Starting phenix.real_space_refine on Mon Aug 25 20:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hls_0241/08_2025/6hls_0241.map" } resolution = 3.21 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= -0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 166 5.16 5 C 19580 2.51 5 N 5376 2.21 5 O 5825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30954 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 11308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1431, 11308 Classifications: {'peptide': 1431} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1371} Chain breaks: 10 Chain: "B" Number of atoms: 9248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1163, 9248 Classifications: {'peptide': 1163} Link IDs: {'PTRANS': 59, 'TRANS': 1103} Chain breaks: 4 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} 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: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} 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: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} 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 461 SG CYS A 62 62.136 51.274 56.118 1.00 58.45 S ATOM 480 SG CYS A 65 65.634 49.840 55.871 1.00 53.69 S ATOM 535 SG CYS A 72 64.578 51.492 59.046 1.00 50.91 S ATOM 781 SG CYS A 102 62.369 101.530 43.631 1.00 74.18 S ATOM 806 SG CYS A 105 65.742 99.891 40.778 1.00 73.06 S ATOM 1575 SG CYS A 233 66.792 102.720 42.781 1.00 81.47 S ATOM 1597 SG CYS A 236 63.853 102.893 40.174 1.00 89.19 S ATOM 19886 SG CYS B1104 76.730 60.405 48.595 1.00 36.57 S ATOM 19912 SG CYS B1107 74.219 63.051 48.457 1.00 43.96 S ATOM 20059 SG CYS B1128 73.130 59.669 48.583 1.00 51.13 S ATOM 28535 SG CYS I 13 33.169 126.428 107.591 1.00 63.09 S ATOM 28655 SG CYS I 30 34.090 128.049 104.458 1.00 77.26 S ATOM 28973 SG CYS I 89 71.399 86.317 155.587 1.00136.54 S ATOM 29171 SG CYS I 114 68.717 87.322 151.553 1.00108.04 S ATOM 29314 SG CYS J 7 79.156 42.644 128.480 1.00 25.29 S ATOM 29337 SG CYS J 10 82.641 42.009 129.097 1.00 24.78 S ATOM 29617 SG CYS J 45 82.811 45.659 129.920 1.00 23.47 S ATOM 29623 SG CYS J 46 80.569 43.167 131.777 1.00 23.27 S ATOM 30638 SG CYS L 31 37.873 42.965 112.755 1.00 47.42 S ATOM 30658 SG CYS L 34 36.247 41.491 115.808 1.00 49.32 S ATOM 30762 SG CYS L 48 34.804 40.130 112.736 1.00 69.01 S ATOM 30785 SG CYS L 51 34.029 44.387 114.355 1.00 68.98 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN I3002 " occ=0.75 Time building chain proxies: 6.46, per 1000 atoms: 0.21 Number of scatterers: 30954 At special positions: 0 Unit cell: (158.08, 162.24, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 166 16.00 O 5825 8.00 N 5376 7.00 C 19580 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.7 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 105 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN I3002 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 89 " pdb="ZN ZN I3002 " - pdb=" SG CYS I 114 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " Number of angles added : 21 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7316 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 51 sheets defined 35.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.977A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.191A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.740A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.559A pdb=" N LYS A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 199 removed outlier: 3.697A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 229 removed outlier: 3.613A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.516A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.536A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.683A pdb=" N ARG A 368 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 405 removed outlier: 3.503A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 439 removed outlier: 3.676A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.172A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.659A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.515A pdb=" N ASN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.528A 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: 3.954A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 802 removed outlier: 3.810A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.642A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 3.786A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 847 Processing helix chain 'A' and resid 848 through 851 removed outlier: 3.894A pdb=" N VAL A 851 " --> pdb=" O LYS A 848 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.629A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 Processing helix chain 'A' and resid 894 through 912 removed outlier: 3.685A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.561A pdb=" N VAL A 940 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1008 removed outlier: 3.558A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 removed outlier: 3.775A 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 removed outlier: 3.733A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.555A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.194A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.566A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.695A pdb=" N ASP A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A1151 " --> pdb=" O PHE A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.794A pdb=" N PHE A1166 " --> pdb=" O ASN A1162 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.875A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A1194 " --> pdb=" O SER A1190 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1195 " --> pdb=" O GLN A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1248 through 1256 removed outlier: 3.553A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1254 " --> pdb=" O GLN A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 4.081A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A1306 " --> pdb=" O TYR A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.507A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A1319 " --> pdb=" O ASN A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.525A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1454 removed outlier: 3.608A pdb=" N ASP A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1451 " --> pdb=" O GLN A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 3.897A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.852A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1554 removed outlier: 3.829A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1566 removed outlier: 3.576A pdb=" N ASN A1560 " --> pdb=" O GLU A1556 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1572 Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.747A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.637A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 removed outlier: 3.582A pdb=" N ASP A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1643 removed outlier: 3.763A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.289A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 4.035A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.049A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 55 through 59 removed outlier: 4.136A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 removed outlier: 3.915A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.529A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 182 removed outlier: 3.665A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.545A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.515A pdb=" N GLY B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.526A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.824A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.703A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.815A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (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: 3.774A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.573A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.835A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 614 removed outlier: 3.594A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.557A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 removed outlier: 3.584A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.508A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 754 through 760 removed outlier: 4.321A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 833 through 839 removed outlier: 3.928A pdb=" N TRP B 836 " --> pdb=" O PRO B 833 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 839' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 959 through 976 removed outlier: 3.968A pdb=" N PHE B 963 " --> pdb=" O THR B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.808A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.686A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.559A pdb=" N GLN B1089 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1193 removed outlier: 3.609A pdb=" N ALA B1191 " --> pdb=" O SER B1187 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 40 removed outlier: 3.533A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.671A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.557A pdb=" N HIS C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 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 174 through 179 removed outlier: 3.820A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 179' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.598A pdb=" N PHE C 219 " --> pdb=" O HIS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.714A pdb=" N CYS C 250 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.641A pdb=" N ARG C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 282' Processing helix chain 'C' and resid 283 through 286 removed outlier: 3.899A pdb=" N ALA C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.567A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 82 through 94 removed outlier: 4.143A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 removed outlier: 4.151A pdb=" N SER E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 removed outlier: 3.656A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 91 through 103 removed outlier: 3.781A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.609A pdb=" N LEU E 123 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 removed outlier: 3.992A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.826A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.573A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 4.129A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 102 removed outlier: 3.885A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 66 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.640A pdb=" N ASP H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 67 removed outlier: 3.770A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.569A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 4.283A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.046A 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: 3.721A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 removed outlier: 3.608A pdb=" N LYS K 122 " --> pdb=" O GLN K 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU K 132 " --> pdb=" O CYS K 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER K 141 " --> pdb=" O GLU K 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA2, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 7.344A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 86 removed outlier: 3.595A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 11.486A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA5, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.967A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.641A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.980A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.578A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB2, first strand: chain 'A' and resid 1507 through 1508 Processing sheet with id=AB3, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.139A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.841A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.841A pdb=" N GLN D 29 " --> pdb=" O ARG G 40 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 40 " --> pdb=" O GLN D 29 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP G 117 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR G 123 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR G 84 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TRP G 125 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 82 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS G 72 " --> pdb=" O VAL G 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 104 removed outlier: 5.948A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB9, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AC1, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.355A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.418A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 236 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.705A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC5, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.803A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.501A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.501A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 752 through 753 removed outlier: 3.527A pdb=" N LYS B 753 " --> pdb=" O GLN B 979 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 775 removed outlier: 8.462A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.684A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD3, first strand: chain 'B' and resid 1010 through 1011 Processing sheet with id=AD4, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD5, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD6, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.686A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN C 301 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA C 225 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU C 303 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 41 through 46 removed outlier: 3.686A pdb=" N GLU C 41 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 168 through 169 removed outlier: 6.677A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.400A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE3, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE4, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE5, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.105A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE7, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.703A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 132 through 133 removed outlier: 3.913A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=AF1, first strand: chain 'G' and resid 167 through 169 removed outlier: 4.009A pdb=" N HIS G 216 " --> pdb=" O VAL G 169 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.945A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.853A pdb=" N LEU I 7 " --> pdb=" O VAL I 4 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 28 through 29 Processing sheet with id=AF5, first strand: chain 'I' and resid 95 through 99 Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 1078 hydrogen bonds defined for protein. 2985 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: 7.76 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9549 1.33 - 1.46: 5634 1.46 - 1.58: 16108 1.58 - 1.70: 0 1.70 - 1.82: 260 Bond restraints: 31551 Sorted by residual: bond pdb=" C GLY B 844 " pdb=" N LEU B 845 " ideal model delta sigma weight residual 1.331 1.257 0.074 2.83e-02 1.25e+03 6.76e+00 bond pdb=" CG1 ILE B 276 " pdb=" CD1 ILE B 276 " ideal model delta sigma weight residual 1.513 1.429 0.084 3.90e-02 6.57e+02 4.68e+00 bond pdb=" CB MET B 936 " pdb=" CG MET B 936 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.12e+00 bond pdb=" CG LEU B1087 " pdb=" CD1 LEU B1087 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.98e+00 bond pdb=" CG LEU A1584 " pdb=" CD1 LEU A1584 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 ... (remaining 31546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 41106 2.22 - 4.44: 1289 4.44 - 6.67: 176 6.67 - 8.89: 51 8.89 - 11.11: 11 Bond angle restraints: 42633 Sorted by residual: angle pdb=" N ILE A 793 " pdb=" CA ILE A 793 " pdb=" C ILE A 793 " ideal model delta sigma weight residual 112.96 108.02 4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" N ILE B 417 " pdb=" CA ILE B 417 " pdb=" C ILE B 417 " ideal model delta sigma weight residual 112.29 107.74 4.55 9.40e-01 1.13e+00 2.35e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ARG L 42 " pdb=" N THR L 43 " pdb=" CA THR L 43 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 angle pdb=" C THR B 18 " pdb=" N LEU B 19 " pdb=" CA LEU B 19 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 ... (remaining 42628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 18068 15.30 - 30.59: 929 30.59 - 45.89: 206 45.89 - 61.19: 8 61.19 - 76.48: 21 Dihedral angle restraints: 19232 sinusoidal: 7905 harmonic: 11327 Sorted by residual: dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA CYS J 7 " pdb=" C CYS J 7 " pdb=" N PHE J 8 " pdb=" CA PHE J 8 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA LEU A 781 " pdb=" C LEU A 781 " pdb=" N ASP A 782 " pdb=" CA ASP A 782 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 19229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4241 0.094 - 0.188: 482 0.188 - 0.282: 28 0.282 - 0.375: 3 0.375 - 0.469: 2 Chirality restraints: 4756 Sorted by residual: chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CB ILE D 22 " pdb=" CA ILE D 22 " pdb=" CG1 ILE D 22 " pdb=" CG2 ILE D 22 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 4753 not shown) Planarity restraints: 5519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO E 151 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " -0.024 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR B1033 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN G 67 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO G 68 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 68 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 68 " -0.039 5.00e-02 4.00e+02 ... (remaining 5516 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5424 2.76 - 3.30: 27483 3.30 - 3.83: 50649 3.83 - 4.37: 62084 4.37 - 4.90: 106492 Nonbonded interactions: 252132 Sorted by model distance: nonbonded pdb=" O PHE B 963 " pdb=" OH TYR B1027 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP B 843 " pdb=" OH TYR L 29 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP B1186 " pdb=" OH TYR B1198 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.289 3.040 nonbonded pdb=" OD2 ASP E 25 " pdb=" OH TYR E 187 " model vdw 2.301 3.040 ... (remaining 252127 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.910 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.010 0.545 31574 Z= 0.365 Angle : 1.056 61.947 42654 Z= 0.502 Chirality : 0.060 0.469 4756 Planarity : 0.007 0.082 5519 Dihedral : 10.209 76.484 11916 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.32 % Allowed : 3.60 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -4.54 (0.10), residues: 3836 helix: -4.39 (0.06), residues: 1228 sheet: -2.49 (0.19), residues: 600 loop : -2.19 (0.12), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 135 TYR 0.049 0.003 TYR B1033 PHE 0.038 0.003 PHE A1610 TRP 0.048 0.004 TRP B 836 HIS 0.013 0.002 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00698 (31551) covalent geometry : angle 0.94309 (42633) hydrogen bonds : bond 0.30255 ( 1037) hydrogen bonds : angle 10.90644 ( 2985) metal coordination : bond 0.25351 ( 23) metal coordination : angle 21.38777 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 979 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8597 (t80) cc_final: 0.8285 (t80) REVERT: A 97 TYR cc_start: 0.8071 (m-80) cc_final: 0.7823 (m-80) REVERT: A 110 LEU cc_start: 0.8697 (tt) cc_final: 0.8451 (tp) REVERT: A 111 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7983 (tptm) REVERT: A 221 HIS cc_start: 0.7377 (m90) cc_final: 0.7047 (m170) REVERT: A 388 LYS cc_start: 0.7789 (tttp) cc_final: 0.7304 (mttt) REVERT: A 516 ILE cc_start: 0.7735 (pp) cc_final: 0.7481 (pp) REVERT: A 547 ILE cc_start: 0.8378 (mt) cc_final: 0.8081 (tt) REVERT: A 627 ASP cc_start: 0.7760 (p0) cc_final: 0.7478 (p0) REVERT: A 662 SER cc_start: 0.8826 (t) cc_final: 0.8485 (m) REVERT: A 1097 TYR cc_start: 0.8489 (t80) cc_final: 0.8242 (t80) REVERT: B 37 LEU cc_start: 0.8800 (tp) cc_final: 0.8380 (mp) REVERT: B 66 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8152 (ttmm) REVERT: B 333 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7543 (ttpt) REVERT: B 343 ASP cc_start: 0.7795 (t0) cc_final: 0.7572 (p0) REVERT: B 677 THR cc_start: 0.8778 (t) cc_final: 0.8450 (p) REVERT: B 990 ASP cc_start: 0.7642 (p0) cc_final: 0.7405 (p0) REVERT: B 1111 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7624 (pp) REVERT: C 31 TRP cc_start: 0.8716 (t60) cc_final: 0.8363 (t60) REVERT: C 43 ASN cc_start: 0.7695 (t0) cc_final: 0.7395 (m-40) REVERT: C 47 LEU cc_start: 0.7914 (mm) cc_final: 0.7278 (mt) REVERT: E 17 ARG cc_start: 0.7638 (ttt180) cc_final: 0.7398 (ttp-170) REVERT: E 20 LYS cc_start: 0.8362 (mmpt) cc_final: 0.8033 (mmtp) REVERT: E 112 TYR cc_start: 0.7873 (p90) cc_final: 0.7134 (p90) REVERT: G 56 ASN cc_start: 0.8138 (m-40) cc_final: 0.7908 (m110) REVERT: H 37 LYS cc_start: 0.8293 (pttt) cc_final: 0.8028 (pttt) REVERT: H 91 ASP cc_start: 0.8396 (m-30) cc_final: 0.8103 (m-30) REVERT: H 144 ILE cc_start: 0.8874 (mm) cc_final: 0.8663 (mt) REVERT: K 48 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8288 (ttpp) REVERT: K 119 LYS cc_start: 0.8450 (tttt) cc_final: 0.7807 (tttm) REVERT: K 131 VAL cc_start: 0.8999 (m) cc_final: 0.8728 (t) REVERT: L 33 GLU cc_start: 0.7739 (tp30) cc_final: 0.7340 (tp30) outliers start: 11 outliers final: 2 residues processed: 986 average time/residue: 0.2071 time to fit residues: 314.2742 Evaluate side-chains 576 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 573 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 1111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 553 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS A 634 ASN A 673 HIS A 798 HIS A 880 GLN A 939 ASN A1047 GLN A1062 HIS A1108 HIS A1293 HIS A1447 GLN B 27 ASN B 473 GLN B 679 GLN B 684 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 745 GLN B 767 ASN B 921 HIS B1115 GLN C 175 GLN C 216 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 136 ASN G 64 GLN G 121 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN K 106 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.149084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124674 restraints weight = 42620.771| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.63 r_work: 0.3244 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31574 Z= 0.135 Angle : 0.643 17.196 42654 Z= 0.334 Chirality : 0.046 0.235 4756 Planarity : 0.005 0.076 5519 Dihedral : 5.642 48.165 4235 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.26 % Allowed : 9.99 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -3.21 (0.12), residues: 3836 helix: -2.70 (0.11), residues: 1284 sheet: -2.08 (0.19), residues: 619 loop : -1.61 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 156 TYR 0.019 0.002 TYR H 95 PHE 0.016 0.001 PHE B1167 TRP 0.023 0.001 TRP B 836 HIS 0.010 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00296 (31551) covalent geometry : angle 0.63062 (42633) hydrogen bonds : bond 0.04837 ( 1037) hydrogen bonds : angle 6.23093 ( 2985) metal coordination : bond 0.00831 ( 23) metal coordination : angle 5.72288 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 667 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8796 (t80) cc_final: 0.8426 (t80) REVERT: A 110 LEU cc_start: 0.8701 (tt) cc_final: 0.8422 (tp) REVERT: A 111 LYS cc_start: 0.8262 (ptpt) cc_final: 0.7968 (tptm) REVERT: A 182 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7948 (mtpt) REVERT: A 205 ARG cc_start: 0.7682 (mtp85) cc_final: 0.6989 (mmt180) REVERT: A 221 HIS cc_start: 0.7914 (m90) cc_final: 0.7509 (m170) REVERT: A 248 PHE cc_start: 0.6833 (m-80) cc_final: 0.6432 (m-80) REVERT: A 388 LYS cc_start: 0.7857 (tttp) cc_final: 0.7265 (mttt) REVERT: A 547 ILE cc_start: 0.8594 (mt) cc_final: 0.8248 (tt) REVERT: A 625 ASN cc_start: 0.8366 (t0) cc_final: 0.8073 (t0) REVERT: A 891 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8598 (mm) REVERT: A 953 GLU cc_start: 0.7824 (pm20) cc_final: 0.7541 (pm20) REVERT: A 1092 GLU cc_start: 0.6617 (tp30) cc_final: 0.6357 (tp30) REVERT: A 1572 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7368 (tpt170) REVERT: B 37 LEU cc_start: 0.8772 (tp) cc_final: 0.8554 (mp) REVERT: B 66 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8466 (ttmm) REVERT: B 179 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8128 (mt-10) REVERT: B 273 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8424 (t) REVERT: B 333 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7142 (ttpt) REVERT: B 343 ASP cc_start: 0.8159 (t0) cc_final: 0.7810 (p0) REVERT: B 502 MET cc_start: 0.8995 (ptm) cc_final: 0.8606 (ptm) REVERT: B 550 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7782 (mmt90) REVERT: B 626 ILE cc_start: 0.8595 (pt) cc_final: 0.8274 (mt) REVERT: B 795 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8286 (mm-30) REVERT: B 896 GLN cc_start: 0.7397 (tt0) cc_final: 0.6727 (mt0) REVERT: C 31 TRP cc_start: 0.8840 (t60) cc_final: 0.8424 (t60) REVERT: E 17 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7650 (ttp-170) REVERT: E 20 LYS cc_start: 0.8487 (mmpt) cc_final: 0.8205 (mmtp) REVERT: E 46 TYR cc_start: 0.7552 (m-80) cc_final: 0.6973 (m-80) REVERT: E 215 MET cc_start: 0.8717 (mmt) cc_final: 0.8489 (mmt) REVERT: G 64 GLN cc_start: 0.8776 (mt0) cc_final: 0.8570 (mt0) REVERT: H 22 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8413 (mttp) REVERT: H 144 ILE cc_start: 0.9141 (mm) cc_final: 0.8937 (mt) REVERT: I 29 GLU cc_start: 0.7620 (tt0) cc_final: 0.7226 (pm20) REVERT: I 96 TYR cc_start: 0.7382 (p90) cc_final: 0.6911 (p90) REVERT: I 112 TYR cc_start: 0.7983 (m-80) cc_final: 0.7733 (m-80) REVERT: K 48 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8400 (ttpp) REVERT: K 85 ASP cc_start: 0.8533 (t0) cc_final: 0.8067 (t0) REVERT: K 119 LYS cc_start: 0.8587 (tttt) cc_final: 0.8161 (tttm) REVERT: L 33 GLU cc_start: 0.7498 (tp30) cc_final: 0.7280 (tp30) outliers start: 78 outliers final: 51 residues processed: 714 average time/residue: 0.2032 time to fit residues: 229.9874 Evaluate side-chains 590 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 536 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 553 GLN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 563 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 39 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 301 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 GLN A 116 HIS A 553 GLN A 634 ASN A 656 GLN A1447 GLN B 101 GLN B 710 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 234 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN E 101 GLN E 106 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS I 32 GLN J 26 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121394 restraints weight = 42914.776| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.68 r_work: 0.3192 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31574 Z= 0.160 Angle : 0.610 11.130 42654 Z= 0.314 Chirality : 0.046 0.259 4756 Planarity : 0.005 0.070 5519 Dihedral : 5.287 51.168 4233 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.93 % Allowed : 12.19 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -2.32 (0.12), residues: 3836 helix: -1.70 (0.13), residues: 1269 sheet: -1.75 (0.19), residues: 618 loop : -1.23 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 329 TYR 0.025 0.002 TYR A 995 PHE 0.017 0.002 PHE B1167 TRP 0.022 0.001 TRP B 836 HIS 0.007 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00381 (31551) covalent geometry : angle 0.60346 (42633) hydrogen bonds : bond 0.04276 ( 1037) hydrogen bonds : angle 5.59221 ( 2985) metal coordination : bond 0.00589 ( 23) metal coordination : angle 4.12525 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 554 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8804 (t80) cc_final: 0.8421 (t80) REVERT: A 110 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 111 LYS cc_start: 0.8343 (ptpt) cc_final: 0.8070 (tptm) REVERT: A 195 LYS cc_start: 0.7309 (tttp) cc_final: 0.7109 (mttt) REVERT: A 205 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7004 (mmt180) REVERT: A 388 LYS cc_start: 0.7882 (tttp) cc_final: 0.7296 (mttt) REVERT: A 424 MET cc_start: 0.7805 (mmm) cc_final: 0.7352 (mmt) REVERT: A 547 ILE cc_start: 0.8519 (mt) cc_final: 0.8167 (tt) REVERT: A 846 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8533 (mp) REVERT: A 1092 GLU cc_start: 0.6567 (tp30) cc_final: 0.6088 (tp30) REVERT: A 1150 LYS cc_start: 0.7566 (mmmt) cc_final: 0.7075 (mttm) REVERT: A 1170 MET cc_start: 0.8975 (mmt) cc_final: 0.8387 (mmt) REVERT: B 37 LEU cc_start: 0.8776 (tp) cc_final: 0.8499 (mp) REVERT: B 66 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8485 (ttmm) REVERT: B 125 GLU cc_start: 0.8693 (tp30) cc_final: 0.8379 (tp30) REVERT: B 179 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8127 (mt-10) REVERT: B 205 MET cc_start: 0.7948 (mtt) cc_final: 0.7628 (mtt) REVERT: B 273 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8639 (p) REVERT: B 333 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7280 (tttt) REVERT: B 502 MET cc_start: 0.8858 (ptm) cc_final: 0.8617 (ptm) REVERT: B 550 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7871 (mmt90) REVERT: B 795 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7926 (mt-10) REVERT: E 17 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7794 (ttp-170) REVERT: E 20 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8298 (mmtp) REVERT: G 62 MET cc_start: 0.8832 (mtt) cc_final: 0.8366 (mtt) REVERT: H 22 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8400 (mttp) REVERT: I 29 GLU cc_start: 0.7687 (tt0) cc_final: 0.7378 (pm20) REVERT: I 96 TYR cc_start: 0.7430 (p90) cc_final: 0.6808 (p90) REVERT: I 120 LYS cc_start: 0.6213 (mtmm) cc_final: 0.5972 (mtmm) REVERT: K 48 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8415 (ttpp) REVERT: K 85 ASP cc_start: 0.8734 (t0) cc_final: 0.8157 (t0) REVERT: K 119 LYS cc_start: 0.8504 (tttt) cc_final: 0.8201 (tttm) REVERT: K 138 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8028 (mmmt) outliers start: 101 outliers final: 60 residues processed: 620 average time/residue: 0.1889 time to fit residues: 186.6912 Evaluate side-chains 570 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 506 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 211 optimal weight: 3.9990 chunk 356 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 93 GLN A 553 GLN A 863 ASN B 600 GLN B 646 HIS B 745 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 106 GLN J 53 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.116973 restraints weight = 42706.966| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.55 r_work: 0.3127 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 31574 Z= 0.283 Angle : 0.709 11.334 42654 Z= 0.363 Chirality : 0.050 0.280 4756 Planarity : 0.005 0.071 5519 Dihedral : 5.516 52.739 4232 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.18 % Allowed : 12.63 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -2.00 (0.13), residues: 3836 helix: -1.34 (0.13), residues: 1285 sheet: -1.57 (0.19), residues: 615 loop : -1.12 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 135 TYR 0.037 0.002 TYR B1033 PHE 0.020 0.002 PHE A 637 TRP 0.028 0.002 TRP B 836 HIS 0.010 0.002 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00683 (31551) covalent geometry : angle 0.70230 (42633) hydrogen bonds : bond 0.04446 ( 1037) hydrogen bonds : angle 5.55416 ( 2985) metal coordination : bond 0.00914 ( 23) metal coordination : angle 4.42480 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 519 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5492 (m90) REVERT: A 57 PHE cc_start: 0.8806 (t80) cc_final: 0.8440 (t80) REVERT: A 110 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8589 (tp) REVERT: A 111 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8173 (tptm) REVERT: A 205 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7170 (mmt180) REVERT: A 388 LYS cc_start: 0.8139 (tttp) cc_final: 0.7594 (mttt) REVERT: A 424 MET cc_start: 0.7946 (mmm) cc_final: 0.7530 (mmt) REVERT: A 547 ILE cc_start: 0.8551 (mt) cc_final: 0.8272 (tt) REVERT: A 846 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 1092 GLU cc_start: 0.6759 (tp30) cc_final: 0.6427 (tp30) REVERT: A 1150 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7580 (mttm) REVERT: A 1474 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6811 (tt) REVERT: B 37 LEU cc_start: 0.8743 (tp) cc_final: 0.8480 (mp) REVERT: B 66 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8524 (ttmm) REVERT: B 125 GLU cc_start: 0.8793 (tp30) cc_final: 0.8433 (tp30) REVERT: B 179 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8108 (mt-10) REVERT: B 205 MET cc_start: 0.7994 (mtt) cc_final: 0.7620 (mtt) REVERT: B 296 ASP cc_start: 0.8641 (p0) cc_final: 0.8438 (p0) REVERT: B 333 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7268 (tttt) REVERT: B 502 MET cc_start: 0.8822 (ptm) cc_final: 0.8516 (ptm) REVERT: B 550 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7864 (mmt90) REVERT: B 803 MET cc_start: 0.8873 (ttp) cc_final: 0.8655 (ttp) REVERT: B 1044 PHE cc_start: 0.8426 (t80) cc_final: 0.8135 (t80) REVERT: B 1185 LEU cc_start: 0.8836 (tm) cc_final: 0.8480 (tp) REVERT: C 47 LEU cc_start: 0.8015 (mt) cc_final: 0.7809 (mt) REVERT: E 17 ARG cc_start: 0.8247 (ttt180) cc_final: 0.7759 (ttp80) REVERT: E 20 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8273 (mmtp) REVERT: E 215 MET cc_start: 0.8824 (mmt) cc_final: 0.8607 (mmt) REVERT: H 142 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8536 (tt) REVERT: I 29 GLU cc_start: 0.7710 (tt0) cc_final: 0.7467 (pm20) REVERT: I 120 LYS cc_start: 0.6213 (mtmm) cc_final: 0.5923 (mtmm) REVERT: K 48 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8484 (ttpp) REVERT: K 85 ASP cc_start: 0.8722 (t0) cc_final: 0.8098 (t0) REVERT: K 119 LYS cc_start: 0.8598 (tttt) cc_final: 0.8293 (tttm) outliers start: 144 outliers final: 104 residues processed: 617 average time/residue: 0.1852 time to fit residues: 181.4217 Evaluate side-chains 599 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 489 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 61 HIS Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 236 optimal weight: 0.5980 chunk 288 optimal weight: 0.9980 chunk 271 optimal weight: 10.0000 chunk 286 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 GLN B 600 GLN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B 952 HIS B1094 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN E 143 ASN G 140 GLN I 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.146052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122697 restraints weight = 42357.969| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.65 r_work: 0.3211 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 31574 Z= 0.105 Angle : 0.551 9.670 42654 Z= 0.286 Chirality : 0.044 0.255 4756 Planarity : 0.004 0.057 5519 Dihedral : 4.970 51.905 4232 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.55 % Allowed : 15.04 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -1.52 (0.13), residues: 3836 helix: -0.80 (0.14), residues: 1286 sheet: -1.36 (0.20), residues: 598 loop : -0.92 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 329 TYR 0.021 0.001 TYR A1302 PHE 0.017 0.001 PHE A1456 TRP 0.017 0.001 TRP B 836 HIS 0.013 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00236 (31551) covalent geometry : angle 0.54658 (42633) hydrogen bonds : bond 0.03430 ( 1037) hydrogen bonds : angle 5.11155 ( 2985) metal coordination : bond 0.00430 ( 23) metal coordination : angle 3.14236 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 547 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8782 (t80) cc_final: 0.8281 (t80) REVERT: A 110 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8512 (tp) REVERT: A 111 LYS cc_start: 0.8231 (ptpt) cc_final: 0.8017 (tptm) REVERT: A 205 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7034 (mmt180) REVERT: A 388 LYS cc_start: 0.8001 (tttp) cc_final: 0.7323 (mttt) REVERT: A 416 ARG cc_start: 0.5436 (tmt170) cc_final: 0.4776 (mmm-85) REVERT: A 424 MET cc_start: 0.7887 (mmm) cc_final: 0.7561 (mmt) REVERT: A 547 ILE cc_start: 0.8416 (mt) cc_final: 0.8181 (tt) REVERT: A 555 LYS cc_start: 0.8203 (tptt) cc_final: 0.7932 (ttmm) REVERT: A 846 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 1092 GLU cc_start: 0.6525 (tp30) cc_final: 0.6282 (tp30) REVERT: A 1611 MET cc_start: 0.9101 (ttp) cc_final: 0.8759 (ttp) REVERT: B 66 LYS cc_start: 0.8681 (ttmt) cc_final: 0.8382 (ttmm) REVERT: B 179 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8034 (mt-10) REVERT: B 333 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7156 (tttt) REVERT: B 451 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6723 (mpp) REVERT: B 502 MET cc_start: 0.8837 (ptm) cc_final: 0.8593 (ptp) REVERT: B 550 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7837 (mmt90) REVERT: B 795 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7938 (mt-10) REVERT: B 1165 ASN cc_start: 0.7174 (t0) cc_final: 0.6898 (m-40) REVERT: B 1185 LEU cc_start: 0.8718 (tm) cc_final: 0.8447 (tp) REVERT: E 17 ARG cc_start: 0.8192 (ttt180) cc_final: 0.7752 (ttp80) REVERT: E 20 LYS cc_start: 0.8454 (mmpt) cc_final: 0.8196 (mmtp) REVERT: E 215 MET cc_start: 0.8752 (mmt) cc_final: 0.8403 (mmt) REVERT: F 59 GLN cc_start: 0.8094 (tp40) cc_final: 0.7847 (tp-100) REVERT: H 129 TYR cc_start: 0.7224 (p90) cc_final: 0.7015 (p90) REVERT: H 142 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8423 (tt) REVERT: I 29 GLU cc_start: 0.7776 (tt0) cc_final: 0.7436 (pm20) REVERT: I 120 LYS cc_start: 0.6180 (mtmm) cc_final: 0.5842 (mtmm) REVERT: K 48 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8471 (ttpp) REVERT: K 85 ASP cc_start: 0.8623 (t0) cc_final: 0.8046 (t0) REVERT: K 119 LYS cc_start: 0.8476 (tttt) cc_final: 0.8204 (tttm) REVERT: K 138 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8112 (mmmt) outliers start: 88 outliers final: 48 residues processed: 605 average time/residue: 0.1963 time to fit residues: 188.2196 Evaluate side-chains 546 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 493 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 346 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 351 optimal weight: 0.6980 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 489 ASN A 521 GLN A 525 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B1094 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN G 140 GLN I 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.115558 restraints weight = 42865.061| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.69 r_work: 0.3109 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31574 Z= 0.262 Angle : 0.675 10.844 42654 Z= 0.344 Chirality : 0.049 0.280 4756 Planarity : 0.005 0.063 5519 Dihedral : 5.265 52.166 4232 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.41 % Allowed : 14.46 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -1.52 (0.13), residues: 3836 helix: -0.83 (0.14), residues: 1292 sheet: -1.35 (0.20), residues: 607 loop : -0.90 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 329 TYR 0.030 0.002 TYR B1033 PHE 0.020 0.002 PHE A1456 TRP 0.023 0.002 TRP B 836 HIS 0.009 0.002 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00640 (31551) covalent geometry : angle 0.66978 (42633) hydrogen bonds : bond 0.04124 ( 1037) hydrogen bonds : angle 5.30808 ( 2985) metal coordination : bond 0.00823 ( 23) metal coordination : angle 3.92861 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 493 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.6007 (OUTLIER) cc_final: 0.5302 (m90) REVERT: A 57 PHE cc_start: 0.8851 (t80) cc_final: 0.8443 (t80) REVERT: A 110 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8699 (tp) REVERT: A 111 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8144 (tptm) REVERT: A 205 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7069 (mmt180) REVERT: A 388 LYS cc_start: 0.8190 (tttp) cc_final: 0.7512 (mttt) REVERT: A 547 ILE cc_start: 0.8441 (mt) cc_final: 0.8185 (tt) REVERT: A 846 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 1092 GLU cc_start: 0.6546 (tp30) cc_final: 0.6236 (tp30) REVERT: A 1474 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6839 (tt) REVERT: B 66 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8477 (ttmm) REVERT: B 125 GLU cc_start: 0.8758 (tp30) cc_final: 0.8467 (tp30) REVERT: B 179 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8058 (mt-10) REVERT: B 333 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7069 (tttt) REVERT: B 462 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: B 502 MET cc_start: 0.8942 (ptm) cc_final: 0.8706 (ptp) REVERT: B 550 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7912 (mmt90) REVERT: B 795 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8111 (mt-10) REVERT: B 1114 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.6933 (pp30) REVERT: B 1165 ASN cc_start: 0.7324 (t0) cc_final: 0.7116 (m-40) REVERT: B 1185 LEU cc_start: 0.8814 (tm) cc_final: 0.8543 (tp) REVERT: D 95 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: E 17 ARG cc_start: 0.8328 (ttt180) cc_final: 0.7773 (ttp80) REVERT: E 20 LYS cc_start: 0.8555 (mmpt) cc_final: 0.8284 (mmtp) REVERT: E 41 ASP cc_start: 0.7377 (t70) cc_final: 0.7097 (t0) REVERT: E 215 MET cc_start: 0.8781 (mmt) cc_final: 0.8559 (mmt) REVERT: H 142 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8543 (tt) REVERT: I 29 GLU cc_start: 0.7764 (tt0) cc_final: 0.7489 (pm20) REVERT: I 120 LYS cc_start: 0.6261 (mtmm) cc_final: 0.5939 (mtmm) REVERT: K 48 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8477 (ttpp) REVERT: K 85 ASP cc_start: 0.8704 (t0) cc_final: 0.8045 (t0) REVERT: K 119 LYS cc_start: 0.8557 (tttt) cc_final: 0.8297 (tttm) outliers start: 152 outliers final: 107 residues processed: 595 average time/residue: 0.1870 time to fit residues: 176.8713 Evaluate side-chains 598 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 482 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1065 ARG Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 332 optimal weight: 4.9990 chunk 367 optimal weight: 0.8980 chunk 66 optimal weight: 0.0070 chunk 126 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 302 optimal weight: 10.0000 chunk 364 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 375 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN I 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.119427 restraints weight = 42857.030| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.69 r_work: 0.3165 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 31574 Z= 0.106 Angle : 0.552 9.511 42654 Z= 0.285 Chirality : 0.044 0.258 4756 Planarity : 0.004 0.049 5519 Dihedral : 4.868 52.120 4232 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.05 % Allowed : 15.97 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -1.17 (0.13), residues: 3836 helix: -0.39 (0.14), residues: 1285 sheet: -1.19 (0.20), residues: 611 loop : -0.78 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 329 TYR 0.024 0.001 TYR A1302 PHE 0.017 0.001 PHE B1167 TRP 0.016 0.001 TRP B 836 HIS 0.025 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00239 (31551) covalent geometry : angle 0.54808 (42633) hydrogen bonds : bond 0.03334 ( 1037) hydrogen bonds : angle 4.98947 ( 2985) metal coordination : bond 0.00405 ( 23) metal coordination : angle 2.83426 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 511 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8757 (t80) cc_final: 0.8266 (t80) REVERT: A 110 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 111 LYS cc_start: 0.8281 (ptpt) cc_final: 0.8048 (tptm) REVERT: A 205 ARG cc_start: 0.7948 (mtp85) cc_final: 0.7109 (mmt180) REVERT: A 388 LYS cc_start: 0.7992 (tttp) cc_final: 0.7344 (mttt) REVERT: A 416 ARG cc_start: 0.5479 (tmt170) cc_final: 0.4780 (mmm-85) REVERT: A 424 MET cc_start: 0.7856 (mmm) cc_final: 0.7569 (mmt) REVERT: A 547 ILE cc_start: 0.8393 (mt) cc_final: 0.8116 (tt) REVERT: A 555 LYS cc_start: 0.8220 (tptt) cc_final: 0.7945 (ttmm) REVERT: A 846 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 1096 LYS cc_start: 0.7499 (mtmm) cc_final: 0.7066 (mmmt) REVERT: A 1272 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8468 (t) REVERT: A 1298 ASP cc_start: 0.7433 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1611 MET cc_start: 0.9088 (ttp) cc_final: 0.8733 (ttp) REVERT: B 66 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8317 (ttmm) REVERT: B 179 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8059 (mt-10) REVERT: B 333 LYS cc_start: 0.8071 (mmtt) cc_final: 0.6977 (tttt) REVERT: B 502 MET cc_start: 0.8958 (ptm) cc_final: 0.8711 (ptp) REVERT: B 550 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7836 (mmt90) REVERT: B 626 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8219 (mp) REVERT: B 795 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7962 (mt-10) REVERT: B 1114 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7060 (pp30) REVERT: B 1115 GLN cc_start: 0.7866 (mm110) cc_final: 0.7409 (mm-40) REVERT: B 1185 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 174 ARG cc_start: 0.7168 (ptp90) cc_final: 0.6785 (ptp-170) REVERT: E 17 ARG cc_start: 0.8265 (ttt180) cc_final: 0.7752 (ttp80) REVERT: E 20 LYS cc_start: 0.8501 (mmpt) cc_final: 0.8259 (mmtp) REVERT: E 215 MET cc_start: 0.8744 (mmt) cc_final: 0.8340 (mmt) REVERT: F 59 GLN cc_start: 0.8206 (tp40) cc_final: 0.7967 (tp-100) REVERT: F 63 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: H 142 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8414 (tt) REVERT: I 29 GLU cc_start: 0.7768 (tt0) cc_final: 0.7407 (pm20) REVERT: I 120 LYS cc_start: 0.6228 (mtmm) cc_final: 0.5920 (mtmm) REVERT: K 48 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8437 (ttpp) REVERT: K 85 ASP cc_start: 0.8681 (t0) cc_final: 0.8109 (t0) REVERT: K 119 LYS cc_start: 0.8470 (tttt) cc_final: 0.8236 (tttm) REVERT: K 138 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8095 (mmmt) outliers start: 105 outliers final: 70 residues processed: 578 average time/residue: 0.1940 time to fit residues: 177.8489 Evaluate side-chains 567 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 488 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1301 GLU Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 330 optimal weight: 9.9990 chunk 85 optimal weight: 0.0070 chunk 23 optimal weight: 20.0000 chunk 348 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 270 optimal weight: 0.4980 chunk 273 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 361 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN E 143 ASN I 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.143441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119990 restraints weight = 42625.303| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.65 r_work: 0.3172 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31574 Z= 0.135 Angle : 0.560 9.789 42654 Z= 0.288 Chirality : 0.045 0.256 4756 Planarity : 0.004 0.047 5519 Dihedral : 4.796 52.401 4232 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.93 % Allowed : 16.49 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -1.02 (0.13), residues: 3836 helix: -0.24 (0.15), residues: 1280 sheet: -1.13 (0.21), residues: 596 loop : -0.72 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 329 TYR 0.022 0.001 TYR A1302 PHE 0.017 0.001 PHE D 39 TRP 0.017 0.001 TRP B 836 HIS 0.006 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00324 (31551) covalent geometry : angle 0.55648 (42633) hydrogen bonds : bond 0.03377 ( 1037) hydrogen bonds : angle 4.94352 ( 2985) metal coordination : bond 0.00459 ( 23) metal coordination : angle 2.91765 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 492 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8741 (t80) cc_final: 0.8200 (t80) REVERT: A 110 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8585 (tp) REVERT: A 111 LYS cc_start: 0.8236 (ptpt) cc_final: 0.7998 (tptm) REVERT: A 205 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7045 (mmt180) REVERT: A 246 ASP cc_start: 0.5370 (t70) cc_final: 0.5076 (t0) REVERT: A 388 LYS cc_start: 0.7962 (tttp) cc_final: 0.7301 (mttt) REVERT: A 416 ARG cc_start: 0.5442 (tmt170) cc_final: 0.4773 (mmm-85) REVERT: A 422 ARG cc_start: 0.6508 (ttp-170) cc_final: 0.6169 (mtp85) REVERT: A 424 MET cc_start: 0.7801 (mmm) cc_final: 0.7524 (mmt) REVERT: A 547 ILE cc_start: 0.8377 (mt) cc_final: 0.8099 (tt) REVERT: A 555 LYS cc_start: 0.8290 (tptt) cc_final: 0.7972 (ttmm) REVERT: A 846 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8551 (mp) REVERT: A 1092 GLU cc_start: 0.6412 (tp30) cc_final: 0.6210 (tp30) REVERT: A 1096 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7127 (mmmt) REVERT: A 1272 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (t) REVERT: A 1298 ASP cc_start: 0.7449 (m-30) cc_final: 0.7119 (m-30) REVERT: B 66 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8349 (ttmm) REVERT: B 179 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7997 (mt-10) REVERT: B 333 LYS cc_start: 0.8131 (mmtt) cc_final: 0.6966 (tttt) REVERT: B 462 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8416 (tp40) REVERT: B 502 MET cc_start: 0.8990 (ptm) cc_final: 0.8731 (ptp) REVERT: B 550 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7843 (mmt90) REVERT: B 795 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7994 (mt-10) REVERT: B 1114 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.6924 (pp30) REVERT: B 1115 GLN cc_start: 0.7799 (mm110) cc_final: 0.7389 (mm-40) REVERT: B 1185 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (tp) REVERT: D 97 LYS cc_start: 0.5991 (mtmm) cc_final: 0.5271 (mtmm) REVERT: E 17 ARG cc_start: 0.8259 (ttt180) cc_final: 0.7741 (ttp80) REVERT: E 20 LYS cc_start: 0.8492 (mmpt) cc_final: 0.8241 (mmtp) REVERT: E 215 MET cc_start: 0.8723 (mmt) cc_final: 0.8354 (mmt) REVERT: H 142 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8445 (tt) REVERT: I 29 GLU cc_start: 0.7687 (tt0) cc_final: 0.7423 (pm20) REVERT: I 120 LYS cc_start: 0.6263 (mtmm) cc_final: 0.5915 (mtmm) REVERT: K 48 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8415 (ttpp) REVERT: K 85 ASP cc_start: 0.8652 (t0) cc_final: 0.8060 (t0) REVERT: K 119 LYS cc_start: 0.8452 (tttt) cc_final: 0.8203 (tttm) REVERT: K 138 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8092 (mmmt) outliers start: 101 outliers final: 78 residues processed: 557 average time/residue: 0.2190 time to fit residues: 191.6020 Evaluate side-chains 567 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 481 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 877 LYS Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 125 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN I 27 ASN I 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.140405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.116400 restraints weight = 42690.275| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.64 r_work: 0.3128 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31574 Z= 0.209 Angle : 0.628 10.623 42654 Z= 0.322 Chirality : 0.047 0.269 4756 Planarity : 0.004 0.049 5519 Dihedral : 5.005 52.730 4232 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.40 % Allowed : 16.05 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -1.09 (0.13), residues: 3836 helix: -0.36 (0.14), residues: 1293 sheet: -1.09 (0.21), residues: 595 loop : -0.74 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 429 TYR 0.022 0.002 TYR A1120 PHE 0.017 0.002 PHE A1456 TRP 0.021 0.002 TRP B 836 HIS 0.008 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00512 (31551) covalent geometry : angle 0.62383 (42633) hydrogen bonds : bond 0.03767 ( 1037) hydrogen bonds : angle 5.07515 ( 2985) metal coordination : bond 0.00676 ( 23) metal coordination : angle 3.46253 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 476 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8822 (t80) cc_final: 0.8375 (t80) REVERT: A 110 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (tp) REVERT: A 111 LYS cc_start: 0.8364 (ptpt) cc_final: 0.8067 (tptm) REVERT: A 205 ARG cc_start: 0.7945 (mtp85) cc_final: 0.7068 (mmt180) REVERT: A 388 LYS cc_start: 0.8147 (tttp) cc_final: 0.7489 (mttt) REVERT: A 416 ARG cc_start: 0.5295 (tmt170) cc_final: 0.4719 (mmm-85) REVERT: A 422 ARG cc_start: 0.6564 (ttp-170) cc_final: 0.6195 (mtp85) REVERT: A 424 MET cc_start: 0.7941 (mmm) cc_final: 0.7676 (mmt) REVERT: A 547 ILE cc_start: 0.8403 (mt) cc_final: 0.8113 (tt) REVERT: A 555 LYS cc_start: 0.8369 (tptt) cc_final: 0.8051 (ttmm) REVERT: A 846 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8534 (mp) REVERT: A 1096 LYS cc_start: 0.7473 (mtmm) cc_final: 0.7234 (mmmt) REVERT: B 66 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8394 (ttmm) REVERT: B 179 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8056 (mt-10) REVERT: B 333 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7002 (tttt) REVERT: B 462 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8493 (tp40) REVERT: B 502 MET cc_start: 0.9030 (ptm) cc_final: 0.8764 (ptp) REVERT: B 550 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7884 (mmt90) REVERT: B 795 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8074 (mt-10) REVERT: B 1114 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7059 (pp30) REVERT: B 1185 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8540 (tp) REVERT: E 17 ARG cc_start: 0.8294 (ttt180) cc_final: 0.7743 (ttp80) REVERT: E 20 LYS cc_start: 0.8523 (mmpt) cc_final: 0.8276 (mmtp) REVERT: E 41 ASP cc_start: 0.7415 (t70) cc_final: 0.7158 (t0) REVERT: E 215 MET cc_start: 0.8764 (mmt) cc_final: 0.8462 (mmt) REVERT: G 102 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7008 (mm-30) REVERT: H 142 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8488 (tt) REVERT: I 29 GLU cc_start: 0.7761 (tt0) cc_final: 0.7461 (pm20) REVERT: I 112 TYR cc_start: 0.8160 (m-10) cc_final: 0.7865 (m-80) REVERT: I 120 LYS cc_start: 0.6223 (mtmm) cc_final: 0.5843 (mtmm) REVERT: K 85 ASP cc_start: 0.8698 (t0) cc_final: 0.8039 (t0) REVERT: K 119 LYS cc_start: 0.8503 (tttt) cc_final: 0.8274 (tttm) REVERT: K 138 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8080 (mmmt) outliers start: 117 outliers final: 95 residues processed: 548 average time/residue: 0.2273 time to fit residues: 196.1404 Evaluate side-chains 576 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 473 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASN Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 242 optimal weight: 0.0770 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 324 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN I 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118623 restraints weight = 42487.661| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.65 r_work: 0.3163 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31574 Z= 0.141 Angle : 0.575 9.720 42654 Z= 0.296 Chirality : 0.045 0.263 4756 Planarity : 0.004 0.044 5519 Dihedral : 4.856 52.695 4232 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.13 % Allowed : 16.37 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -0.98 (0.13), residues: 3836 helix: -0.21 (0.14), residues: 1288 sheet: -1.05 (0.21), residues: 598 loop : -0.71 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 429 TYR 0.026 0.001 TYR A1302 PHE 0.019 0.001 PHE D 39 TRP 0.019 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00335 (31551) covalent geometry : angle 0.57077 (42633) hydrogen bonds : bond 0.03415 ( 1037) hydrogen bonds : angle 4.96282 ( 2985) metal coordination : bond 0.00478 ( 23) metal coordination : angle 3.06214 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 481 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8753 (t80) cc_final: 0.8272 (t80) REVERT: A 110 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 111 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8049 (tptm) REVERT: A 205 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7095 (mmt180) REVERT: A 388 LYS cc_start: 0.8052 (tttp) cc_final: 0.7422 (mttt) REVERT: A 416 ARG cc_start: 0.5337 (tmt170) cc_final: 0.4767 (mmm-85) REVERT: A 422 ARG cc_start: 0.6604 (ttp-170) cc_final: 0.6262 (mtp85) REVERT: A 424 MET cc_start: 0.7828 (mmm) cc_final: 0.7575 (mmt) REVERT: A 547 ILE cc_start: 0.8377 (mt) cc_final: 0.8099 (tt) REVERT: A 555 LYS cc_start: 0.8225 (tptt) cc_final: 0.7985 (ttmm) REVERT: A 557 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 846 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 868 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8386 (p) REVERT: A 1096 LYS cc_start: 0.7428 (mtmm) cc_final: 0.7128 (mmmt) REVERT: A 1149 ASP cc_start: 0.7023 (m-30) cc_final: 0.6822 (m-30) REVERT: A 1272 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8451 (t) REVERT: A 1455 ARG cc_start: 0.6137 (ttm110) cc_final: 0.5733 (mtp180) REVERT: A 1611 MET cc_start: 0.9113 (ttp) cc_final: 0.8740 (ttp) REVERT: B 66 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8346 (ttmm) REVERT: B 179 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8000 (mt-10) REVERT: B 333 LYS cc_start: 0.8088 (mmtt) cc_final: 0.6980 (tttt) REVERT: B 462 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8387 (tp-100) REVERT: B 502 MET cc_start: 0.8980 (ptm) cc_final: 0.8739 (ptp) REVERT: B 550 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7846 (mmt90) REVERT: B 795 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8001 (mt-10) REVERT: B 1114 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.6986 (pp30) REVERT: B 1185 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (tp) REVERT: E 17 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7756 (ttp80) REVERT: E 20 LYS cc_start: 0.8472 (mmpt) cc_final: 0.8232 (mmtp) REVERT: E 215 MET cc_start: 0.8705 (mmt) cc_final: 0.8336 (mmt) REVERT: H 142 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8478 (tt) REVERT: I 29 GLU cc_start: 0.7736 (tt0) cc_final: 0.7459 (pm20) REVERT: I 112 TYR cc_start: 0.8050 (m-10) cc_final: 0.7690 (m-80) REVERT: I 120 LYS cc_start: 0.6306 (mtmm) cc_final: 0.5911 (mtmm) REVERT: K 85 ASP cc_start: 0.8658 (t0) cc_final: 0.8077 (t0) REVERT: K 119 LYS cc_start: 0.8468 (tttt) cc_final: 0.8250 (tttm) REVERT: K 138 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8128 (mmmt) outliers start: 108 outliers final: 91 residues processed: 549 average time/residue: 0.2095 time to fit residues: 181.4746 Evaluate side-chains 571 residues out of total 3445 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 470 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1035 ASP Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1185 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1114 GLN Chi-restraints excluded: chain B residue 1166 LYS Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 63 LYS Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 36 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 304 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 229 optimal weight: 5.9990 chunk 179 optimal weight: 20.0000 chunk 191 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 239 optimal weight: 0.0970 chunk 124 optimal weight: 9.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.141774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.117706 restraints weight = 42827.264| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.69 r_work: 0.3142 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31574 Z= 0.134 Angle : 0.571 9.688 42654 Z= 0.293 Chirality : 0.045 0.259 4756 Planarity : 0.004 0.043 5519 Dihedral : 4.812 52.721 4232 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.22 % Allowed : 16.31 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.31 % 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 aren not related in a simple way. whole: -0.89 (0.14), residues: 3836 helix: -0.11 (0.15), residues: 1284 sheet: -1.02 (0.21), residues: 587 loop : -0.67 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 429 TYR 0.025 0.001 TYR A1302 PHE 0.019 0.001 PHE D 39 TRP 0.019 0.001 TRP B 836 HIS 0.005 0.001 HIS A 596 Details of bonding type rmsd covalent geometry : bond 0.00320 (31551) covalent geometry : angle 0.56682 (42633) hydrogen bonds : bond 0.03377 ( 1037) hydrogen bonds : angle 4.91972 ( 2985) metal coordination : bond 0.00471 ( 23) metal coordination : angle 2.99175 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8055.77 seconds wall clock time: 138 minutes 42.28 seconds (8322.28 seconds total)