5615 (mmp-170) cc_final: 0.4909 (mpp-170) REVERT: K 98 GLU cc_start: 0.6284 (pp20) cc_final: 0.5887 (pp20) REVERT: L 29 TYR cc_start: 0.7644 (m-80) cc_final: 0.7348 (m-80) REVERT: L 40 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.6042 (pp) REVERT: N 33 LYS cc_start: 0.6899 (pmmt) cc_final: 0.6112 (mmtt) outliers start: 176 outliers final: 82 residues processed: 821 average time/residue: 0.2129 time to fit residues: 282.7772 Evaluate side-chains 657 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 566 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 85 CYS 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 451 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 635 MET 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 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 1013 THR Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1070 LEU 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 1538 VAL Chi-restraints excluded: chain A residue 1571 SER 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 131 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 259 THR 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 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 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 746 THR Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 92 ILE 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 66 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 GLU 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 89 CYS Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 142 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 322 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 386 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 chunk 411 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 290 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 580 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS ** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1453 HIS B 209 GLN ** B 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 710 ASN B 767 ASN B 921 HIS C 216 HIS ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142733 restraints weight = 53687.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141941 restraints weight = 46574.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142857 restraints weight = 40657.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143249 restraints weight = 32809.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143498 restraints weight = 29217.702| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 35562 Z= 0.228 Angle : 0.763 27.592 48221 Z= 0.372 Chirality : 0.047 0.214 5380 Planarity : 0.006 0.121 6085 Dihedral : 10.928 81.230 5115 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.37 % Rotamer: Outliers : 5.42 % Allowed : 16.25 % Favored : 78.34 % 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: -2.63 (0.12), residues: 4211 helix: -1.22 (0.14), residues: 1224 sheet: -1.83 (0.20), residues: 586 loop : -2.04 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 52 TYR 0.027 0.002 TYR A 95 PHE 0.025 0.002 PHE A1456 TRP 0.023 0.002 TRP B 595 HIS 0.017 0.002 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00537 (35538) covalent geometry : angle 0.72263 (48194) hydrogen bonds : bond 0.04569 ( 1083) hydrogen bonds : angle 6.12117 ( 3078) metal coordination : bond 0.01236 ( 24) metal coordination : angle 10.31536 ( 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 819 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 614 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8284 (pttt) cc_final: 0.7667 (pttm) REVERT: A 182 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8386 (ttmt) REVERT: A 191 MET cc_start: 0.6901 (ppp) cc_final: 0.6571 (ppp) REVERT: A 225 LYS cc_start: 0.8293 (tptm) cc_final: 0.7796 (tmmt) REVERT: A 446 ARG cc_start: 0.4021 (OUTLIER) cc_final: 0.3462 (mmm160) REVERT: A 451 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5338 (m) REVERT: A 471 MET cc_start: 0.7942 (mmt) cc_final: 0.6868 (mmt) REVERT: A 540 ASP cc_start: 0.7928 (t70) cc_final: 0.7667 (t0) REVERT: A 928 MET cc_start: 0.8392 (ttp) cc_final: 0.7928 (ptt) REVERT: A 1020 GLN cc_start: 0.8097 (mt0) cc_final: 0.7698 (tt0) REVERT: A 1073 TYR cc_start: 0.8779 (t80) cc_final: 0.8528 (t80) REVERT: A 1085 LEU cc_start: 0.8376 (mt) cc_final: 0.7780 (tt) REVERT: A 1108 HIS cc_start: 0.6789 (t70) cc_final: 0.6566 (t-90) REVERT: A 1175 MET cc_start: 0.8386 (tmm) cc_final: 0.7968 (tmm) REVERT: A 1227 MET cc_start: 0.7301 (mmm) cc_final: 0.6367 (mmm) REVERT: A 1275 THR cc_start: 0.7629 (OUTLIER) cc_final: 0.7325 (p) REVERT: A 1439 MET cc_start: 0.6233 (ppp) cc_final: 0.5907 (ptm) REVERT: A 1485 MET cc_start: 0.6994 (mmm) cc_final: 0.6565 (mmm) REVERT: A 1573 TYR cc_start: 0.4688 (OUTLIER) cc_final: 0.4067 (t80) REVERT: A 1634 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7909 (pp) REVERT: B 37 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8672 (tm) REVERT: B 243 GLN cc_start: 0.8653 (mp-120) cc_final: 0.8194 (mm-40) REVERT: B 302 LEU cc_start: 0.8626 (mp) cc_final: 0.8365 (mt) REVERT: B 305 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7384 (tmt-80) REVERT: B 346 ASP cc_start: 0.6957 (p0) cc_final: 0.6442 (p0) REVERT: B 434 ARG cc_start: 0.7906 (mmt90) cc_final: 0.7575 (tpt90) REVERT: B 443 LYS cc_start: 0.7416 (mmmt) cc_final: 0.7084 (mmmt) REVERT: B 446 MET cc_start: 0.6528 (tpp) cc_final: 0.6158 (tmm) REVERT: B 447 SER cc_start: 0.8327 (m) cc_final: 0.7802 (p) REVERT: B 497 ILE cc_start: 0.9284 (tp) cc_final: 0.9050 (tp) REVERT: B 552 SER cc_start: 0.8695 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 576 THR cc_start: 0.6143 (OUTLIER) cc_final: 0.5565 (p) REVERT: B 746 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 930 LYS cc_start: 0.8816 (mttt) cc_final: 0.8531 (mtpp) REVERT: B 946 ASP cc_start: 0.8946 (p0) cc_final: 0.8722 (p0) REVERT: B 967 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 1013 MET cc_start: 0.8720 (mtp) cc_final: 0.8002 (mtp) REVERT: B 1089 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7727 (tm-30) REVERT: C 45 SER cc_start: 0.8523 (p) cc_final: 0.8128 (p) REVERT: C 53 ASN cc_start: 0.8587 (t0) cc_final: 0.8382 (t0) REVERT: C 107 LYS cc_start: 0.7702 (mttt) cc_final: 0.7250 (tmmt) REVERT: C 142 ARG cc_start: 0.8038 (tpp80) cc_final: 0.7672 (tpp-160) REVERT: E 54 GLN cc_start: 0.7540 (tp-100) cc_final: 0.6860 (mp10) REVERT: E 58 MET cc_start: 0.8551 (mtp) cc_final: 0.8325 (mtp) REVERT: E 146 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.8062 (m90) REVERT: E 164 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8645 (tp) REVERT: E 174 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: F 60 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8457 (mt0) REVERT: F 61 HIS cc_start: 0.7323 (m90) cc_final: 0.6917 (m-70) REVERT: F 79 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7192 (ptt90) REVERT: F 150 GLU cc_start: 0.8063 (pt0) cc_final: 0.7728 (pt0) REVERT: G 80 VAL cc_start: 0.8307 (t) cc_final: 0.8017 (p) REVERT: G 97 LYS cc_start: 0.7186 (pptt) cc_final: 0.6908 (ptmm) REVERT: G 125 TRP cc_start: 0.7534 (t60) cc_final: 0.6973 (t60) REVERT: H 62 SER cc_start: 0.8576 (t) cc_final: 0.8255 (m) REVERT: H 89 LEU cc_start: 0.8425 (mt) cc_final: 0.7930 (tt) REVERT: I 32 GLN cc_start: 0.6766 (mp-120) cc_final: 0.6557 (mp10) REVERT: J 49 MET cc_start: 0.7575 (mmm) cc_final: 0.6303 (mmm) REVERT: K 44 ARG cc_start: 0.5511 (mmp-170) cc_final: 0.4751 (mpp-170) REVERT: K 98 GLU cc_start: 0.6253 (pp20) cc_final: 0.5817 (pp20) REVERT: K 140 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7830 (tptt) REVERT: L 29 TYR cc_start: 0.7901 (m-80) cc_final: 0.7653 (m-80) REVERT: L 40 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.5911 (pp) REVERT: M 108 LEU cc_start: 0.7324 (pt) cc_final: 0.7096 (pp) REVERT: N 33 LYS cc_start: 0.7231 (pmmt) cc_final: 0.6283 (mmtt) outliers start: 205 outliers final: 104 residues processed: 781 average time/residue: 0.2106 time to fit residues: 269.4736 Evaluate side-chains 658 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 538 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 92 ASN 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 314 TYR Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 VAL 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 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 907 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 1030 VAL 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 1263 LEU Chi-restraints excluded: chain A residue 1275 THR 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 1583 ASP 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 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 259 THR 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 385 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN 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 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 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU 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 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 146 HIS Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 174 GLN 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 47 VAL Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain J residue 14 VAL 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 M residue 69 SER Chi-restraints excluded: chain N residue 36 LYS Chi-restraints excluded: chain N residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 70 optimal weight: 2.9990 chunk 366 optimal weight: 8.9990 chunk 290 optimal weight: 0.0060 chunk 281 optimal weight: 5.9990 chunk 246 optimal weight: 0.2980 chunk 423 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 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 669 GLN B 764 ASN B1157 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN L 53 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.176280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144846 restraints weight = 52997.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144163 restraints weight = 41639.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145130 restraints weight = 36544.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145967 restraints weight = 28678.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145904 restraints weight = 25128.851| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35562 Z= 0.150 Angle : 0.678 18.714 48221 Z= 0.331 Chirality : 0.045 0.240 5380 Planarity : 0.005 0.075 6085 Dihedral : 10.837 81.479 5113 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.90 % Rotamer: Outliers : 4.44 % Allowed : 17.89 % Favored : 77.68 % 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: -2.34 (0.12), residues: 4211 helix: -0.87 (0.14), residues: 1233 sheet: -1.65 (0.20), residues: 569 loop : -1.93 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 40 TYR 0.020 0.002 TYR B 420 PHE 0.031 0.002 PHE A 355 TRP 0.020 0.001 TRP B 595 HIS 0.012 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00348 (35538) covalent geometry : angle 0.65186 (48194) hydrogen bonds : bond 0.03889 ( 1083) hydrogen bonds : angle 5.75817 ( 3078) metal coordination : bond 0.00894 ( 24) metal coordination : angle 7.85927 ( 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 753 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 585 time to evaluate : 1.004 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: A 70 LYS cc_start: 0.8261 (pttt) cc_final: 0.7634 (pttm) REVERT: A 182 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8323 (ttmt) REVERT: A 191 MET cc_start: 0.6846 (ppp) cc_final: 0.6496 (ppp) REVERT: A 225 LYS cc_start: 0.8269 (tptm) cc_final: 0.7819 (tmmt) REVERT: A 378 HIS cc_start: 0.6825 (m-70) cc_final: 0.6625 (m170) REVERT: A 446 ARG cc_start: 0.3704 (OUTLIER) cc_final: 0.3420 (mmm160) REVERT: A 451 VAL cc_start: 0.5575 (OUTLIER) cc_final: 0.5342 (m) REVERT: A 540 ASP cc_start: 0.7751 (t70) cc_final: 0.7539 (t0) REVERT: A 543 LEU cc_start: 0.7770 (tp) cc_final: 0.7315 (mp) REVERT: A 928 MET cc_start: 0.8653 (ttp) cc_final: 0.8309 (tmm) REVERT: A 977 MET cc_start: 0.7966 (tmm) cc_final: 0.7644 (tmm) REVERT: A 1020 GLN cc_start: 0.8051 (mt0) cc_final: 0.7691 (tt0) REVERT: A 1040 ASP cc_start: 0.8923 (m-30) cc_final: 0.8722 (m-30) REVERT: A 1073 TYR cc_start: 0.8715 (t80) cc_final: 0.8443 (t80) REVERT: A 1085 LEU cc_start: 0.8415 (mt) cc_final: 0.7849 (tt) REVERT: A 1175 MET cc_start: 0.8370 (tmm) cc_final: 0.8154 (tmm) REVERT: A 1227 MET cc_start: 0.7239 (mmm) cc_final: 0.6340 (mmm) REVERT: A 1275 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7409 (p) REVERT: A 1439 MET cc_start: 0.6245 (ppp) cc_final: 0.5922 (ptm) REVERT: A 1573 TYR cc_start: 0.4940 (OUTLIER) cc_final: 0.4324 (t80) REVERT: A 1588 MET cc_start: 0.8968 (mmm) cc_final: 0.8311 (tpt) REVERT: A 1603 MET cc_start: 0.7710 (ttt) cc_final: 0.7015 (ttt) REVERT: A 1611 MET cc_start: 0.9032 (tmm) cc_final: 0.8217 (tmm) REVERT: A 1634 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7932 (pp) REVERT: B 37 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8604 (tm) REVERT: B 205 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6601 (ttp) REVERT: B 243 GLN cc_start: 0.8746 (mp-120) cc_final: 0.8158 (mm-40) REVERT: B 302 LEU cc_start: 0.8542 (mp) cc_final: 0.8299 (mt) REVERT: B 373 MET cc_start: 0.7747 (tpp) cc_final: 0.7324 (tpt) REVERT: B 434 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7416 (tpt90) REVERT: B 443 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7338 (mmmt) REVERT: B 446 MET cc_start: 0.6445 (tpp) cc_final: 0.6025 (tmm) REVERT: B 447 SER cc_start: 0.8388 (m) cc_final: 0.7874 (p) REVERT: B 497 ILE cc_start: 0.9319 (tp) cc_final: 0.9084 (tp) REVERT: B 708 ASP cc_start: 0.8395 (p0) cc_final: 0.8187 (p0) REVERT: B 725 THR cc_start: 0.9332 (p) cc_final: 0.8930 (t) REVERT: B 746 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7189 (p) REVERT: B 760 TYR cc_start: 0.8344 (m-80) cc_final: 0.8079 (m-80) REVERT: B 930 LYS cc_start: 0.8802 (mttt) cc_final: 0.8558 (mtpp) REVERT: B 1013 MET cc_start: 0.8763 (mtp) cc_final: 0.8133 (mtp) REVERT: C 45 SER cc_start: 0.8486 (p) cc_final: 0.8167 (p) REVERT: C 63 ILE cc_start: 0.9166 (mm) cc_final: 0.8887 (mt) REVERT: C 107 LYS cc_start: 0.7676 (mttt) cc_final: 0.7179 (tmmt) REVERT: C 142 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7765 (tpp-160) REVERT: E 50 MET cc_start: 0.5496 (tmm) cc_final: 0.5062 (tmm) REVERT: E 54 GLN cc_start: 0.7442 (tp-100) cc_final: 0.6772 (mp10) REVERT: E 58 MET cc_start: 0.8405 (mtp) cc_final: 0.8203 (mtp) REVERT: E 164 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8550 (tp) REVERT: F 60 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8531 (mt0) REVERT: F 61 HIS cc_start: 0.7288 (m90) cc_final: 0.6886 (m-70) REVERT: G 80 VAL cc_start: 0.8234 (t) cc_final: 0.7995 (p) REVERT: G 125 TRP cc_start: 0.7356 (t60) cc_final: 0.6857 (t60) REVERT: H 9 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7433 (mt) REVERT: H 62 SER cc_start: 0.8469 (t) cc_final: 0.8148 (m) REVERT: H 89 LEU cc_start: 0.8357 (mt) cc_final: 0.7880 (tt) REVERT: I 7 LEU cc_start: 0.7567 (mt) cc_final: 0.7175 (mt) REVERT: I 32 GLN cc_start: 0.6622 (mp-120) cc_final: 0.6396 (mp10) REVERT: J 49 MET cc_start: 0.7403 (mmm) cc_final: 0.6164 (mmm) REVERT: K 98 GLU cc_start: 0.5992 (pp20) cc_final: 0.5729 (pp20) REVERT: K 140 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7757 (tptt) REVERT: M 90 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.6767 (mm) REVERT: N 33 LYS cc_start: 0.7254 (pmmt) cc_final: 0.6279 (mmtt) outliers start: 168 outliers final: 93 residues processed: 713 average time/residue: 0.2014 time to fit residues: 237.4152 Evaluate side-chains 653 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 549 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 316 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 451 VAL 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 737 LEU 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 892 LEU 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 982 VAL 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 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 1504 ILE Chi-restraints excluded: chain A residue 1538 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 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 263 SER 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 385 VAL Chi-restraints excluded: chain B residue 478 LEU 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 746 THR Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1056 THR 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 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU 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 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 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 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 114 VAL 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 J residue 13 VAL Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 139 ILE 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: 5.9990 chunk 402 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 282 optimal weight: 0.4980 chunk 226 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 209 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 GLN B 767 ASN J 53 HIS N 106 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.175783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144185 restraints weight = 53264.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143146 restraints weight = 43046.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.144294 restraints weight = 38342.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144912 restraints weight = 29763.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144955 restraints weight = 26495.398| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35562 Z= 0.154 Angle : 0.667 16.375 48221 Z= 0.327 Chirality : 0.045 0.261 5380 Planarity : 0.005 0.063 6085 Dihedral : 10.793 80.899 5113 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 4.68 % Allowed : 18.52 % Favored : 76.80 % 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: -2.11 (0.12), residues: 4211 helix: -0.59 (0.15), residues: 1221 sheet: -1.52 (0.21), residues: 571 loop : -1.84 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 609 TYR 0.021 0.002 TYR H 93 PHE 0.024 0.001 PHE A 355 TRP 0.018 0.001 TRP B 525 HIS 0.011 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00361 (35538) covalent geometry : angle 0.64954 (48194) hydrogen bonds : bond 0.03786 ( 1083) hydrogen bonds : angle 5.57184 ( 3078) metal coordination : bond 0.00806 ( 24) metal coordination : angle 6.46840 ( 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 752 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 575 time to evaluate : 1.287 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: 0.8309 (pttt) cc_final: 0.7656 (pttm) REVERT: A 182 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8254 (ttmt) REVERT: A 191 MET cc_start: 0.6876 (ppp) cc_final: 0.6581 (ppp) REVERT: A 446 ARG cc_start: 0.3744 (OUTLIER) cc_final: 0.3471 (mmm160) REVERT: A 451 VAL cc_start: 0.5785 (OUTLIER) cc_final: 0.5536 (m) REVERT: A 471 MET cc_start: 0.7775 (mmt) cc_final: 0.6585 (mmt) REVERT: A 543 LEU cc_start: 0.7759 (tp) cc_final: 0.7350 (mp) REVERT: A 632 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 642 ASN cc_start: 0.8210 (t0) cc_final: 0.7923 (t0) REVERT: A 925 MET cc_start: 0.8284 (tmm) cc_final: 0.7851 (tmm) REVERT: A 977 MET cc_start: 0.7953 (tmm) cc_final: 0.7573 (tmm) REVERT: A 1020 GLN cc_start: 0.8064 (mt0) cc_final: 0.7590 (tt0) REVERT: A 1073 TYR cc_start: 0.8707 (t80) cc_final: 0.8442 (t80) REVERT: A 1085 LEU cc_start: 0.8431 (mt) cc_final: 0.7857 (tt) REVERT: A 1124 LEU cc_start: 0.8884 (tp) cc_final: 0.8672 (mt) REVERT: A 1175 MET cc_start: 0.8383 (tmm) cc_final: 0.8171 (tmm) REVERT: A 1227 MET cc_start: 0.7216 (mmm) cc_final: 0.6307 (mmm) REVERT: A 1439 MET cc_start: 0.6312 (ppp) cc_final: 0.5815 (ptt) REVERT: A 1571 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7736 (t) REVERT: A 1573 TYR cc_start: 0.4789 (OUTLIER) cc_final: 0.4162 (t80) REVERT: A 1588 MET cc_start: 0.9042 (mmm) cc_final: 0.8376 (tpt) REVERT: A 1634 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7931 (pp) REVERT: B 37 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8528 (tm) REVERT: B 205 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6743 (ttp) REVERT: B 243 GLN cc_start: 0.8813 (mp-120) cc_final: 0.8103 (mm-40) REVERT: B 302 LEU cc_start: 0.8493 (mp) cc_final: 0.8250 (mt) REVERT: B 308 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7328 (mm) REVERT: B 373 MET cc_start: 0.7773 (tpp) cc_final: 0.7513 (tpp) REVERT: B 443 LYS cc_start: 0.7599 (mmmt) cc_final: 0.7302 (mmmt) REVERT: B 446 MET cc_start: 0.6374 (tpp) cc_final: 0.5931 (tmm) REVERT: B 447 SER cc_start: 0.8301 (m) cc_final: 0.6997 (p) REVERT: B 480 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: B 497 ILE cc_start: 0.9317 (tp) cc_final: 0.9110 (tp) REVERT: B 502 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (tmm) REVERT: B 668 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6542 (tp30) REVERT: B 708 ASP cc_start: 0.8434 (p0) cc_final: 0.8184 (p0) REVERT: B 746 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7231 (p) REVERT: B 760 TYR cc_start: 0.8370 (m-80) cc_final: 0.8084 (m-80) REVERT: B 930 LYS cc_start: 0.8842 (mttt) cc_final: 0.8622 (mtpp) REVERT: B 1013 MET cc_start: 0.8764 (mtp) cc_final: 0.8055 (mtp) REVERT: C 63 ILE cc_start: 0.9181 (mm) cc_final: 0.8910 (mt) REVERT: C 107 LYS cc_start: 0.7640 (mttt) cc_final: 0.7219 (tmmt) REVERT: C 200 GLN cc_start: 0.9034 (mt0) cc_final: 0.8539 (mt0) REVERT: D 88 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6557 (tm-30) REVERT: E 54 GLN cc_start: 0.7472 (tp-100) cc_final: 0.6810 (mp10) REVERT: E 58 MET cc_start: 0.8516 (mtp) cc_final: 0.8257 (mtp) REVERT: E 164 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8571 (tp) REVERT: E 174 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8414 (mt0) REVERT: F 61 HIS cc_start: 0.7306 (m90) cc_final: 0.6876 (m-70) REVERT: F 79 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7061 (ptt90) REVERT: F 144 GLU cc_start: 0.8642 (pp20) cc_final: 0.8338 (pp20) REVERT: F 150 GLU cc_start: 0.8079 (pt0) cc_final: 0.7867 (pt0) REVERT: G 80 VAL cc_start: 0.8218 (t) cc_final: 0.7910 (p) REVERT: G 125 TRP cc_start: 0.7365 (t60) cc_final: 0.6824 (t60) REVERT: H 9 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7436 (mt) REVERT: H 62 SER cc_start: 0.8499 (t) cc_final: 0.8197 (m) REVERT: H 130 ARG cc_start: 0.5813 (mtm-85) cc_final: 0.5492 (ptp90) REVERT: I 32 GLN cc_start: 0.6517 (mp-120) cc_final: 0.5891 (mm110) REVERT: I 46 LYS cc_start: 0.8489 (tptp) cc_final: 0.7599 (tptm) REVERT: J 49 MET cc_start: 0.7432 (mmm) cc_final: 0.6189 (mmm) REVERT: K 52 GLN cc_start: 0.7806 (mp10) cc_final: 0.7250 (mt0) REVERT: K 98 GLU cc_start: 0.5762 (pp20) cc_final: 0.5489 (pp20) REVERT: K 140 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7676 (tptt) REVERT: L 40 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5890 (pp) REVERT: N 33 LYS cc_start: 0.7259 (pmmt) cc_final: 0.6299 (mmtt) outliers start: 177 outliers final: 111 residues processed: 703 average time/residue: 0.2004 time to fit residues: 233.2366 Evaluate side-chains 661 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 534 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 ILE 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 813 LEU Chi-restraints excluded: chain A residue 821 ILE 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 982 VAL 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 1123 VAL Chi-restraints excluded: chain A residue 1137 SER 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 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 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 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 259 THR Chi-restraints excluded: chain B residue 263 SER 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 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 502 MET 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 885 VAL 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 151 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU 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 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 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 66 LEU Chi-restraints excluded: chain G residue 108 THR 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 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 I residue 3 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS 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 M residue 51 PHE Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 106 ASN Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 125 optimal weight: 9.9990 chunk 318 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 326 optimal weight: 3.9990 chunk 378 optimal weight: 0.9990 chunk 332 optimal weight: 0.7980 chunk 404 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS A 378 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 673 HIS 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 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146228 restraints weight = 52894.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146541 restraints weight = 44121.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147355 restraints weight = 35410.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147858 restraints weight = 29073.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148065 restraints weight = 24851.426| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35562 Z= 0.119 Angle : 0.637 15.737 48221 Z= 0.314 Chirality : 0.043 0.218 5380 Planarity : 0.004 0.060 6085 Dihedral : 10.692 80.598 5113 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.84 % Favored : 94.13 % Rotamer: Outliers : 4.02 % Allowed : 19.52 % Favored : 76.46 % 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: -0.31 (0.15), residues: 1205 sheet: -1.37 (0.21), residues: 572 loop : -1.73 (0.12), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 609 TYR 0.022 0.001 TYR E 28 PHE 0.025 0.001 PHE A 355 TRP 0.016 0.001 TRP B 525 HIS 0.020 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00272 (35538) covalent geometry : angle 0.62370 (48194) hydrogen bonds : bond 0.03433 ( 1083) hydrogen bonds : angle 5.36532 ( 3078) metal coordination : bond 0.00589 ( 24) metal coordination : angle 5.51846 ( 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 745 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 593 time to evaluate : 1.333 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: 0.8139 (pttt) cc_final: 0.7486 (pttm) REVERT: A 182 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8343 (ttmt) REVERT: A 191 MET cc_start: 0.6605 (ppp) cc_final: 0.6294 (ppp) REVERT: A 208 PHE cc_start: 0.6068 (t80) cc_final: 0.5846 (t80) REVERT: A 451 VAL cc_start: 0.5775 (OUTLIER) cc_final: 0.5563 (m) REVERT: A 471 MET cc_start: 0.8062 (mmt) cc_final: 0.7043 (mmt) REVERT: A 543 LEU cc_start: 0.7704 (tp) cc_final: 0.7394 (mp) REVERT: A 642 ASN cc_start: 0.8022 (t0) cc_final: 0.7817 (t0) REVERT: A 925 MET cc_start: 0.8153 (tmm) cc_final: 0.7838 (tmm) REVERT: A 977 MET cc_start: 0.7911 (tmm) cc_final: 0.7522 (tmm) REVERT: A 1020 GLN cc_start: 0.7928 (mt0) cc_final: 0.7644 (tt0) REVERT: A 1040 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: A 1073 TYR cc_start: 0.8642 (t80) cc_final: 0.8401 (t80) REVERT: A 1085 LEU cc_start: 0.8402 (mt) cc_final: 0.7887 (tt) REVERT: A 1124 LEU cc_start: 0.8845 (tp) cc_final: 0.8631 (mt) REVERT: A 1227 MET cc_start: 0.7169 (mmm) cc_final: 0.6192 (mmm) REVERT: A 1439 MET cc_start: 0.6264 (ppp) cc_final: 0.5808 (ptt) REVERT: A 1571 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7656 (t) REVERT: A 1573 TYR cc_start: 0.4664 (OUTLIER) cc_final: 0.4129 (t80) REVERT: A 1588 MET cc_start: 0.9038 (mmm) cc_final: 0.8305 (tpt) REVERT: A 1634 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7959 (pp) REVERT: B 37 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8536 (tm) REVERT: B 71 LYS cc_start: 0.7170 (mtpp) cc_final: 0.6628 (mmtt) REVERT: B 128 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: B 205 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6700 (ttp) REVERT: B 243 GLN cc_start: 0.8722 (mp-120) cc_final: 0.8127 (mm-40) REVERT: B 302 LEU cc_start: 0.8497 (mp) cc_final: 0.8225 (mt) REVERT: B 308 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7191 (mm) REVERT: B 373 MET cc_start: 0.7788 (tpp) cc_final: 0.7432 (tpp) REVERT: B 446 MET cc_start: 0.6290 (tpp) cc_final: 0.5960 (tmm) REVERT: B 480 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7735 (mp10) REVERT: B 502 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8323 (tmm) REVERT: B 668 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6193 (tp30) REVERT: B 760 TYR cc_start: 0.8322 (m-80) cc_final: 0.7942 (m-80) REVERT: B 1013 MET cc_start: 0.8498 (mtp) cc_final: 0.7797 (mtp) REVERT: B 1077 ASP cc_start: 0.7657 (p0) cc_final: 0.7380 (p0) REVERT: C 63 ILE cc_start: 0.9226 (mm) cc_final: 0.8932 (mt) REVERT: C 107 LYS cc_start: 0.7567 (mttt) cc_final: 0.7190 (tmmt) REVERT: D 38 GLN cc_start: 0.5865 (tp-100) cc_final: 0.5107 (mt0) REVERT: E 54 GLN cc_start: 0.7471 (tp-100) cc_final: 0.6846 (mp10) REVERT: E 58 MET cc_start: 0.8384 (mtp) cc_final: 0.8162 (mtp) REVERT: F 61 HIS cc_start: 0.7596 (m90) cc_final: 0.7144 (m-70) REVERT: F 79 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7115 (ptt90) REVERT: F 144 GLU cc_start: 0.8496 (pp20) cc_final: 0.8255 (pp20) REVERT: F 150 GLU cc_start: 0.8063 (pt0) cc_final: 0.7851 (pt0) REVERT: G 125 TRP cc_start: 0.7302 (t60) cc_final: 0.6803 (t60) REVERT: H 9 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7424 (mt) REVERT: H 62 SER cc_start: 0.8617 (t) cc_final: 0.8274 (m) REVERT: H 89 LEU cc_start: 0.8285 (mt) cc_final: 0.7875 (tt) REVERT: H 130 ARG cc_start: 0.5783 (mtm-85) cc_final: 0.5491 (ptp90) REVERT: I 32 GLN cc_start: 0.6454 (mp-120) cc_final: 0.5842 (mm110) REVERT: I 46 LYS cc_start: 0.8432 (tptp) cc_final: 0.7594 (tptm) REVERT: I 51 THR cc_start: 0.7772 (t) cc_final: 0.7503 (m) REVERT: K 81 MET cc_start: 0.8798 (mmm) cc_final: 0.8366 (mmt) REVERT: K 125 MET cc_start: 0.7768 (mmt) cc_final: 0.7387 (mmp) REVERT: K 140 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7758 (tppt) REVERT: L 40 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5856 (pp) REVERT: M 90 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.6730 (mm) REVERT: N 33 LYS cc_start: 0.7245 (pmmt) cc_final: 0.6305 (mmtt) outliers start: 152 outliers final: 98 residues processed: 705 average time/residue: 0.2052 time to fit residues: 238.6294 Evaluate side-chains 655 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 542 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 221 HIS 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 395 LEU Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 490 ILE 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 727 THR Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 750 ILE 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 892 LEU 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 1040 ASP 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 1504 ILE Chi-restraints excluded: chain A residue 1571 SER 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 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 128 GLN 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 283 THR 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 425 ILE 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 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 885 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR 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 147 HIS Chi-restraints excluded: chain E residue 149 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 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 J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS 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 L residue 68 GLU 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 107 MET 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: 8.9990 chunk 64 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 341 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 56 ASN G 237 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.178158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145084 restraints weight = 52965.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145414 restraints weight = 39135.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146065 restraints weight = 32345.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146778 restraints weight = 26958.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146911 restraints weight = 24379.006| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35562 Z= 0.123 Angle : 0.638 12.166 48221 Z= 0.314 Chirality : 0.043 0.210 5380 Planarity : 0.004 0.056 6085 Dihedral : 10.614 79.901 5109 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 4.23 % Allowed : 19.71 % Favored : 76.06 % 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: -1.75 (0.12), residues: 4211 helix: -0.22 (0.15), residues: 1205 sheet: -1.27 (0.21), residues: 570 loop : -1.65 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 606 TYR 0.021 0.001 TYR H 93 PHE 0.019 0.001 PHE A 223 TRP 0.019 0.001 TRP B 525 HIS 0.021 0.001 HIS L 53 Details of bonding type rmsd covalent geometry : bond 0.00285 (35538) covalent geometry : angle 0.62517 (48194) hydrogen bonds : bond 0.03364 ( 1083) hydrogen bonds : angle 5.27006 ( 3078) metal coordination : bond 0.00559 ( 24) metal coordination : angle 5.34024 ( 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 723 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 563 time to evaluate : 1.312 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: 0.8221 (pttt) cc_final: 0.7574 (pttm) REVERT: A 182 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8334 (ttmt) REVERT: A 191 MET cc_start: 0.6694 (ppp) cc_final: 0.6410 (ppp) REVERT: A 238 MET cc_start: 0.5106 (ptt) cc_final: 0.4817 (ptm) REVERT: A 451 VAL cc_start: 0.5790 (OUTLIER) cc_final: 0.5573 (m) REVERT: A 471 MET cc_start: 0.8090 (mmt) cc_final: 0.7309 (mmt) REVERT: A 543 LEU cc_start: 0.7693 (tp) cc_final: 0.7426 (mp) REVERT: A 925 MET cc_start: 0.8198 (tmm) cc_final: 0.7839 (tmm) REVERT: A 977 MET cc_start: 0.7817 (tmm) cc_final: 0.7484 (tmm) REVERT: A 1020 GLN cc_start: 0.7958 (mt0) cc_final: 0.7621 (tt0) REVERT: A 1073 TYR cc_start: 0.8629 (t80) cc_final: 0.8387 (t80) REVERT: A 1175 MET cc_start: 0.8442 (tmm) cc_final: 0.8200 (tmm) REVERT: A 1227 MET cc_start: 0.7179 (mmm) cc_final: 0.6206 (mmm) REVERT: A 1439 MET cc_start: 0.6352 (ppp) cc_final: 0.5872 (ptt) REVERT: A 1573 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.3946 (t80) REVERT: A 1588 MET cc_start: 0.9065 (mmm) cc_final: 0.8317 (tpt) REVERT: A 1616 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: A 1634 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7999 (pp) REVERT: B 37 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8466 (tm) REVERT: B 60 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7236 (mp) REVERT: B 71 LYS cc_start: 0.7074 (mtpp) cc_final: 0.6494 (mmtt) REVERT: B 128 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7070 (mp10) REVERT: B 205 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6695 (ttp) REVERT: B 243 GLN cc_start: 0.8750 (mp-120) cc_final: 0.8170 (mm-40) REVERT: B 302 LEU cc_start: 0.8559 (mp) cc_final: 0.8224 (mt) REVERT: B 305 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7019 (tpt90) REVERT: B 308 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7277 (mm) REVERT: B 359 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6074 (mt) REVERT: B 374 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8637 (pt) REVERT: B 446 MET cc_start: 0.6354 (tpp) cc_final: 0.5967 (tmm) REVERT: B 480 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7722 (mp10) REVERT: B 502 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8454 (tmm) REVERT: B 668 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6269 (tp30) REVERT: B 760 TYR cc_start: 0.8330 (m-80) cc_final: 0.7951 (m-80) REVERT: B 912 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: B 1013 MET cc_start: 0.8462 (mtp) cc_final: 0.7971 (mtp) REVERT: B 1134 ARG cc_start: 0.6531 (mpt-90) cc_final: 0.6142 (mpt-90) REVERT: C 63 ILE cc_start: 0.9218 (mm) cc_final: 0.8914 (mt) REVERT: C 107 LYS cc_start: 0.7567 (mttt) cc_final: 0.7189 (tmmt) REVERT: D 88 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6651 (tp40) REVERT: E 50 MET cc_start: 0.5748 (tmm) cc_final: 0.5257 (tmm) REVERT: E 54 GLN cc_start: 0.7457 (tp-100) cc_final: 0.6859 (mp10) REVERT: E 78 LEU cc_start: 0.8774 (pp) cc_final: 0.8437 (pp) REVERT: E 164 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8359 (tp) REVERT: F 61 HIS cc_start: 0.7346 (m90) cc_final: 0.7019 (m-70) REVERT: F 79 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7128 (ptt90) REVERT: G 125 TRP cc_start: 0.7358 (t60) cc_final: 0.6933 (t60) REVERT: H 9 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7411 (mt) REVERT: H 62 SER cc_start: 0.8634 (t) cc_final: 0.8293 (m) REVERT: H 89 LEU cc_start: 0.8310 (mt) cc_final: 0.7881 (tt) REVERT: H 126 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: H 130 ARG cc_start: 0.5747 (mtm-85) cc_final: 0.5511 (ptp90) REVERT: I 46 LYS cc_start: 0.8488 (tptp) cc_final: 0.7708 (tptm) REVERT: I 51 THR cc_start: 0.7713 (t) cc_final: 0.7462 (m) REVERT: K 52 GLN cc_start: 0.7916 (mp10) cc_final: 0.7391 (mt0) REVERT: K 81 MET cc_start: 0.8848 (mmm) cc_final: 0.8389 (mmt) REVERT: K 140 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7752 (tppt) REVERT: L 29 TYR cc_start: 0.7575 (m-80) cc_final: 0.7290 (m-10) REVERT: L 40 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5896 (pp) REVERT: M 60 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.6304 (tm) REVERT: M 90 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.6850 (mm) REVERT: N 33 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6257 (mmtt) outliers start: 160 outliers final: 100 residues processed: 680 average time/residue: 0.2090 time to fit residues: 234.7707 Evaluate side-chains 647 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 524 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 316 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 369 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 451 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 616 LEU 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 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 868 THR 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 1070 LEU Chi-restraints excluded: chain A residue 1123 VAL 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 1322 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1573 TYR 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 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 128 GLN 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 283 THR 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 425 ILE 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 558 VAL 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 885 VAL Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 75 MET 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 147 HIS Chi-restraints excluded: chain E residue 149 LEU 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 66 LEU 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 9 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU 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 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 45 CYS 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 68 GLU Chi-restraints excluded: chain M residue 51 PHE Chi-restraints excluded: chain M residue 60 LEU 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 Chi-restraints excluded: chain N residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 103 optimal weight: 0.0870 chunk 69 optimal weight: 5.9990 chunk 383 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 304 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 537 GLN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1581 HIS B 251 HIS ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B1041 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 237 HIS ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.174610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142918 restraints weight = 53143.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142066 restraints weight = 41964.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143095 restraints weight = 37269.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143491 restraints weight = 30853.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143730 restraints weight = 25966.161| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 35562 Z= 0.172 Angle : 0.676 12.154 48221 Z= 0.336 Chirality : 0.045 0.231 5380 Planarity : 0.005 0.058 6085 Dihedral : 10.677 79.942 5109 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 4.39 % Allowed : 19.47 % Favored : 76.14 % 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: -1.76 (0.12), residues: 4211 helix: -0.25 (0.15), residues: 1212 sheet: -1.25 (0.21), residues: 572 loop : -1.66 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 606 TYR 0.025 0.002 TYR A1615 PHE 0.016 0.002 PHE B1135 TRP 0.018 0.002 TRP B 525 HIS 0.021 0.001 HIS L 53 Details of bonding type rmsd covalent geometry : bond 0.00408 (35538) covalent geometry : angle 0.66374 (48194) hydrogen bonds : bond 0.03674 ( 1083) hydrogen bonds : angle 5.33854 ( 3078) metal coordination : bond 0.00746 ( 24) metal coordination : angle 5.54468 ( 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 714 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 548 time to evaluate : 1.271 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: A 70 LYS cc_start: 0.8272 (pttt) cc_final: 0.7559 (pttm) REVERT: A 191 MET cc_start: 0.6546 (ppp) cc_final: 0.6245 (ppp) REVERT: A 543 LEU cc_start: 0.7755 (tp) cc_final: 0.7459 (mp) REVERT: A 1020 GLN cc_start: 0.8007 (mt0) cc_final: 0.7665 (tt0) REVERT: A 1065 GLN cc_start: 0.7566 (mm110) cc_final: 0.7075 (tp40) REVERT: A 1073 TYR cc_start: 0.8708 (t80) cc_final: 0.8467 (t80) REVERT: A 1175 MET cc_start: 0.8372 (tmm) cc_final: 0.8099 (tmm) REVERT: A 1195 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: A 1227 MET cc_start: 0.7214 (mmm) cc_final: 0.6405 (mmm) REVERT: A 1439 MET cc_start: 0.6401 (ppp) cc_final: 0.5887 (ptt) REVERT: A 1573 TYR cc_start: 0.4825 (OUTLIER) cc_final: 0.4324 (t80) REVERT: A 1588 MET cc_start: 0.9127 (mmm) cc_final: 0.8506 (tpt) REVERT: A 1634 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8030 (pp) REVERT: B 37 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8484 (tm) REVERT: B 71 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6830 (mtpp) REVERT: B 128 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: B 205 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6785 (mtt) REVERT: B 243 GLN cc_start: 0.8802 (mp-120) cc_final: 0.8143 (mm-40) REVERT: B 302 LEU cc_start: 0.8590 (mp) cc_final: 0.8329 (mt) REVERT: B 305 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7029 (tpt90) REVERT: B 308 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7349 (mm) REVERT: B 359 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6135 (mt) REVERT: B 373 MET cc_start: 0.7815 (tpp) cc_final: 0.7593 (tpp) REVERT: B 446 MET cc_start: 0.6473 (tpp) cc_final: 0.6144 (tmm) REVERT: B 480 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7797 (mp10) REVERT: B 502 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8569 (tmm) REVERT: B 650 LEU cc_start: 0.8527 (mm) cc_final: 0.8319 (mp) REVERT: B 668 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6819 (mm-30) REVERT: B 912 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: B 1013 MET cc_start: 0.8526 (mtp) cc_final: 0.7725 (mtp) REVERT: D 88 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6658 (tp40) REVERT: E 50 MET cc_start: 0.5617 (tmm) cc_final: 0.4795 (tmm) REVERT: E 54 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7031 (mp10) REVERT: E 164 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8342 (tp) REVERT: F 61 HIS cc_start: 0.7695 (m90) cc_final: 0.7382 (m-70) REVERT: G 125 TRP cc_start: 0.7501 (t60) cc_final: 0.7107 (t60) REVERT: H 9 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7409 (mt) REVERT: H 62 SER cc_start: 0.8531 (t) cc_final: 0.8229 (m) REVERT: H 89 LEU cc_start: 0.8413 (mt) cc_final: 0.7933 (tt) REVERT: H 126 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: H 130 ARG cc_start: 0.5921 (mtm-85) cc_final: 0.5654 (ptp90) REVERT: I 46 LYS cc_start: 0.8465 (tptp) cc_final: 0.7658 (tptm) REVERT: J 49 MET cc_start: 0.7335 (mmm) cc_final: 0.5847 (mmm) REVERT: K 68 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8129 (mm-30) REVERT: K 81 MET cc_start: 0.8891 (mmm) cc_final: 0.8390 (mmt) REVERT: L 40 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5837 (pp) REVERT: M 90 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6719 (mm) REVERT: N 33 LYS cc_start: 0.6877 (pmmt) cc_final: 0.6025 (mmtt) outliers start: 166 outliers final: 126 residues processed: 669 average time/residue: 0.2091 time to fit residues: 232.8820 Evaluate side-chains 664 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 521 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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 85 CYS Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 VAL 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 369 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 490 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 616 LEU 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 793 ILE Chi-restraints excluded: chain A residue 813 LEU 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 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 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 1137 SER 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 1195 GLU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE 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 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN 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 263 SER Chi-restraints excluded: chain B residue 283 THR 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 425 ILE 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 558 VAL 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 672 MET Chi-restraints excluded: chain B residue 681 ILE 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 964 VAL Chi-restraints excluded: chain B residue 965 GLU Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1056 THR Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 222 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 D residue 82 LEU Chi-restraints excluded: chain E residue 75 MET 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 147 HIS Chi-restraints excluded: chain E residue 149 LEU 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 145 ILE Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 216 HIS 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 H residue 126 GLU 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 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 45 CYS 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 68 GLU 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 66 LYS 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: 4.9990 chunk 25 optimal weight: 0.9990 chunk 417 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 318 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 322 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 422 optimal weight: 10.0000 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS I 32 GLN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.177029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145027 restraints weight = 53062.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144517 restraints weight = 40364.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145384 restraints weight = 33542.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145856 restraints weight = 27930.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145967 restraints weight = 26762.067| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35562 Z= 0.129 Angle : 0.655 11.443 48221 Z= 0.325 Chirality : 0.044 0.183 5380 Planarity : 0.004 0.076 6085 Dihedral : 10.634 80.870 5109 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.75 % Favored : 94.23 % Rotamer: Outliers : 3.96 % Allowed : 19.89 % Favored : 76.14 % 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: -1.63 (0.13), residues: 4211 helix: -0.11 (0.15), residues: 1212 sheet: -1.15 (0.21), residues: 573 loop : -1.60 (0.12), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 609 TYR 0.020 0.002 TYR A1615 PHE 0.020 0.001 PHE A 355 TRP 0.020 0.001 TRP B 525 HIS 0.013 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00300 (35538) covalent geometry : angle 0.64358 (48194) hydrogen bonds : bond 0.03422 ( 1083) hydrogen bonds : angle 5.19687 ( 3078) metal coordination : bond 0.00601 ( 24) metal coordination : angle 5.14504 ( 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 704 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 554 time to evaluate : 1.556 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: 0.8189 (pttt) cc_final: 0.7579 (pttm) REVERT: A 191 MET cc_start: 0.6440 (ppp) cc_final: 0.6113 (ppp) REVERT: A 238 MET cc_start: 0.5160 (ptt) cc_final: 0.4888 (ppp) REVERT: A 471 MET cc_start: 0.7880 (mmt) cc_final: 0.6965 (mmt) REVERT: A 543 LEU cc_start: 0.7740 (tp) cc_final: 0.7480 (mp) REVERT: A 925 MET cc_start: 0.8231 (tmm) cc_final: 0.7813 (tmm) REVERT: A 1020 GLN cc_start: 0.7964 (mt0) cc_final: 0.7646 (tt0) REVERT: A 1065 GLN cc_start: 0.7421 (mm110) cc_final: 0.6984 (tp40) REVERT: A 1073 TYR cc_start: 0.8658 (t80) cc_final: 0.8414 (t80) REVERT: A 1085 LEU cc_start: 0.8499 (mt) cc_final: 0.7915 (tt) REVERT: A 1195 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: A 1227 MET cc_start: 0.7196 (mmm) cc_final: 0.6434 (mmm) REVERT: A 1439 MET cc_start: 0.6412 (ppp) cc_final: 0.5866 (ptt) REVERT: A 1573 TYR cc_start: 0.4671 (OUTLIER) cc_final: 0.4192 (t80) REVERT: A 1588 MET cc_start: 0.9040 (mmm) cc_final: 0.8212 (tpt) REVERT: A 1634 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8049 (pp) REVERT: B 37 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8227 (tm) REVERT: B 71 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6512 (mmtt) REVERT: B 128 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7102 (mp10) REVERT: B 205 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6771 (mtt) REVERT: B 243 GLN cc_start: 0.8798 (mp-120) cc_final: 0.8557 (mm-40) REVERT: B 268 GLU cc_start: 0.8150 (pm20) cc_final: 0.7841 (mt-10) REVERT: B 302 LEU cc_start: 0.8500 (mp) cc_final: 0.8280 (mt) REVERT: B 305 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7135 (tpt90) REVERT: B 308 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7277 (mm) REVERT: B 359 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6365 (mt) REVERT: B 446 MET cc_start: 0.6394 (tpp) cc_final: 0.5988 (tmm) REVERT: B 480 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7796 (mp10) REVERT: B 502 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8526 (tmm) REVERT: B 654 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7054 (ptm160) REVERT: B 667 PHE cc_start: 0.8305 (t80) cc_final: 0.7582 (t80) REVERT: B 912 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.5995 (pm20) REVERT: B 1013 MET cc_start: 0.8513 (mtp) cc_final: 0.7836 (mtp) REVERT: B 1134 ARG cc_start: 0.6520 (mpt-90) cc_final: 0.6255 (mpt-90) REVERT: C 63 ILE cc_start: 0.9196 (mm) cc_final: 0.8859 (mt) REVERT: C 107 LYS cc_start: 0.7677 (mttt) cc_final: 0.7331 (tmmt) REVERT: D 88 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6667 (tp40) REVERT: E 54 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7122 (mp10) REVERT: E 164 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8292 (tp) REVERT: F 61 HIS cc_start: 0.7674 (m90) cc_final: 0.7437 (m90) REVERT: F 84 TYR cc_start: 0.7940 (m-80) cc_final: 0.7507 (m-80) REVERT: F 97 ARG cc_start: 0.8424 (tpt170) cc_final: 0.8202 (tpt170) REVERT: G 71 MET cc_start: 0.7799 (mmm) cc_final: 0.7359 (tpt) REVERT: G 125 TRP cc_start: 0.7459 (t60) cc_final: 0.7065 (t60) REVERT: H 9 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7400 (mt) REVERT: H 62 SER cc_start: 0.8634 (t) cc_final: 0.8298 (m) REVERT: H 89 LEU cc_start: 0.8318 (mt) cc_final: 0.7878 (tt) REVERT: H 126 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: H 130 ARG cc_start: 0.5790 (mtm-85) cc_final: 0.5515 (ptp90) REVERT: I 46 LYS cc_start: 0.8532 (tptp) cc_final: 0.7759 (tptm) REVERT: I 51 THR cc_start: 0.7663 (t) cc_final: 0.7428 (m) REVERT: J 49 MET cc_start: 0.7082 (mmm) cc_final: 0.5622 (mmm) REVERT: K 52 GLN cc_start: 0.7827 (mp10) cc_final: 0.7274 (mt0) REVERT: K 68 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8047 (mm-30) REVERT: K 81 MET cc_start: 0.8853 (mmm) cc_final: 0.8314 (mmt) REVERT: L 29 TYR cc_start: 0.7619 (m-80) cc_final: 0.7216 (m-10) REVERT: L 40 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5807 (pp) REVERT: M 90 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.6738 (mm) REVERT: N 33 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6173 (mmtt) REVERT: N 65 SER cc_start: 0.6142 (m) cc_final: 0.5612 (t) outliers start: 150 outliers final: 111 residues processed: 660 average time/residue: 0.2091 time to fit residues: 229.7613 Evaluate side-chains 661 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 531 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 220 VAL 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 369 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 490 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 616 LEU 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 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain A residue 868 THR 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 982 VAL 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 1070 LEU Chi-restraints excluded: chain A residue 1137 SER 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 1195 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1542 THR 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 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 128 GLN 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 283 THR 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 369 ASP Chi-restraints excluded: chain B residue 425 ILE 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 558 VAL 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 672 MET Chi-restraints excluded: chain B residue 681 ILE 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 964 VAL Chi-restraints excluded: chain B residue 965 GLU 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 162 VAL Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 222 VAL 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 75 MET 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 147 HIS Chi-restraints excluded: chain E residue 149 LEU 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 145 ILE Chi-restraints excluded: chain G residue 167 THR 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 H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU 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 5 VAL Chi-restraints excluded: chain J residue 7 CYS 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 L residue 68 GLU 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 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 420 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 319 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 HIS G 237 HIS ** J 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 = 0.4040 r_free = 0.4040 target = 0.173257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141737 restraints weight = 53430.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140821 restraints weight = 43644.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141775 restraints weight = 37585.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142305 restraints weight = 29872.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142397 restraints weight = 27552.211| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 35562 Z= 0.190 Angle : 0.705 11.788 48221 Z= 0.352 Chirality : 0.046 0.234 5380 Planarity : 0.005 0.058 6085 Dihedral : 10.717 80.168 5109 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.93 % Favored : 93.02 % Rotamer: Outliers : 3.86 % Allowed : 20.34 % Favored : 75.80 % 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: -1.71 (0.12), residues: 4211 helix: -0.18 (0.15), residues: 1216 sheet: -1.25 (0.21), residues: 568 loop : -1.64 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 452 TYR 0.019 0.002 TYR B 717 PHE 0.027 0.002 PHE A 355 TRP 0.029 0.002 TRP A 530 HIS 0.016 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.00453 (35538) covalent geometry : angle 0.69293 (48194) hydrogen bonds : bond 0.03770 ( 1083) hydrogen bonds : angle 5.30854 ( 3078) metal coordination : bond 0.00792 ( 24) metal coordination : angle 5.49204 ( 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 683 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 537 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8253 (pttt) cc_final: 0.7467 (pttm) REVERT: A 182 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8134 (mptt) REVERT: A 238 MET cc_start: 0.5387 (ptt) cc_final: 0.5030 (ppp) REVERT: A 356 PHE cc_start: 0.7131 (m-80) cc_final: 0.6916 (m-80) REVERT: A 357 MET cc_start: 0.7821 (mpp) cc_final: 0.7438 (mtm) REVERT: A 471 MET cc_start: 0.7719 (mmt) cc_final: 0.7345 (mmt) REVERT: A 543 LEU cc_start: 0.7875 (tp) cc_final: 0.7517 (mp) REVERT: A 1020 GLN cc_start: 0.8053 (mt0) cc_final: 0.7708 (tt0) REVERT: A 1065 GLN cc_start: 0.7492 (mm110) cc_final: 0.7057 (tp40) REVERT: A 1073 TYR cc_start: 0.8738 (t80) cc_final: 0.8472 (t80) REVERT: A 1195 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: A 1227 MET cc_start: 0.7219 (mmm) cc_final: 0.6496 (mmm) REVERT: A 1439 MET cc_start: 0.6382 (ppp) cc_final: 0.5898 (ptt) REVERT: A 1464 ASP cc_start: 0.5934 (p0) cc_final: 0.5729 (m-30) REVERT: A 1573 TYR cc_start: 0.5088 (OUTLIER) cc_final: 0.4583 (t80) REVERT: A 1588 MET cc_start: 0.9189 (mmm) cc_final: 0.8621 (tpt) REVERT: A 1634 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8027 (pp) REVERT: B 37 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8336 (tm) REVERT: B 71 LYS cc_start: 0.7303 (mtpp) cc_final: 0.6634 (mmtt) REVERT: B 128 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: B 205 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7017 (mtt) REVERT: B 236 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7283 (tt) REVERT: B 243 GLN cc_start: 0.8841 (mp-120) cc_final: 0.8489 (mm-40) REVERT: B 268 GLU cc_start: 0.8108 (pm20) cc_final: 0.7890 (mt-10) REVERT: B 302 LEU cc_start: 0.8645 (mp) cc_final: 0.8393 (mt) REVERT: B 305 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6860 (tpt90) REVERT: B 308 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7379 (mm) REVERT: B 359 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.5932 (mt) REVERT: B 373 MET cc_start: 0.7736 (tpp) cc_final: 0.7436 (tpt) REVERT: B 446 MET cc_start: 0.6520 (tpp) cc_final: 0.6098 (tmm) REVERT: B 480 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: B 650 LEU cc_start: 0.8573 (mm) cc_final: 0.8364 (mp) REVERT: B 654 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7069 (ptm160) REVERT: B 875 HIS cc_start: 0.6809 (p-80) cc_final: 0.6267 (p90) REVERT: B 912 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6160 (pm20) REVERT: B 946 ASP cc_start: 0.8901 (p0) cc_final: 0.8608 (p0) REVERT: B 1013 MET cc_start: 0.8497 (mtp) cc_final: 0.7760 (mtp) REVERT: B 1089 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 1134 ARG cc_start: 0.6628 (mpt-90) cc_final: 0.6376 (mpt-90) REVERT: C 63 ILE cc_start: 0.9187 (mm) cc_final: 0.8838 (mt) REVERT: C 107 LYS cc_start: 0.7865 (mttt) cc_final: 0.7417 (tmmt) REVERT: C 224 THR cc_start: 0.6562 (OUTLIER) cc_final: 0.6152 (p) REVERT: D 88 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6695 (tp40) REVERT: E 54 GLN cc_start: 0.7474 (tp-100) cc_final: 0.6988 (mp10) REVERT: E 164 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8285 (tp) REVERT: F 61 HIS cc_start: 0.7627 (m90) cc_final: 0.7338 (m90) REVERT: G 71 MET cc_start: 0.7803 (mmm) cc_final: 0.7392 (tpt) REVERT: G 125 TRP cc_start: 0.7524 (t60) cc_final: 0.7148 (t60) REVERT: H 62 SER cc_start: 0.8547 (t) cc_final: 0.8274 (m) REVERT: H 126 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: H 130 ARG cc_start: 0.5893 (mtm-85) cc_final: 0.5624 (ptp90) REVERT: I 46 LYS cc_start: 0.8522 (tptp) cc_final: 0.7720 (tptm) REVERT: K 52 GLN cc_start: 0.7911 (mp10) cc_final: 0.7365 (mt0) REVERT: K 68 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8177 (mm-30) REVERT: K 98 GLU cc_start: 0.6252 (pp20) cc_final: 0.5970 (pp20) REVERT: L 40 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5778 (pp) REVERT: M 90 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.6742 (mm) REVERT: N 33 LYS cc_start: 0.6751 (pmmt) cc_final: 0.5920 (mmtt) REVERT: N 65 SER cc_start: 0.6226 (m) cc_final: 0.5659 (t) outliers start: 146 outliers final: 121 residues processed: 636 average time/residue: 0.2022 time to fit residues: 214.3098 Evaluate side-chains 658 residues out of total 3785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 519 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 220 VAL 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 369 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 490 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 616 LEU 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 764 SER Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 831 ASP Chi-restraints excluded: chain A residue 868 THR 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 982 VAL 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 1036 ASN Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1137 SER Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1176 ARG Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1195 GLU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1573 TYR Chi-restraints excluded: chain A residue 1585 ILE 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 106 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 130 LEU 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 236 ILE Chi-restraints excluded: chain B residue 283 THR 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 425 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 558 VAL 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 672 MET Chi-restraints excluded: chain B residue 681 ILE 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 965 GLU Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 1158 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 178 THR 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 311 GLU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 75 MET 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 147 HIS Chi-restraints excluded: chain E residue 149 LEU 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 167 THR Chi-restraints excluded: chain G residue 216 HIS Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU 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 5 VAL Chi-restraints excluded: chain J residue 7 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 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 68 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 382 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.0070 chunk 326 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 353 optimal weight: 0.0270 chunk 365 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS ** A1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN H 134 ASN ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145501 restraints weight = 52772.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144854 restraints weight = 40329.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145921 restraints weight = 32976.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146651 restraints weight = 27867.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146812 restraints weight = 24769.205| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 35562 Z= 0.124 Angle : 0.667 11.255 48221 Z= 0.330 Chirality : 0.043 0.193 5380 Planarity : 0.004 0.056 6085 Dihedral : 10.624 81.224 5109 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.30 % Rotamer: Outliers : 3.38 % Allowed : 21.11 % Favored : 75.51 % 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: -1.52 (0.13), residues: 4211 helix: 0.05 (0.15), residues: 1195 sheet: -1.18 (0.21), residues: 568 loop : -1.54 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 606 TYR 0.017 0.001 TYR B 420 PHE 0.031 0.001 PHE A 355 TRP 0.026 0.001 TRP A 530 HIS 0.013 0.001 HIS J 53 Details of bonding type rmsd covalent geometry : bond 0.00287 (35538) covalent geometry : angle 0.65618 (48194) hydrogen bonds : bond 0.03350 ( 1083) hydrogen bonds : angle 5.12103 ( 3078) metal coordination : bond 0.00578 ( 24) metal coordination : angle 5.02019 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5944.31 seconds wall clock time: 103 minutes 49.32 seconds (6229.32 seconds total)