Starting phenix.real_space_refine on Sat Mar 7 08:48:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z0h_14421/03_2026/7z0h_14421.map" } resolution = 2.6 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 Mg 2 5.21 5 S 217 5.16 5 C 25772 2.51 5 N 7010 2.21 5 O 7657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40665 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1419, 11123 Classifications: {'peptide': 1419} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1354} Chain breaks: 3 Chain: "B" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8701 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 41, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1140 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 11} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain breaks: 1 Chain: "W" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 141 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 101.437 117.004 91.083 1.00 71.78 S ATOM 510 SG CYS A 70 99.702 120.472 90.415 1.00 50.43 S ATOM 557 SG CYS A 77 98.691 117.421 91.466 1.00 52.82 S ATOM 795 SG CYS A 107 71.701 94.701 59.649 1.00 65.84 S ATOM 818 SG CYS A 110 71.797 96.028 57.099 1.00 67.08 S ATOM 1184 SG CYS A 154 68.283 95.973 58.215 1.00 67.55 S ATOM 1208 SG CYS A 157 71.753 93.984 56.272 1.00 74.15 S ATOM 19397 SG CYS B1095 85.303 124.964 81.080 1.00 47.06 S ATOM 19420 SG CYS B1098 84.950 121.122 79.492 1.00 42.70 S ATOM 19486 SG CYS B1107 88.322 123.064 80.306 1.00 51.12 S ATOM 19506 SG CYS B1110 86.546 123.177 77.862 1.00 50.38 S ATOM 28735 SG CYS I 5 58.899 36.570 89.132 1.00 44.07 S ATOM 28754 SG CYS I 8 62.695 38.696 89.098 1.00 55.94 S ATOM 28882 SG CYS I 26 59.500 39.350 87.065 1.00 59.30 S ATOM 28905 SG CYS I 29 60.656 37.096 86.606 1.00 59.70 S ATOM 29232 SG CYS I 69 43.371 100.188 129.414 1.00 68.87 S ATOM 29280 SG CYS I 75 39.308 99.972 128.316 1.00 60.84 S ATOM 29482 SG CYS I 100 42.477 97.172 129.215 1.00 64.55 S ATOM 29503 SG CYS I 103 41.570 98.893 126.164 1.00 63.33 S ATOM 29622 SG CYS J 7 87.949 100.659 157.718 1.00 0.00 S ATOM 29645 SG CYS J 10 85.523 102.910 160.762 1.00 53.68 S ATOM 29925 SG CYS J 45 84.983 100.053 159.101 1.00 2.24 S ATOM 29931 SG CYS J 46 87.887 99.700 161.270 1.00 13.70 S ATOM 30982 SG CYS L 31 122.301 86.884 134.517 1.00 33.71 S ATOM 31002 SG CYS L 34 123.999 86.083 137.105 1.00 41.80 S ATOM 31106 SG CYS L 48 125.520 87.114 134.133 1.00 30.82 S ATOM 31129 SG CYS L 51 123.791 83.370 134.510 1.00 36.00 S Time building chain proxies: 8.75, per 1000 atoms: 0.22 Number of scatterers: 40665 At special positions: 0 Unit cell: (139.92, 193.98, 199.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 217 16.00 Mg 2 11.99 O 7657 8.00 N 7010 7.00 C 25772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 75 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " Number of angles added : 39 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 49 sheets defined 40.4% alpha, 12.6% 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 30 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.569A pdb=" N ILE A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.683A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.314A pdb=" N TYR A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 233 through 234 No H-bonds generated for 'chain 'A' and resid 233 through 234' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.822A pdb=" N ASP A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 283 through 306 removed outlier: 4.085A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 removed outlier: 3.592A pdb=" N ALA A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.685A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.993A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.157A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.649A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 720 through 748 removed outlier: 3.615A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 784 removed outlier: 4.045A pdb=" N LEU A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 857 through 882 Processing helix chain 'A' and resid 884 through 894 Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.658A pdb=" N MET A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.524A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 974 removed outlier: 3.660A pdb=" N LEU A 974 " --> pdb=" O LEU A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1037 through 1042 removed outlier: 4.462A pdb=" N GLY A1041 " --> pdb=" O GLU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1063 through 1082 removed outlier: 3.656A pdb=" N ARG A1082 " --> pdb=" O TYR A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1100 through 1103 Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1153 through 1161 removed outlier: 4.146A pdb=" N VAL A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.738A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 removed outlier: 3.698A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1299 through 1306 removed outlier: 3.823A pdb=" N VAL A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1345 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.918A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 3.621A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1391 through 1403 removed outlier: 3.587A pdb=" N HIS A1395 " --> pdb=" O LYS A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing helix chain 'A' and resid 1423 through 1427 Processing helix chain 'A' and resid 1447 through 1455 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.835A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 5.266A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 266 through 274 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.807A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.514A pdb=" N ALA B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 321 through 322 No H-bonds generated for 'chain 'B' and resid 321 through 322' Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.797A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.767A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.704A pdb=" N ALA B 488 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 536 removed outlier: 3.565A pdb=" N LEU B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 Processing helix chain 'B' and resid 624 through 633 Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.513A pdb=" N PHE B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.888A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 707 removed outlier: 4.048A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.597A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 945 through 949 Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.719A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1122 through 1135 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.579A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.693A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 29 through 35 removed outlier: 3.733A pdb=" N ALA D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.789A pdb=" N VAL D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.177A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.881A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.933A pdb=" N TYR E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.548A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.340A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.654A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 4.275A pdb=" N LYS J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.636A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 183 through 195 Processing helix chain 'M' and resid 229 through 240 removed outlier: 3.867A pdb=" N ALA M 233 " --> pdb=" O GLY M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 265 removed outlier: 3.518A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 281 removed outlier: 3.597A pdb=" N ASP M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 223 removed outlier: 4.312A pdb=" N GLU N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 297 Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'O' and resid 37 through 42 removed outlier: 3.750A pdb=" N THR O 41 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 removed outlier: 3.691A pdb=" N TYR O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 71 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 Processing helix chain 'O' and resid 125 through 132 removed outlier: 3.960A pdb=" N ILE O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 4.295A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 Processing helix chain 'O' and resid 170 through 178 removed outlier: 3.912A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 197 removed outlier: 3.944A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.678A pdb=" N LYS O 221 " --> pdb=" O PHE O 217 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR O 223 " --> pdb=" O TYR O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 304 Processing helix chain 'O' and resid 305 through 316 removed outlier: 4.206A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU O 316 " --> pdb=" O TYR O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 356 Processing helix chain 'O' and resid 362 through 368 removed outlier: 3.941A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 463 Processing helix chain 'O' and resid 482 through 500 removed outlier: 4.028A pdb=" N VAL O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 514 Processing helix chain 'O' and resid 520 through 527 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.982A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.932A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG O 578 " --> pdb=" O TYR O 574 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN O 579 " --> pdb=" O ASN O 575 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU O 581 " --> pdb=" O MET O 577 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 620 through 645 Processing helix chain 'P' and resid 171 through 180 Processing helix chain 'P' and resid 181 through 190 removed outlier: 3.823A pdb=" N PHE P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 199 Processing helix chain 'P' and resid 201 through 205 removed outlier: 4.012A pdb=" N ASN P 205 " --> pdb=" O PRO P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 229 removed outlier: 3.556A pdb=" N ILE P 221 " --> pdb=" O THR P 217 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN P 229 " --> pdb=" O ILE P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 248 Processing helix chain 'P' and resid 265 through 271 Processing helix chain 'Q' and resid 48 through 68 removed outlier: 4.628A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 138 removed outlier: 4.051A pdb=" N ASN Q 138 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.692A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 6.710A pdb=" N VAL A 32 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS A 85 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.970A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.830A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.555A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 392 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG A 493 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL A 394 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.640A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA8, first strand: chain 'A' and resid 597 through 599 removed outlier: 5.975A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.074A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.419A pdb=" N GLY A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 Processing sheet with id=AB3, first strand: chain 'A' and resid 1278 through 1285 removed outlier: 4.367A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1293 " --> pdb=" O ALA A1143 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AB5, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.863A pdb=" N LEU B 93 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB8, first strand: chain 'B' and resid 375 through 378 Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 222 Processing sheet with id=AC2, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AC3, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.677A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 444 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 449 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 619 through 620 current: chain 'B' and resid 672 through 673 Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 removed outlier: 5.596A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 725 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 785 through 795 current: chain 'B' and resid 879 through 888 removed outlier: 8.029A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 904 current: chain 'L' and resid 37 through 39 Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC8, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 7.401A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE B 942 " --> pdb=" O ASN B 754 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR B 756 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N MET B 944 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.661A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD2, first strand: chain 'B' and resid 1043 through 1044 removed outlier: 3.650A pdb=" N GLN B1049 " --> pdb=" O ALA B1044 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.084A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'C' and resid 51 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 57 current: chain 'C' and resid 289 through 304 Processing sheet with id=AD5, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.297A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 106 through 107 removed outlier: 4.232A pdb=" N VAL C 185 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD9, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 5 removed outlier: 5.248A pdb=" N VAL D 3 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA G 8 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 5 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS G 6 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ASN G 69 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL G 54 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL G 75 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE G 48 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.563A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.532A pdb=" N VAL E 88 " --> pdb=" O ASN E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE5, first strand: chain 'I' and resid 15 through 16 removed outlier: 3.603A pdb=" N PHE I 33 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR I 31 " --> pdb=" O CYS I 26 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 80 through 85 Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 54 removed outlier: 4.523A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLN K 52 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N SER K 60 " --> pdb=" O GLN K 52 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 75 through 78 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 75 through 78 current: chain 'M' and resid 118 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 153 current: chain 'M' and resid 168 through 172 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 168 through 172 current: chain 'N' and resid 371 through 374 removed outlier: 6.323A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 380 through 383 current: chain 'N' and resid 404 through 420 Processing sheet with id=AE9, first strand: chain 'O' and resid 106 through 109 removed outlier: 3.538A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR O 117 " --> pdb=" O GLU O 109 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 168 through 169 removed outlier: 3.788A pdb=" N THR O 281 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AF3, first strand: chain 'O' and resid 469 through 472 removed outlier: 4.033A pdb=" N THR O 471 " --> pdb=" O VAL O 475 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 547 through 548 removed outlier: 3.645A pdb=" N GLU O 547 " --> pdb=" O ARG O 567 " (cutoff:3.500A) 1567 hydrogen bonds defined for protein. 4365 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: 10.35 Time building geometry restraints manager: 4.44 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: 11520 1.33 - 1.46: 7182 1.46 - 1.58: 22337 1.58 - 1.70: 2 1.70 - 1.82: 352 Bond restraints: 41393 Sorted by residual: bond pdb=" N ILE Q 33 " pdb=" CA ILE Q 33 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" N TYR P 249 " pdb=" CA TYR P 249 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.22e-02 6.72e+03 9.13e+00 bond pdb=" N TYR E 46 " pdb=" CA TYR E 46 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.10e-02 8.26e+03 8.94e+00 bond pdb=" N VAL E 88 " pdb=" CA VAL E 88 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.22e-02 6.72e+03 8.92e+00 bond pdb=" N HIS Q 32 " pdb=" CA HIS Q 32 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.88e+00 ... (remaining 41388 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 54780 2.10 - 4.20: 967 4.20 - 6.30: 98 6.30 - 8.41: 24 8.41 - 10.51: 11 Bond angle restraints: 55880 Sorted by residual: angle pdb=" N GLY B1053 " pdb=" CA GLY B1053 " pdb=" C GLY B1053 " ideal model delta sigma weight residual 111.38 121.83 -10.45 1.63e+00 3.76e-01 4.11e+01 angle pdb=" N GLU B1052 " pdb=" CA GLU B1052 " pdb=" C GLU B1052 " ideal model delta sigma weight residual 113.28 120.40 -7.12 1.22e+00 6.72e-01 3.41e+01 angle pdb=" CA PRO M 114 " pdb=" N PRO M 114 " pdb=" CD PRO M 114 " ideal model delta sigma weight residual 112.00 104.81 7.19 1.40e+00 5.10e-01 2.64e+01 angle pdb=" CA PHE N 200 " pdb=" C PHE N 200 " pdb=" N PRO N 201 " ideal model delta sigma weight residual 117.47 122.72 -5.25 1.16e+00 7.43e-01 2.05e+01 angle pdb=" N VAL P 248 " pdb=" CA VAL P 248 " pdb=" C VAL P 248 " ideal model delta sigma weight residual 109.34 100.25 9.09 2.08e+00 2.31e-01 1.91e+01 ... (remaining 55875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21857 17.96 - 35.92: 2694 35.92 - 53.89: 638 53.89 - 71.85: 135 71.85 - 89.81: 63 Dihedral angle restraints: 25387 sinusoidal: 10470 harmonic: 14917 Sorted by residual: dihedral pdb=" CA SER C 223 " pdb=" C SER C 223 " pdb=" N THR C 224 " pdb=" CA THR C 224 " ideal model delta harmonic sigma weight residual 180.00 155.36 24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LYS B 448 " pdb=" C LYS B 448 " pdb=" N MET B 449 " pdb=" CA MET B 449 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY A 968 " pdb=" C GLY A 968 " pdb=" N PRO A 969 " pdb=" CA PRO A 969 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 25384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5401 0.066 - 0.132: 833 0.132 - 0.198: 49 0.198 - 0.264: 5 0.264 - 0.330: 2 Chirality restraints: 6290 Sorted by residual: chirality pdb=" CB ILE E 127 " pdb=" CA ILE E 127 " pdb=" CG1 ILE E 127 " pdb=" CG2 ILE E 127 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA GLU B1052 " pdb=" N GLU B1052 " pdb=" C GLU B1052 " pdb=" CB GLU B1052 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA VAL P 248 " pdb=" N VAL P 248 " pdb=" C VAL P 248 " pdb=" CB VAL P 248 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 6287 not shown) Planarity restraints: 7201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 48 " -0.078 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO D 49 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 52 " 0.421 9.50e-02 1.11e+02 1.89e-01 2.18e+01 pdb=" NE ARG E 52 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 52 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 52 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 52 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS M 113 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO M 114 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO M 114 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 114 " 0.061 5.00e-02 4.00e+02 ... (remaining 7198 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 418 2.60 - 3.17: 35031 3.17 - 3.75: 66199 3.75 - 4.32: 92583 4.32 - 4.90: 148636 Nonbonded interactions: 342867 Sorted by model distance: nonbonded pdb=" OD2 ASP I 91 " pdb="MG MG I 201 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A1503 " model vdw 2.054 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A1503 " model vdw 2.055 2.170 nonbonded pdb=" OD1 ASP A 515 " pdb="MG MG A1503 " model vdw 2.065 2.170 nonbonded pdb=" O PRO A 264 " pdb=" NH1 ARG A 269 " model vdw 2.198 3.120 ... (remaining 342862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 42.020 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 41421 Z= 0.195 Angle : 0.880 52.933 55919 Z= 0.391 Chirality : 0.046 0.330 6290 Planarity : 0.005 0.189 7201 Dihedral : 17.034 89.811 15739 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.91 % Favored : 94.01 % Rotamer: Outliers : 1.82 % Allowed : 19.11 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5039 helix: 0.27 (0.12), residues: 1808 sheet: -0.80 (0.20), residues: 643 loop : -1.24 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1023 TYR 0.022 0.002 TYR O 476 PHE 0.037 0.002 PHE M 252 TRP 0.017 0.001 TRP B 442 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00355 (41393) covalent geometry : angle 0.67296 (55880) hydrogen bonds : bond 0.15544 ( 1567) hydrogen bonds : angle 6.26177 ( 4365) metal coordination : bond 0.04321 ( 28) metal coordination : angle 21.45679 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 430 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 275 GLN cc_start: 0.2137 (OUTLIER) cc_final: 0.1854 (mm110) REVERT: E 50 MET cc_start: 0.3815 (OUTLIER) cc_final: 0.3252 (tpt) REVERT: I 87 ILE cc_start: 0.3667 (OUTLIER) cc_final: 0.3425 (pp) REVERT: J 32 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7854 (mp0) outliers start: 82 outliers final: 40 residues processed: 492 average time/residue: 0.7476 time to fit residues: 446.9777 Evaluate side-chains 461 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 417 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 184 LYS Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 203 ILE Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain Q residue 34 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1185 GLN B 159 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 423 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN C 14 ASN C 130 ASN D 8 ASN D 71 ASN D 126 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN J 23 ASN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN M 92 ASN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN N 287 HIS N 366 HIS N 377 ASN N 421 GLN O 254 ASN O 587 ASN O 607 ASN P 176 ASN Q 14 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.197354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142778 restraints weight = 49843.211| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.55 r_work: 0.3342 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 41421 Z= 0.215 Angle : 0.691 22.485 55919 Z= 0.346 Chirality : 0.046 0.242 6290 Planarity : 0.005 0.112 7201 Dihedral : 6.347 81.293 5629 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 3.46 % Allowed : 18.02 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5039 helix: 0.28 (0.12), residues: 1828 sheet: -0.83 (0.21), residues: 617 loop : -1.24 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 292 TYR 0.019 0.002 TYR O 494 PHE 0.021 0.002 PHE B 678 TRP 0.018 0.002 TRP C 31 HIS 0.015 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00502 (41393) covalent geometry : angle 0.65294 (55880) hydrogen bonds : bond 0.04867 ( 1567) hydrogen bonds : angle 5.32657 ( 4365) metal coordination : bond 0.01256 ( 28) metal coordination : angle 8.60545 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 453 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 93 ILE cc_start: 0.5902 (OUTLIER) cc_final: 0.5696 (mp) REVERT: B 74 LYS cc_start: 0.7667 (mmmt) cc_final: 0.7295 (mptt) REVERT: B 269 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7455 (ptm) REVERT: B 280 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: B 383 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8168 (mm) REVERT: B 628 ARG cc_start: 0.7743 (tpp-160) cc_final: 0.7436 (tpp80) REVERT: B 1135 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.7064 (mtt) REVERT: C 196 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7248 (pp) REVERT: C 256 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7764 (pp) REVERT: D 107 MET cc_start: 0.3224 (OUTLIER) cc_final: 0.2657 (mmm) REVERT: E 137 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6812 (mt-10) REVERT: E 204 THR cc_start: 0.5548 (p) cc_final: 0.4863 (m) REVERT: G 84 ILE cc_start: 0.4315 (mp) cc_final: 0.3995 (mm) REVERT: G 88 TRP cc_start: 0.3832 (m-10) cc_final: 0.3563 (m100) REVERT: H 135 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7696 (mt) REVERT: M 262 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5668 (mt-10) REVERT: N 274 LYS cc_start: 0.4731 (pptt) cc_final: 0.4498 (pptt) REVERT: N 312 ARG cc_start: 0.5327 (ttp-170) cc_final: 0.5101 (ttp-170) REVERT: O 86 MET cc_start: 0.2840 (OUTLIER) cc_final: 0.2495 (ppp) REVERT: O 617 GLU cc_start: 0.2940 (pt0) cc_final: 0.2508 (pm20) REVERT: P 294 PHE cc_start: 0.2354 (m-80) cc_final: 0.1913 (m-80) outliers start: 156 outliers final: 52 residues processed: 563 average time/residue: 0.7166 time to fit residues: 499.0162 Evaluate side-chains 485 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 422 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain O residue 159 ILE Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 46 optimal weight: 4.9990 chunk 397 optimal weight: 9.9990 chunk 403 optimal weight: 20.0000 chunk 304 optimal weight: 9.9990 chunk 278 optimal weight: 0.3980 chunk 139 optimal weight: 0.3980 chunk 341 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 302 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 488 optimal weight: 7.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A 828 GLN A1180 ASN A1395 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 198 GLN N 287 HIS N 377 ASN O 225 ASN O 464 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.196582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126717 restraints weight = 49777.871| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.26 r_work: 0.3257 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 41421 Z= 0.237 Angle : 0.695 17.462 55919 Z= 0.352 Chirality : 0.047 0.227 6290 Planarity : 0.005 0.106 7201 Dihedral : 6.065 59.805 5591 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 4.24 % Allowed : 18.78 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.11), residues: 5039 helix: 0.19 (0.12), residues: 1840 sheet: -0.83 (0.21), residues: 604 loop : -1.29 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 277 TYR 0.020 0.002 TYR C 282 PHE 0.022 0.002 PHE B 678 TRP 0.019 0.002 TRP C 31 HIS 0.015 0.002 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00557 (41393) covalent geometry : angle 0.66969 (55880) hydrogen bonds : bond 0.04732 ( 1567) hydrogen bonds : angle 5.25457 ( 4365) metal coordination : bond 0.01273 ( 28) metal coordination : angle 7.10788 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 444 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.3798 (ptt180) REVERT: B 74 LYS cc_start: 0.7661 (mmmt) cc_final: 0.7233 (mptm) REVERT: B 202 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7742 (mmmt) REVERT: B 539 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 552 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7757 (m110) REVERT: B 628 ARG cc_start: 0.7746 (tpp-160) cc_final: 0.7350 (tpp80) REVERT: B 632 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: C 196 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7357 (pp) REVERT: C 256 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7831 (pp) REVERT: E 137 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6864 (mt-10) REVERT: E 204 THR cc_start: 0.5612 (p) cc_final: 0.4870 (m) REVERT: H 135 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7756 (mt) REVERT: M 262 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5334 (mt-10) REVERT: N 274 LYS cc_start: 0.4697 (pptt) cc_final: 0.4436 (pptt) REVERT: N 393 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6403 (t70) REVERT: O 86 MET cc_start: 0.3133 (ttm) cc_final: 0.2680 (ppp) REVERT: O 236 LYS cc_start: 0.3037 (OUTLIER) cc_final: 0.2657 (tmtp) REVERT: O 567 ARG cc_start: 0.2754 (mtm-85) cc_final: 0.2176 (ttp-170) REVERT: O 617 GLU cc_start: 0.2904 (pt0) cc_final: 0.2600 (pm20) REVERT: P 198 PHE cc_start: 0.2404 (m-10) cc_final: 0.2193 (m-10) REVERT: P 294 PHE cc_start: 0.2377 (m-80) cc_final: 0.2020 (m-80) outliers start: 191 outliers final: 84 residues processed: 590 average time/residue: 0.6801 time to fit residues: 493.3465 Evaluate side-chains 515 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 422 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1348 MET Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 393 ASP Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 82 LYS Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 466 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 488 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 425 optimal weight: 8.9990 chunk 471 optimal weight: 20.0000 chunk 212 optimal weight: 1.9990 chunk 494 optimal weight: 7.9990 chunk 370 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 300 GLN B 800 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.197237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129924 restraints weight = 49699.636| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.70 r_work: 0.3251 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 41421 Z= 0.187 Angle : 0.639 15.047 55919 Z= 0.325 Chirality : 0.045 0.249 6290 Planarity : 0.005 0.102 7201 Dihedral : 5.861 59.676 5588 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 4.42 % Allowed : 19.40 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 5039 helix: 0.35 (0.12), residues: 1840 sheet: -0.81 (0.21), residues: 601 loop : -1.25 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 277 TYR 0.019 0.002 TYR O 494 PHE 0.022 0.002 PHE B 678 TRP 0.018 0.002 TRP C 31 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00434 (41393) covalent geometry : angle 0.61806 (55880) hydrogen bonds : bond 0.04246 ( 1567) hydrogen bonds : angle 5.08843 ( 4365) metal coordination : bond 0.01145 ( 28) metal coordination : angle 6.12598 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 454 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 TRP cc_start: 0.4908 (OUTLIER) cc_final: 0.3613 (t60) REVERT: A 1287 ASP cc_start: 0.4904 (OUTLIER) cc_final: 0.3902 (t70) REVERT: A 1417 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 74 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7326 (mptt) REVERT: B 202 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7773 (mmmt) REVERT: B 217 GLN cc_start: 0.7404 (pp30) cc_final: 0.7155 (pp30) REVERT: B 907 GLU cc_start: 0.8914 (pt0) cc_final: 0.8704 (pt0) REVERT: C 196 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7397 (pp) REVERT: C 245 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7101 (mpp-170) REVERT: C 256 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7800 (pp) REVERT: E 106 GLN cc_start: 0.6671 (tp40) cc_final: 0.6419 (tp40) REVERT: E 137 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6936 (mt-10) REVERT: G 97 ILE cc_start: 0.3223 (tt) cc_final: 0.2648 (mm) REVERT: N 274 LYS cc_start: 0.4598 (pptt) cc_final: 0.4349 (pptt) REVERT: N 393 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.6363 (t70) REVERT: O 86 MET cc_start: 0.2886 (OUTLIER) cc_final: 0.2518 (ppp) REVERT: O 201 ILE cc_start: 0.3448 (tp) cc_final: 0.3090 (mp) REVERT: O 236 LYS cc_start: 0.3037 (OUTLIER) cc_final: 0.2668 (tmtp) REVERT: O 258 GLU cc_start: 0.3214 (OUTLIER) cc_final: 0.2216 (tt0) REVERT: O 567 ARG cc_start: 0.2796 (mtm-85) cc_final: 0.2335 (ttp-170) REVERT: O 627 LEU cc_start: 0.2460 (OUTLIER) cc_final: 0.2234 (mm) REVERT: O 635 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5185 (tp) REVERT: P 294 PHE cc_start: 0.3060 (m-80) cc_final: 0.2671 (m-80) outliers start: 199 outliers final: 77 residues processed: 599 average time/residue: 0.6505 time to fit residues: 484.2711 Evaluate side-chains 513 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 424 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1003 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 393 ASP Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 129 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 386 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 356 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1142 ASN A1180 ASN A1233 ASN A1345 ASN A1453 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN Q 128 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.198187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.3554 r_free = 0.3554 target = 0.129623 restraints weight = 49528.976| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.04 r_work: 0.3304 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 41421 Z= 0.140 Angle : 0.593 15.034 55919 Z= 0.301 Chirality : 0.044 0.256 6290 Planarity : 0.004 0.099 7201 Dihedral : 5.523 58.438 5583 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 4.02 % Allowed : 20.47 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 5039 helix: 0.55 (0.12), residues: 1845 sheet: -0.72 (0.22), residues: 593 loop : -1.19 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 292 TYR 0.017 0.001 TYR O 494 PHE 0.022 0.001 PHE P 174 TRP 0.017 0.001 TRP C 31 HIS 0.009 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00321 (41393) covalent geometry : angle 0.57572 (55880) hydrogen bonds : bond 0.03809 ( 1567) hydrogen bonds : angle 4.91854 ( 4365) metal coordination : bond 0.00956 ( 28) metal coordination : angle 5.43584 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 463 time to evaluate : 1.626 Fit side-chains revert: symmetry clash REVERT: A 316 TRP cc_start: 0.4796 (OUTLIER) cc_final: 0.3750 (t60) REVERT: A 1172 TYR cc_start: 0.6950 (p90) cc_final: 0.6713 (p90) REVERT: A 1260 MET cc_start: 0.6963 (ttt) cc_final: 0.5927 (ttt) REVERT: A 1287 ASP cc_start: 0.4689 (OUTLIER) cc_final: 0.3823 (t70) REVERT: A 1417 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (mt) REVERT: B 74 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7358 (mptt) REVERT: B 202 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7750 (mmmt) REVERT: B 632 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: B 907 GLU cc_start: 0.8846 (pt0) cc_final: 0.8606 (pt0) REVERT: C 256 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7814 (pp) REVERT: E 106 GLN cc_start: 0.6657 (tp40) cc_final: 0.6386 (tp40) REVERT: E 137 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6835 (mt-10) REVERT: M 262 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5451 (mt-10) REVERT: N 393 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.6055 (t70) REVERT: O 32 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.3196 (ttm) REVERT: O 86 MET cc_start: 0.2900 (ttm) cc_final: 0.2626 (ppp) REVERT: O 196 GLU cc_start: 0.3582 (tp30) cc_final: 0.2772 (mm-30) REVERT: O 201 ILE cc_start: 0.3548 (tp) cc_final: 0.3192 (mp) REVERT: O 236 LYS cc_start: 0.2926 (OUTLIER) cc_final: 0.2593 (tmtp) REVERT: O 258 GLU cc_start: 0.3371 (OUTLIER) cc_final: 0.2407 (tt0) REVERT: O 567 ARG cc_start: 0.2570 (mtm-85) cc_final: 0.2135 (ttp-170) REVERT: O 627 LEU cc_start: 0.2066 (OUTLIER) cc_final: 0.1839 (mm) outliers start: 181 outliers final: 81 residues processed: 602 average time/residue: 0.6722 time to fit residues: 501.4715 Evaluate side-chains 526 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 434 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1071 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 393 ASP Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 9 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 263 optimal weight: 0.3980 chunk 174 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 411 optimal weight: 5.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A 789 ASN A 828 GLN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN B 800 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 115 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN O 572 HIS O 587 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138959 restraints weight = 49688.342| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.78 r_work: 0.3301 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 41421 Z= 0.241 Angle : 0.686 15.554 55919 Z= 0.350 Chirality : 0.047 0.256 6290 Planarity : 0.005 0.098 7201 Dihedral : 5.776 59.457 5575 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.59 % Favored : 93.35 % Rotamer: Outliers : 4.84 % Allowed : 20.18 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 5039 helix: 0.35 (0.12), residues: 1835 sheet: -0.81 (0.21), residues: 595 loop : -1.24 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 277 TYR 0.020 0.002 TYR F 88 PHE 0.022 0.002 PHE B 51 TRP 0.021 0.002 TRP C 31 HIS 0.012 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00567 (41393) covalent geometry : angle 0.66883 (55880) hydrogen bonds : bond 0.04504 ( 1567) hydrogen bonds : angle 5.10700 ( 4365) metal coordination : bond 0.01091 ( 28) metal coordination : angle 5.87144 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 442 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.4211 (OUTLIER) cc_final: 0.3635 (ptt90) REVERT: A 289 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5050 (mp) REVERT: A 316 TRP cc_start: 0.4862 (OUTLIER) cc_final: 0.3677 (t60) REVERT: A 446 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.6944 (p90) REVERT: A 785 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7933 (mp) REVERT: A 991 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6354 (tptt) REVERT: A 993 GLU cc_start: 0.7731 (pm20) cc_final: 0.7506 (pm20) REVERT: A 1287 ASP cc_start: 0.4963 (OUTLIER) cc_final: 0.3981 (t70) REVERT: A 1417 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8629 (mt) REVERT: B 74 LYS cc_start: 0.7712 (mmmt) cc_final: 0.7319 (mptm) REVERT: B 202 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7720 (mmmt) REVERT: B 632 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7211 (m-30) REVERT: B 907 GLU cc_start: 0.8849 (pt0) cc_final: 0.8636 (pt0) REVERT: C 196 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7421 (pp) REVERT: C 245 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7029 (mpp-170) REVERT: C 256 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7867 (pp) REVERT: E 106 GLN cc_start: 0.6531 (tp40) cc_final: 0.6237 (tp40) REVERT: E 131 THR cc_start: 0.6688 (t) cc_final: 0.6482 (p) REVERT: E 137 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6834 (mt-10) REVERT: E 192 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7228 (ttp-110) REVERT: G 58 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8619 (mt0) REVERT: H 135 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7686 (mt) REVERT: M 255 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4250 (t80) REVERT: N 292 ARG cc_start: 0.5402 (tmm-80) cc_final: 0.5185 (tmm-80) REVERT: O 196 GLU cc_start: 0.3550 (tp30) cc_final: 0.2757 (mm-30) REVERT: O 201 ILE cc_start: 0.3608 (tp) cc_final: 0.3222 (mp) REVERT: O 236 LYS cc_start: 0.2813 (OUTLIER) cc_final: 0.2403 (tmtp) REVERT: O 258 GLU cc_start: 0.3335 (OUTLIER) cc_final: 0.2367 (tt0) REVERT: O 567 ARG cc_start: 0.2679 (mtm-85) cc_final: 0.2236 (ttp-170) REVERT: O 627 LEU cc_start: 0.2371 (OUTLIER) cc_final: 0.2114 (mm) REVERT: O 635 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5071 (tp) outliers start: 218 outliers final: 108 residues processed: 599 average time/residue: 0.6696 time to fit residues: 496.3393 Evaluate side-chains 553 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 425 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1348 MET Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 810 ARG Chi-restraints excluded: chain B residue 820 GLN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1117 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 255 PHE Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 137 ILE Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 469 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 446 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 353 optimal weight: 0.0570 chunk 171 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 314 optimal weight: 0.9990 chunk 384 optimal weight: 0.8980 chunk 290 optimal weight: 6.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 GLN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 ASN ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 100 GLN O 464 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.197174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.130026 restraints weight = 49582.884| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.72 r_work: 0.3268 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 41421 Z= 0.172 Angle : 0.624 14.969 55919 Z= 0.318 Chirality : 0.045 0.253 6290 Planarity : 0.005 0.096 7201 Dihedral : 5.603 57.966 5575 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 4.06 % Allowed : 21.15 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.12), residues: 5039 helix: 0.44 (0.12), residues: 1849 sheet: -0.81 (0.21), residues: 596 loop : -1.20 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 292 TYR 0.025 0.002 TYR O 494 PHE 0.021 0.002 PHE B 678 TRP 0.018 0.002 TRP C 31 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00399 (41393) covalent geometry : angle 0.60733 (55880) hydrogen bonds : bond 0.04041 ( 1567) hydrogen bonds : angle 4.98920 ( 4365) metal coordination : bond 0.01035 ( 28) metal coordination : angle 5.38039 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 459 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 83 HIS cc_start: 0.5787 (p-80) cc_final: 0.4493 (p90) REVERT: A 289 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4952 (mp) REVERT: A 316 TRP cc_start: 0.4870 (OUTLIER) cc_final: 0.3776 (t60) REVERT: A 446 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6959 (p90) REVERT: A 993 GLU cc_start: 0.7804 (pm20) cc_final: 0.7590 (pm20) REVERT: A 1260 MET cc_start: 0.7036 (ttt) cc_final: 0.5948 (ttt) REVERT: A 1287 ASP cc_start: 0.4700 (OUTLIER) cc_final: 0.3891 (t70) REVERT: A 1417 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8675 (mt) REVERT: B 74 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7393 (mptt) REVERT: B 202 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7767 (mmmt) REVERT: B 632 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7332 (m-30) REVERT: B 907 GLU cc_start: 0.8875 (pt0) cc_final: 0.8649 (pt0) REVERT: C 196 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7627 (pp) REVERT: C 256 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7879 (pp) REVERT: D 98 MET cc_start: 0.0979 (ptp) cc_final: 0.0713 (mtm) REVERT: E 106 GLN cc_start: 0.6516 (tp40) cc_final: 0.6214 (tp40) REVERT: E 131 THR cc_start: 0.6426 (t) cc_final: 0.6182 (p) REVERT: E 137 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6846 (mt-10) REVERT: E 192 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7281 (ttp-110) REVERT: G 58 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: N 292 ARG cc_start: 0.5371 (tmm-80) cc_final: 0.5142 (tmm-80) REVERT: O 32 MET cc_start: 0.3609 (OUTLIER) cc_final: 0.3245 (ttm) REVERT: O 196 GLU cc_start: 0.3460 (tp30) cc_final: 0.2731 (mm-30) REVERT: O 197 MET cc_start: 0.2125 (mtp) cc_final: 0.1783 (mtp) REVERT: O 201 ILE cc_start: 0.3539 (tp) cc_final: 0.3178 (mp) REVERT: O 236 LYS cc_start: 0.2761 (OUTLIER) cc_final: 0.2411 (tmtp) REVERT: O 258 GLU cc_start: 0.3433 (OUTLIER) cc_final: 0.2520 (tt0) REVERT: O 567 ARG cc_start: 0.2664 (mtm-85) cc_final: 0.2188 (ttp-170) REVERT: O 627 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.2215 (mm) REVERT: O 635 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.5074 (tp) REVERT: P 312 PHE cc_start: 0.4203 (m-80) cc_final: 0.4002 (m-80) outliers start: 183 outliers final: 100 residues processed: 595 average time/residue: 0.6798 time to fit residues: 500.6145 Evaluate side-chains 552 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 437 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 820 GLN Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1051 THR Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 259 ILE Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 638 PHE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 465 optimal weight: 10.0000 chunk 343 optimal weight: 9.9990 chunk 450 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 453 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 266 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.196549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128278 restraints weight = 49482.923| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.29 r_work: 0.3256 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 41421 Z= 0.205 Angle : 0.654 14.992 55919 Z= 0.334 Chirality : 0.046 0.263 6290 Planarity : 0.005 0.096 7201 Dihedral : 5.691 58.162 5575 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 4.15 % Allowed : 21.51 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 5039 helix: 0.38 (0.12), residues: 1847 sheet: -0.80 (0.21), residues: 591 loop : -1.24 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 292 TYR 0.020 0.002 TYR O 106 PHE 0.024 0.002 PHE M 252 TRP 0.020 0.002 TRP C 31 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00480 (41393) covalent geometry : angle 0.63858 (55880) hydrogen bonds : bond 0.04250 ( 1567) hydrogen bonds : angle 5.04234 ( 4365) metal coordination : bond 0.01018 ( 28) metal coordination : angle 5.46092 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 445 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.4336 (OUTLIER) cc_final: 0.3781 (ptt90) REVERT: A 93 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5659 (mp) REVERT: A 289 LEU cc_start: 0.5303 (OUTLIER) cc_final: 0.4908 (mp) REVERT: A 316 TRP cc_start: 0.4834 (OUTLIER) cc_final: 0.3662 (t60) REVERT: A 446 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6770 (p90) REVERT: A 785 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7879 (mp) REVERT: A 993 GLU cc_start: 0.7822 (pm20) cc_final: 0.7613 (pm20) REVERT: A 1287 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.3955 (t70) REVERT: A 1417 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8665 (mt) REVERT: B 74 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7409 (mptt) REVERT: B 202 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7765 (mmmt) REVERT: B 296 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.5606 (m-10) REVERT: B 489 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8215 (tt) REVERT: B 539 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7982 (mt-10) REVERT: B 632 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: B 907 GLU cc_start: 0.8864 (pt0) cc_final: 0.8644 (pt0) REVERT: C 196 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7656 (pp) REVERT: C 256 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7897 (pp) REVERT: D 5 GLU cc_start: 0.5321 (OUTLIER) cc_final: 0.4981 (pp20) REVERT: E 106 GLN cc_start: 0.6666 (tp40) cc_final: 0.6316 (tp40) REVERT: E 137 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6878 (mt-10) REVERT: E 192 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7260 (ttp-110) REVERT: G 58 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: N 390 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5487 (p90) REVERT: O 196 GLU cc_start: 0.3362 (tp30) cc_final: 0.2670 (mm-30) REVERT: O 197 MET cc_start: 0.2088 (mtp) cc_final: 0.1840 (mtp) REVERT: O 201 ILE cc_start: 0.3498 (tp) cc_final: 0.3150 (mp) REVERT: O 236 LYS cc_start: 0.2815 (OUTLIER) cc_final: 0.2446 (tmtp) REVERT: O 258 GLU cc_start: 0.3562 (OUTLIER) cc_final: 0.2691 (tt0) REVERT: O 453 ILE cc_start: 0.0777 (OUTLIER) cc_final: 0.0537 (mp) REVERT: O 567 ARG cc_start: 0.2622 (mtm-85) cc_final: 0.2190 (ttp-170) REVERT: O 627 LEU cc_start: 0.2239 (OUTLIER) cc_final: 0.2008 (mm) REVERT: O 635 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5084 (tp) outliers start: 187 outliers final: 116 residues processed: 585 average time/residue: 0.6602 time to fit residues: 477.7141 Evaluate side-chains 570 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 432 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1348 MET Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 296 TYR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 810 ARG Chi-restraints excluded: chain B residue 820 GLN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 259 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 305 MET Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 379 VAL Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 638 PHE Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 400 optimal weight: 10.0000 chunk 427 optimal weight: 8.9990 chunk 386 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 chunk 453 optimal weight: 9.9990 chunk 303 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 350 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.196715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.128766 restraints weight = 49836.725| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.46 r_work: 0.3260 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 41421 Z= 0.195 Angle : 0.648 14.855 55919 Z= 0.331 Chirality : 0.046 0.257 6290 Planarity : 0.005 0.096 7201 Dihedral : 5.683 57.788 5575 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.09 % Rotamer: Outliers : 3.95 % Allowed : 22.00 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.12), residues: 5039 helix: 0.39 (0.12), residues: 1851 sheet: -0.80 (0.21), residues: 595 loop : -1.22 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 292 TYR 0.020 0.002 TYR O 106 PHE 0.021 0.002 PHE B 678 TRP 0.019 0.002 TRP C 31 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00456 (41393) covalent geometry : angle 0.63298 (55880) hydrogen bonds : bond 0.04191 ( 1567) hydrogen bonds : angle 5.02122 ( 4365) metal coordination : bond 0.01006 ( 28) metal coordination : angle 5.35479 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 446 time to evaluate : 1.222 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.4325 (OUTLIER) cc_final: 0.3813 (ptt90) REVERT: A 289 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.4969 (mp) REVERT: A 316 TRP cc_start: 0.4827 (OUTLIER) cc_final: 0.3707 (t60) REVERT: A 446 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6804 (p90) REVERT: A 743 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.6951 (m) REVERT: A 785 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 993 GLU cc_start: 0.7792 (pm20) cc_final: 0.7569 (pm20) REVERT: A 1260 MET cc_start: 0.7124 (ttt) cc_final: 0.6049 (ttt) REVERT: A 1287 ASP cc_start: 0.4882 (OUTLIER) cc_final: 0.4023 (t70) REVERT: A 1417 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8653 (mt) REVERT: B 74 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7403 (mptt) REVERT: B 202 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7769 (mmmt) REVERT: B 217 GLN cc_start: 0.7360 (pp30) cc_final: 0.7108 (pp30) REVERT: B 489 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8195 (tt) REVERT: B 539 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7889 (mt-10) REVERT: B 907 GLU cc_start: 0.8877 (pt0) cc_final: 0.8629 (pt0) REVERT: C 196 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7636 (pp) REVERT: C 256 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7884 (pp) REVERT: D 5 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.5080 (pp20) REVERT: E 106 GLN cc_start: 0.6656 (tp40) cc_final: 0.6331 (tp40) REVERT: E 137 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6950 (mt-10) REVERT: E 192 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7256 (ttp-110) REVERT: G 58 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8627 (mt0) REVERT: G 207 LEU cc_start: 0.1600 (tp) cc_final: 0.1339 (mt) REVERT: N 390 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5427 (p90) REVERT: O 196 GLU cc_start: 0.3382 (tp30) cc_final: 0.2704 (mm-30) REVERT: O 197 MET cc_start: 0.2275 (mtp) cc_final: 0.2013 (mtp) REVERT: O 201 ILE cc_start: 0.3521 (tp) cc_final: 0.3169 (mp) REVERT: O 236 LYS cc_start: 0.2824 (OUTLIER) cc_final: 0.2442 (tmtp) REVERT: O 258 GLU cc_start: 0.3566 (OUTLIER) cc_final: 0.2694 (tt0) REVERT: O 284 LEU cc_start: 0.4497 (pp) cc_final: 0.3772 (tm) REVERT: O 567 ARG cc_start: 0.2644 (mtm-85) cc_final: 0.2216 (ttp-170) REVERT: O 627 LEU cc_start: 0.2245 (OUTLIER) cc_final: 0.2007 (mm) REVERT: O 635 LEU cc_start: 0.5424 (OUTLIER) cc_final: 0.5073 (tp) outliers start: 178 outliers final: 118 residues processed: 580 average time/residue: 0.6647 time to fit residues: 476.4889 Evaluate side-chains 571 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 434 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 952 LYS Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1262 GLN Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1348 MET Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 199 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 625 ILE Chi-restraints excluded: chain B residue 810 ARG Chi-restraints excluded: chain B residue 820 GLN Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 5 GLU Chi-restraints excluded: chain D residue 8 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 259 ILE Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 207 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain N residue 417 VAL Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 116 LYS Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 379 SER Chi-restraints excluded: chain O residue 476 TYR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 563 VAL Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 635 LEU Chi-restraints excluded: chain O residue 638 PHE Chi-restraints excluded: chain P residue 186 ILE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 293 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 613 THR Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 31 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 210 optimal weight: 0.9980 chunk 307 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 391 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN L 53 HIS ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN O 464 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.199042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147582 restraints weight = 49498.838| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.40 r_work: 0.3407 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 41421 Z= 0.118 Angle : 0.580 13.754 55919 Z= 0.295 Chirality : 0.043 0.297 6290 Planarity : 0.004 0.095 7201 Dihedral : 5.277 58.445 5575 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 2.80 % Allowed : 23.24 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.12), residues: 5039 helix: 0.74 (0.12), residues: 1827 sheet: -0.69 (0.21), residues: 597 loop : -1.09 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 292 TYR 0.016 0.001 TYR O 106 PHE 0.032 0.001 PHE M 252 TRP 0.017 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00267 (41393) covalent geometry : angle 0.56704 (55880) hydrogen bonds : bond 0.03533 ( 1567) hydrogen bonds : angle 4.79979 ( 4365) metal coordination : bond 0.00886 ( 28) metal coordination : angle 4.67391 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 461 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 37 ARG cc_start: 0.3951 (OUTLIER) cc_final: 0.3530 (mpp80) REVERT: A 289 LEU cc_start: 0.5421 (OUTLIER) cc_final: 0.5091 (mp) REVERT: A 316 TRP cc_start: 0.4967 (OUTLIER) cc_final: 0.3959 (t60) REVERT: A 320 GLN cc_start: 0.5397 (tm-30) cc_final: 0.5064 (tm-30) REVERT: A 517 MET cc_start: 0.9252 (mtp) cc_final: 0.8993 (mtm) REVERT: A 741 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6968 (tt) REVERT: A 743 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7031 (m) REVERT: A 1117 MET cc_start: 0.5516 (mtm) cc_final: 0.4384 (pmm) REVERT: A 1172 TYR cc_start: 0.7141 (p90) cc_final: 0.6888 (p90) REVERT: A 1287 ASP cc_start: 0.4471 (OUTLIER) cc_final: 0.3650 (t70) REVERT: A 1446 CYS cc_start: 0.3441 (OUTLIER) cc_final: 0.3086 (m) REVERT: B 74 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7424 (mptt) REVERT: B 202 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7726 (mmmt) REVERT: B 539 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7649 (mt-10) REVERT: C 196 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7472 (pp) REVERT: C 256 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7754 (pp) REVERT: D 98 MET cc_start: 0.1279 (ptp) cc_final: 0.0949 (mtm) REVERT: E 106 GLN cc_start: 0.6566 (tp40) cc_final: 0.6274 (tp40) REVERT: G 58 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: G 84 ILE cc_start: 0.4225 (mp) cc_final: 0.3948 (mm) REVERT: I 33 PHE cc_start: 0.6657 (t80) cc_final: 0.6451 (t80) REVERT: J 30 LEU cc_start: 0.7965 (mt) cc_final: 0.7711 (mt) REVERT: M 154 GLU cc_start: 0.6360 (tp30) cc_final: 0.5688 (pm20) REVERT: O 32 MET cc_start: 0.3710 (OUTLIER) cc_final: 0.3285 (ttm) REVERT: O 196 GLU cc_start: 0.3369 (tp30) cc_final: 0.2853 (mm-30) REVERT: O 197 MET cc_start: 0.2513 (mtp) cc_final: 0.2123 (mtp) REVERT: O 201 ILE cc_start: 0.3564 (tp) cc_final: 0.3085 (mp) REVERT: O 236 LYS cc_start: 0.3092 (OUTLIER) cc_final: 0.2679 (tmtp) REVERT: O 258 GLU cc_start: 0.3868 (OUTLIER) cc_final: 0.2829 (tt0) REVERT: O 284 LEU cc_start: 0.4450 (pp) cc_final: 0.3731 (tm) REVERT: O 453 ILE cc_start: 0.0933 (OUTLIER) cc_final: 0.0672 (mp) REVERT: O 484 MET cc_start: 0.4036 (tpp) cc_final: 0.3274 (tpp) REVERT: O 528 MET cc_start: 0.2616 (OUTLIER) cc_final: 0.2332 (mmm) REVERT: O 567 ARG cc_start: 0.2602 (mtm-85) cc_final: 0.2227 (ttp-170) REVERT: O 627 LEU cc_start: 0.2206 (OUTLIER) cc_final: 0.1964 (mm) outliers start: 126 outliers final: 71 residues processed: 562 average time/residue: 0.6832 time to fit residues: 474.3304 Evaluate side-chains 519 residues out of total 4516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 432 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 810 ARG Chi-restraints excluded: chain B residue 864 THR Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 168 VAL Chi-restraints excluded: chain M residue 259 ILE Chi-restraints excluded: chain N residue 202 VAL Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 372 SER Chi-restraints excluded: chain N residue 382 ILE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 397 LEU Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 140 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 236 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 280 LEU Chi-restraints excluded: chain O residue 453 ILE Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 528 MET Chi-restraints excluded: chain O residue 554 THR Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 638 PHE Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain Q residue 105 ILE Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain W residue 619 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 377 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 437 optimal weight: 9.9990 chunk 387 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 252 optimal weight: 5.9990 chunk 447 optimal weight: 0.4980 chunk 413 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 481 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN A1180 ASN A1345 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1025 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** M 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 287 HIS N 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.197004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128765 restraints weight = 49687.749| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.51 r_work: 0.3258 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 41421 Z= 0.195 Angle : 0.642 14.320 55919 Z= 0.327 Chirality : 0.046 0.296 6290 Planarity : 0.005 0.095 7201 Dihedral : 5.523 57.877 5574 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 2.60 % Allowed : 23.68 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.12), residues: 5039 helix: 0.57 (0.12), residues: 1840 sheet: -0.77 (0.21), residues: 617 loop : -1.14 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 292 TYR 0.028 0.002 TYR O 494 PHE 0.028 0.002 PHE M 252 TRP 0.019 0.002 TRP B 442 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00459 (41393) covalent geometry : angle 0.62788 (55880) hydrogen bonds : bond 0.04068 ( 1567) hydrogen bonds : angle 4.92599 ( 4365) metal coordination : bond 0.00895 ( 28) metal coordination : angle 5.02519 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21125.90 seconds wall clock time: 358 minutes 23.80 seconds (21503.80 seconds total)