Starting phenix.real_space_refine on Thu Dec 26 03:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.map" model { file = "/net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1o_14451/12_2024/7z1o_14451.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 26659 2.51 5 N 7301 2.21 5 O 8124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42375 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11228 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 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: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1083 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} 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: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1196 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 2 Chain: "O" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4562 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10} Chain: "S" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "T" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 597 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 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: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 500 SG CYS A 67 114.110 78.495 108.016 1.00 53.58 S ATOM 518 SG CYS A 70 112.829 74.993 107.055 1.00 54.80 S ATOM 565 SG CYS A 77 111.387 78.163 105.337 1.00 45.88 S ATOM 803 SG CYS A 107 82.264 100.569 137.711 1.00 40.77 S ATOM 826 SG CYS A 110 83.280 97.430 139.680 1.00 44.92 S ATOM 1192 SG CYS A 154 79.582 98.500 139.471 1.00 53.98 S ATOM 1216 SG CYS A 157 82.129 100.405 141.529 1.00 54.88 S ATOM 19494 SG CYS B1095 99.299 70.114 117.025 1.00 43.11 S ATOM 19517 SG CYS B1098 98.719 73.893 117.473 1.00 43.33 S ATOM 19583 SG CYS B1107 102.124 72.680 116.902 1.00 47.69 S ATOM 19603 SG CYS B1110 100.483 71.830 120.205 1.00 48.48 S ATOM 28899 SG CYS I 5 63.942 153.726 108.724 1.00 74.07 S ATOM 28918 SG CYS I 8 67.645 152.759 107.959 1.00 74.28 S ATOM 29046 SG CYS I 26 65.881 150.974 110.707 1.00 75.01 S ATOM 29069 SG CYS I 29 66.581 154.746 111.006 1.00 77.94 S ATOM 29396 SG CYS I 69 15.258 125.229 101.551 1.00162.84 S ATOM 29646 SG CYS I 100 15.666 124.848 97.072 1.00150.09 S ATOM 29667 SG CYS I 103 17.487 126.778 98.789 1.00153.60 S ATOM 29786 SG CYS J 7 93.922 91.311 38.742 1.00 32.27 S ATOM 29809 SG CYS J 10 93.339 88.437 36.224 1.00 34.22 S ATOM 30089 SG CYS J 45 90.475 90.804 37.376 1.00 33.82 S ATOM 30095 SG CYS J 46 93.278 91.781 34.951 1.00 34.66 S ATOM 31152 SG CYS L 31 127.336 110.667 59.172 1.00 59.34 S ATOM 31172 SG CYS L 34 129.174 111.554 56.007 1.00 61.23 S ATOM 31276 SG CYS L 48 131.164 110.964 59.159 1.00 66.10 S ATOM 31299 SG CYS L 51 129.028 114.069 58.915 1.00 67.77 S Time building chain proxies: 20.33, per 1000 atoms: 0.48 Number of scatterers: 42375 At special positions: 0 Unit cell: (148.863, 193.626, 196.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 217 16.00 P 66 15.00 Mg 1 11.99 O 8124 8.00 N 7301 7.00 C 26659 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: 10.17 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 69 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " 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 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 33 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9720 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 50 sheets defined 41.9% alpha, 14.8% beta 14 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 14.14 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 133 through 150 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.580A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.861A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 215 " --> pdb=" O GLU A 212 " (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 243 removed outlier: 4.244A pdb=" N GLU A 240 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 283 through 306 Processing helix chain 'A' and resid 308 through 328 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 450 through 455 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 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.029A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.552A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 649 removed outlier: 6.198A pdb=" N GLN A 647 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 648 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 708 removed outlier: 3.808A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 748 Processing helix chain 'A' and resid 757 through 783 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 894 removed outlier: 4.409A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 973 Proline residue: A 969 - end of helix Processing helix chain 'A' and resid 985 through 989 removed outlier: 3.656A pdb=" N LEU A 989 " --> pdb=" O ARG A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 995 Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1051 through 1060 removed outlier: 3.862A pdb=" N SER A1055 " --> pdb=" O ASN A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1100 through 1102 No H-bonds generated for 'chain 'A' and resid 1100 through 1102' Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.521A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 removed outlier: 3.553A pdb=" N ILE A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1212 Processing helix chain 'A' and resid 1213 through 1216 Processing helix chain 'A' and resid 1254 through 1267 removed outlier: 3.644A pdb=" N TYR A1258 " --> pdb=" O ASN A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1318 through 1326 removed outlier: 3.845A pdb=" N VAL A1322 " --> pdb=" O HIS A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1347 removed outlier: 3.755A pdb=" N HIS A1346 " --> pdb=" O THR A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1363 removed outlier: 3.953A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1380 Processing helix chain 'A' and resid 1382 through 1388 removed outlier: 3.955A pdb=" N LEU A1386 " --> pdb=" O SER A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1423 through 1426 removed outlier: 3.543A pdb=" N GLY A1426 " --> pdb=" O ILE A1423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1423 through 1426' Processing helix chain 'A' and resid 1438 through 1442 removed outlier: 3.791A pdb=" N VAL A1442 " --> pdb=" O LYS A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1452 removed outlier: 3.535A pdb=" N SER A1450 " --> pdb=" O CYS A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 4.396A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.833A pdb=" N ALA B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 71 removed outlier: 4.198A pdb=" N LEU B 62 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.592A pdb=" N CYS B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.988A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 363 through 366 removed outlier: 3.739A pdb=" N ILE B 366 " --> pdb=" O PRO B 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 363 through 366' 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 removed outlier: 3.644A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 422 through 439 removed outlier: 3.704A pdb=" N ASN B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.593A pdb=" N MET B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 623 through 633 Processing helix chain 'B' and resid 636 through 643 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.754A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.557A pdb=" N ILE B 666 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 removed outlier: 3.616A pdb=" N THR B 679 " --> pdb=" O GLU B 676 " (cutoff:3.500A) 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 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 738 through 744 Processing helix chain 'B' and resid 763 through 767 removed outlier: 3.918A pdb=" N ASP B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 767 " --> pdb=" O GLY B 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 767' Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 818 through 822 removed outlier: 3.512A pdb=" N GLN B 822 " --> pdb=" O TRP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.700A pdb=" N GLY B 948 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.888A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 removed outlier: 3.648A pdb=" N MET B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1053 through 1057 removed outlier: 3.506A pdb=" N ASP B1057 " --> pdb=" O ARG B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 32 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.637A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 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 250 removed outlier: 3.579A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.576A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.558A pdb=" N PHE C 285 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 30 through 37 removed outlier: 3.729A pdb=" N LEU D 37 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.513A pdb=" N GLN D 56 " --> pdb=" O HIS D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 112 removed outlier: 3.806A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 127 Processing helix chain 'D' and resid 130 through 138 removed outlier: 3.580A pdb=" N LEU D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.743A pdb=" N GLY D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.943A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.808A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.524A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.886A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) 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 removed outlier: 3.726A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 162 through 175 removed outlier: 3.512A pdb=" N GLU G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.924A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.770A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.741A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain '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: 4.536A 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 removed outlier: 3.637A pdb=" N ALA M 136 " --> pdb=" O ASN M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 229 through 240 Processing helix chain 'M' and resid 251 through 266 removed outlier: 3.599A pdb=" N PHE M 255 " --> pdb=" O THR M 251 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 280 removed outlier: 3.572A pdb=" N ILE M 278 " --> pdb=" O GLN M 274 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN M 280 " --> pdb=" O ASP M 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 200 removed outlier: 3.558A pdb=" N GLN N 198 " --> pdb=" O ARG N 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 212 removed outlier: 3.643A pdb=" N VAL N 212 " --> pdb=" O HIS N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 223 removed outlier: 3.562A pdb=" N GLU N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 297 Processing helix chain 'O' and resid 27 through 35 Processing helix chain 'O' and resid 38 through 42 removed outlier: 3.820A pdb=" N THR O 41 " --> pdb=" O GLU O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 57 Processing helix chain 'O' and resid 58 through 72 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 removed outlier: 3.514A pdb=" N LEU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 132 removed outlier: 4.057A pdb=" N ILE O 127 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.787A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 167 Processing helix chain 'O' and resid 171 through 176 Processing helix chain 'O' and resid 180 through 197 removed outlier: 3.547A pdb=" N MET O 197 " --> pdb=" O GLN O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 209 Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 233 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 4.322A pdb=" N LEU O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 301 removed outlier: 3.686A pdb=" N PHE O 287 " --> pdb=" O ASN O 283 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 319 Processing helix chain 'O' and resid 328 through 333 Processing helix chain 'O' and resid 338 through 356 removed outlier: 3.779A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR O 356 " --> pdb=" O VAL O 352 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 368 removed outlier: 3.904A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 462 Processing helix chain 'O' and resid 479 through 501 removed outlier: 3.851A pdb=" N MET O 484 " --> pdb=" O TYR O 480 " (cutoff:3.500A) Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 501 through 514 removed outlier: 3.623A pdb=" N ASN O 514 " --> pdb=" O CYS O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 526 Processing helix chain 'O' and resid 529 through 542 removed outlier: 3.767A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.718A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 614 through 619 Processing helix chain 'O' and resid 620 through 649 Processing helix chain 'P' and resid 171 through 191 Processing helix chain 'P' and resid 218 through 228 Processing helix chain 'P' and resid 236 through 250 Processing helix chain 'P' and resid 264 through 271 removed outlier: 3.687A pdb=" N ILE P 268 " --> pdb=" O THR P 264 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 299 Processing helix chain 'Q' and resid 41 through 45 removed outlier: 3.809A pdb=" N ASN Q 44 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY Q 45 " --> pdb=" O PRO Q 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 45' Processing helix chain 'Q' and resid 48 through 67 Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.699A pdb=" N LYS Q 111 " --> pdb=" O TYR Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 132 removed outlier: 3.655A pdb=" N PHE Q 132 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 1405 through 1407 removed outlier: 6.734A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.378A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LYS A 85 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A 259 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N LEU A 88 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ILE A 257 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.526A pdb=" N ASP A 220 " --> pdb=" O HIS A 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.621A pdb=" N LYS A 371 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1037 removed outlier: 3.761A pdb=" N LEU A 500 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.855A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.295A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 814 through 815 Processing sheet with id=AB2, first strand: chain 'A' and resid 897 through 898 removed outlier: 7.044A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1280 through 1285 removed outlier: 3.707A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N ILE A1140 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N THR A1314 " --> pdb=" O ILE A1140 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N ASN A1142 " --> pdb=" O SER A1312 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N SER A1312 " --> pdb=" O ASN A1142 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL A1144 " --> pdb=" O ILE A1310 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 3.742A pdb=" N LYS A1273 " --> pdb=" O THR A1164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.455A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1173 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 40 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1365 through 1366 removed outlier: 3.781A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1428 through 1432 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1428 through 1432 current: chain 'F' and resid 145 through 147 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 145 through 147 current: chain 'G' and resid 43 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 54 current: chain 'G' and resid 66 through 77 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.737A pdb=" N LEU B 93 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR B 136 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 95 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 134 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP B 97 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA B 127 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY B 150 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 129 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 148 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 131 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 146 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 375 through 378 removed outlier: 6.651A pdb=" N VAL B 196 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.459A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 441 through 444 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: 5.460A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 554 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 601 " --> pdb=" O GLY B 554 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR B 556 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 724 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: 6.617A pdb=" N LEU B 899 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 884 " --> pdb=" O LYS B 897 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS B 897 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET B 886 " --> pdb=" O LEU B 895 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 895 " --> pdb=" O MET B 886 " (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 38 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: 7.254A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 4.225A 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: 3.922A 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 1101 through 1102 removed outlier: 4.100A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.409A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD6, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD7, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.431A pdb=" N THR C 334 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.598A pdb=" N LEU G 197 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU G 153 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA G 195 " --> pdb=" O GLU G 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 120 through 121 Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.930A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 13 through 15 removed outlier: 4.667A pdb=" N TYR I 31 " --> pdb=" O CYS I 26 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 64 through 66 removed outlier: 5.182A pdb=" N CYS I 100 " --> pdb=" O HIS I 105 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N HIS I 105 " --> pdb=" O CYS I 100 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 70 through 78 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 70 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 154 current: chain 'M' and resid 168 through 182 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 168 through 182 current: chain 'N' and resid 371 through 375 removed outlier: 6.478A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 4.464A 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 378 through 383 current: chain 'N' and resid 405 through 420 Processing sheet with id=AE7, first strand: chain 'M' and resid 96 through 97 Processing sheet with id=AE8, first strand: chain 'O' and resid 106 through 110 Processing sheet with id=AE9, first strand: chain 'O' and resid 168 through 170 Processing sheet with id=AF1, first strand: chain 'O' and resid 380 through 381 Processing sheet with id=AF2, first strand: chain 'O' and resid 469 through 470 Processing sheet with id=AF3, first strand: chain 'O' and resid 547 through 551 Processing sheet with id=AF4, first strand: chain 'P' and resid 165 through 166 Processing sheet with id=AF5, first strand: chain 'P' and resid 216 through 217 removed outlier: 7.217A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) 1685 hydrogen bonds defined for protein. 4683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 22.37 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13402 1.34 - 1.46: 7764 1.46 - 1.58: 21622 1.58 - 1.70: 138 1.70 - 1.82: 352 Bond restraints: 43278 Sorted by residual: bond pdb=" C LEU A1267 " pdb=" N PRO A1268 " ideal model delta sigma weight residual 1.334 1.363 -0.029 8.40e-03 1.42e+04 1.20e+01 bond pdb=" C15 1N7 C 401 " pdb=" C16 1N7 C 401 " ideal model delta sigma weight residual 1.530 1.594 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C16 1N7 C 401 " pdb=" C17 1N7 C 401 " ideal model delta sigma weight residual 1.527 1.590 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C15 1N7 A2003 " pdb=" C16 1N7 A2003 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.76e+00 bond pdb=" C19 1N7 A2003 " pdb=" C2 1N7 A2003 " ideal model delta sigma weight residual 1.551 1.613 -0.062 2.00e-02 2.50e+03 9.52e+00 ... (remaining 43273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 57963 2.34 - 4.68: 652 4.68 - 7.03: 91 7.03 - 9.37: 21 9.37 - 11.71: 6 Bond angle restraints: 58733 Sorted by residual: angle pdb=" CA PRO O 473 " pdb=" N PRO O 473 " pdb=" CD PRO O 473 " ideal model delta sigma weight residual 112.00 103.76 8.24 1.40e+00 5.10e-01 3.46e+01 angle pdb=" CA PRO O 256 " pdb=" N PRO O 256 " pdb=" CD PRO O 256 " ideal model delta sigma weight residual 112.00 104.92 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.53 108.68 4.85 9.80e-01 1.04e+00 2.45e+01 angle pdb=" N ALA D 129 " pdb=" CA ALA D 129 " pdb=" C ALA D 129 " ideal model delta sigma weight residual 114.04 108.09 5.95 1.24e+00 6.50e-01 2.30e+01 angle pdb=" C GLU P 314 " pdb=" N TRP P 315 " pdb=" CA TRP P 315 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 ... (remaining 58728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 25365 27.48 - 54.95: 1027 54.95 - 82.43: 115 82.43 - 109.91: 2 109.91 - 137.39: 2 Dihedral angle restraints: 26511 sinusoidal: 11488 harmonic: 15023 Sorted by residual: dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual 180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA MET B 469 " pdb=" C MET B 469 " pdb=" N MET B 470 " pdb=" CA MET B 470 " ideal model delta harmonic sigma weight residual 180.00 157.26 22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLU O 149 " pdb=" C GLU O 149 " pdb=" N GLU O 150 " pdb=" CA GLU O 150 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 26508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5738 0.068 - 0.135: 857 0.135 - 0.203: 30 0.203 - 0.270: 7 0.270 - 0.338: 4 Chirality restraints: 6636 Sorted by residual: chirality pdb=" C9 1N7 C 401 " pdb=" C20 1N7 C 401 " pdb=" C5 1N7 C 401 " pdb=" C8 1N7 C 401 " both_signs ideal model delta sigma weight residual False 2.62 2.96 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C9 1N7 A2003 " pdb=" C20 1N7 A2003 " pdb=" C5 1N7 A2003 " pdb=" C8 1N7 A2003 " both_signs ideal model delta sigma weight residual False 2.62 2.95 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C17 1N7 C 401 " pdb=" C16 1N7 C 401 " pdb=" C18 1N7 C 401 " pdb=" O3 1N7 C 401 " both_signs ideal model delta sigma weight residual False 2.40 2.71 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 6633 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 255 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PRO O 256 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO O 256 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO O 256 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 472 " -0.078 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO O 473 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO O 473 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO O 473 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 124 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO E 125 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " -0.043 5.00e-02 4.00e+02 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 349 2.63 - 3.20: 35659 3.20 - 3.76: 64935 3.76 - 4.33: 91307 4.33 - 4.90: 152553 Nonbonded interactions: 344803 Sorted by model distance: nonbonded pdb=" O3' C R 19 " pdb="MG MG A2002 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.083 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.156 2.170 nonbonded pdb=" O VAL O 31 " pdb=" OG SER O 35 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 231 " pdb=" O VAL B 331 " model vdw 2.218 3.040 ... (remaining 344798 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: 4.980 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: 0.000 Extract box with map and model: 1.360 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 108.560 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 0.103 43278 Z= 0.238 Angle : 0.654 11.709 58733 Z= 0.349 Chirality : 0.046 0.338 6636 Planarity : 0.005 0.132 7320 Dihedral : 14.182 137.386 16791 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.11), residues: 5092 helix: 0.59 (0.11), residues: 1877 sheet: 0.33 (0.20), residues: 697 loop : -0.42 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 185 HIS 0.007 0.001 HIS L 53 PHE 0.027 0.001 PHE B1018 TYR 0.017 0.001 TYR B 416 ARG 0.015 0.000 ARG B 915 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 4.544 Fit side-chains REVERT: A 775 GLU cc_start: 0.6899 (tp30) cc_final: 0.6681 (mm-30) REVERT: A 819 SER cc_start: 0.8265 (t) cc_final: 0.8046 (m) REVERT: A 890 MET cc_start: 0.7585 (tpp) cc_final: 0.7344 (tpp) REVERT: A 1060 TYR cc_start: 0.7638 (m-80) cc_final: 0.7430 (m-80) REVERT: A 1127 LYS cc_start: 0.7852 (tttm) cc_final: 0.7427 (ttpt) REVERT: A 1210 THR cc_start: 0.8126 (m) cc_final: 0.7908 (m) REVERT: A 1337 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7319 (mtm110) REVERT: B 882 ASP cc_start: 0.7060 (t0) cc_final: 0.6808 (t0) REVERT: B 1084 MET cc_start: 0.8018 (ttp) cc_final: 0.7812 (ttm) REVERT: C 9 TYR cc_start: 0.8608 (p90) cc_final: 0.8300 (p90) REVERT: F 115 THR cc_start: 0.8847 (p) cc_final: 0.8639 (p) REVERT: G 75 VAL cc_start: 0.7387 (t) cc_final: 0.7132 (m) REVERT: H 25 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8167 (ttm-80) REVERT: O 629 MET cc_start: 0.6716 (mmp) cc_final: 0.6399 (mpp) REVERT: Q 65 VAL cc_start: 0.7936 (t) cc_final: 0.7734 (t) outliers start: 0 outliers final: 2 residues processed: 593 average time/residue: 1.8058 time to fit residues: 1289.7167 Evaluate side-chains 493 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 491 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 722 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 402 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 465 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 630 ASN A 808 GLN A 821 ASN A1262 GLN B 80 ASN B 237 ASN B 837 GLN C 158 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN O 652 GLN Q 138 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 43278 Z= 0.452 Angle : 0.610 9.674 58733 Z= 0.318 Chirality : 0.047 0.262 6636 Planarity : 0.005 0.082 7320 Dihedral : 11.572 144.618 6494 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.34 % Allowed : 8.46 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.12), residues: 5092 helix: 1.08 (0.12), residues: 1898 sheet: 0.28 (0.19), residues: 746 loop : -0.28 (0.12), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 79 HIS 0.013 0.002 HIS A 427 PHE 0.028 0.002 PHE B1018 TYR 0.021 0.002 TYR E 112 ARG 0.010 0.001 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 526 time to evaluate : 4.959 Fit side-chains REVERT: A 361 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: A 775 GLU cc_start: 0.6831 (tp30) cc_final: 0.6624 (mm-30) REVERT: A 843 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: A 909 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 915 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7724 (t) REVERT: A 1294 LEU cc_start: 0.7993 (pp) cc_final: 0.7734 (pt) REVERT: B 628 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7250 (ttm-80) REVERT: B 631 LEU cc_start: 0.8056 (mt) cc_final: 0.7854 (mt) REVERT: C 9 TYR cc_start: 0.8664 (p90) cc_final: 0.8313 (p90) REVERT: D 154 LEU cc_start: 0.5888 (mm) cc_final: 0.5606 (tm) REVERT: E 50 MET cc_start: 0.6291 (OUTLIER) cc_final: 0.5984 (pp-130) REVERT: E 73 PRO cc_start: 0.8601 (Cg_endo) cc_final: 0.8391 (Cg_exo) REVERT: G 75 VAL cc_start: 0.7500 (t) cc_final: 0.7155 (m) REVERT: I 1 MET cc_start: 0.8053 (tpp) cc_final: 0.7805 (tpp) REVERT: M 261 LYS cc_start: 0.7469 (tmmt) cc_final: 0.7201 (tmmm) REVERT: O 183 MET cc_start: 0.7390 (tpp) cc_final: 0.6998 (mmp) REVERT: O 317 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7071 (mpt180) REVERT: O 343 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7156 (mppt) REVERT: O 542 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6914 (mmm160) REVERT: O 628 LYS cc_start: 0.7095 (tptp) cc_final: 0.6866 (tptt) REVERT: O 629 MET cc_start: 0.6733 (mmp) cc_final: 0.6409 (mpp) REVERT: P 308 GLU cc_start: 0.7481 (mp0) cc_final: 0.6986 (mm-30) outliers start: 61 outliers final: 24 residues processed: 552 average time/residue: 1.7601 time to fit residues: 1173.3034 Evaluate side-chains 523 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 491 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 472 ARG Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 387 optimal weight: 1.9990 chunk 317 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 466 optimal weight: 0.6980 chunk 504 optimal weight: 2.9990 chunk 415 optimal weight: 6.9990 chunk 462 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 374 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1262 GLN B 550 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 61 ASN D 64 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43278 Z= 0.251 Angle : 0.519 9.991 58733 Z= 0.272 Chirality : 0.043 0.233 6636 Planarity : 0.004 0.066 7320 Dihedral : 11.463 140.750 6491 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.78 % Allowed : 10.55 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 5092 helix: 1.40 (0.12), residues: 1897 sheet: 0.32 (0.19), residues: 733 loop : -0.20 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 215 HIS 0.008 0.001 HIS A 427 PHE 0.021 0.001 PHE B 678 TYR 0.017 0.001 TYR J 44 ARG 0.007 0.000 ARG B 874 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 509 time to evaluate : 4.793 Fit side-chains REVERT: A 505 CYS cc_start: 0.7236 (p) cc_final: 0.6951 (p) REVERT: A 775 GLU cc_start: 0.6832 (tp30) cc_final: 0.6622 (mm-30) REVERT: A 784 GLU cc_start: 0.6974 (tp30) cc_final: 0.6686 (tp30) REVERT: A 819 SER cc_start: 0.8453 (t) cc_final: 0.8153 (m) REVERT: A 909 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7977 (t0) REVERT: A 915 THR cc_start: 0.7926 (m) cc_final: 0.7721 (t) REVERT: A 1210 THR cc_start: 0.8077 (m) cc_final: 0.7851 (m) REVERT: A 1294 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7615 (pp) REVERT: B 109 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7297 (mtmm) REVERT: B 250 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: B 281 ASP cc_start: 0.7283 (m-30) cc_final: 0.6847 (m-30) REVERT: B 628 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.7212 (ttm-80) REVERT: B 631 LEU cc_start: 0.8064 (mt) cc_final: 0.7864 (mt) REVERT: B 639 ASP cc_start: 0.6996 (t70) cc_final: 0.6743 (t0) REVERT: B 882 ASP cc_start: 0.7062 (t0) cc_final: 0.6723 (t0) REVERT: C 9 TYR cc_start: 0.8650 (p90) cc_final: 0.8266 (p90) REVERT: C 38 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7894 (ttpp) REVERT: D 107 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6457 (tpp) REVERT: E 169 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7780 (mtt180) REVERT: G 167 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5659 (mp0) REVERT: M 261 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7161 (tppt) REVERT: O 343 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7137 (mppt) REVERT: O 542 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6839 (mmm160) REVERT: O 628 LYS cc_start: 0.7106 (tptp) cc_final: 0.6793 (ttmm) REVERT: O 629 MET cc_start: 0.6734 (mmp) cc_final: 0.6383 (mpp) REVERT: P 308 GLU cc_start: 0.7516 (mp0) cc_final: 0.7061 (mm-30) REVERT: Q 65 VAL cc_start: 0.8193 (t) cc_final: 0.7968 (t) outliers start: 81 outliers final: 30 residues processed: 541 average time/residue: 1.6879 time to fit residues: 1109.6730 Evaluate side-chains 537 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 498 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 353 GLU Chi-restraints excluded: chain O residue 542 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 0.0270 chunk 350 optimal weight: 4.9990 chunk 242 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 313 optimal weight: 1.9990 chunk 468 optimal weight: 3.9990 chunk 495 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 443 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 61 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43278 Z= 0.221 Angle : 0.503 8.132 58733 Z= 0.263 Chirality : 0.042 0.231 6636 Planarity : 0.004 0.061 7320 Dihedral : 11.423 140.695 6489 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.11 % Allowed : 12.02 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 5092 helix: 1.58 (0.12), residues: 1900 sheet: 0.32 (0.19), residues: 745 loop : -0.14 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 197 HIS 0.007 0.001 HIS A 427 PHE 0.020 0.001 PHE B 678 TYR 0.015 0.001 TYR J 44 ARG 0.008 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 503 time to evaluate : 4.958 Fit side-chains REVERT: A 361 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7660 (mm-40) REVERT: A 658 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.6973 (mm110) REVERT: A 784 GLU cc_start: 0.6989 (tp30) cc_final: 0.6646 (tp30) REVERT: A 819 SER cc_start: 0.8480 (t) cc_final: 0.8167 (m) REVERT: A 909 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7972 (t0) REVERT: A 1117 MET cc_start: 0.7234 (mmt) cc_final: 0.6798 (mmt) REVERT: A 1173 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7435 (t) REVERT: A 1210 THR cc_start: 0.8086 (m) cc_final: 0.7864 (m) REVERT: A 1294 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7541 (pt) REVERT: A 1380 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6754 (mmp-170) REVERT: B 109 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7291 (mtmm) REVERT: B 239 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7912 (mtpt) REVERT: B 250 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: B 281 ASP cc_start: 0.7279 (m-30) cc_final: 0.6825 (m-30) REVERT: B 628 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7191 (ttm-80) REVERT: B 631 LEU cc_start: 0.8067 (mt) cc_final: 0.7864 (mt) REVERT: B 639 ASP cc_start: 0.7079 (t70) cc_final: 0.6810 (t0) REVERT: B 882 ASP cc_start: 0.7035 (t0) cc_final: 0.6696 (t0) REVERT: B 958 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: C 9 TYR cc_start: 0.8647 (p90) cc_final: 0.8305 (p90) REVERT: C 38 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7921 (ttpp) REVERT: E 169 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7729 (mtt180) REVERT: G 16 ASP cc_start: 0.7750 (p0) cc_final: 0.7540 (p0) REVERT: G 84 ILE cc_start: 0.8464 (pt) cc_final: 0.8227 (pp) REVERT: G 167 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: H 8 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6690 (t70) REVERT: H 55 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7513 (pp) REVERT: M 261 LYS cc_start: 0.7488 (tmmt) cc_final: 0.7172 (tppt) REVERT: M 282 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7307 (t) REVERT: O 317 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7123 (mpt-90) REVERT: O 343 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7141 (mppt) REVERT: O 542 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6824 (mmm160) REVERT: O 628 LYS cc_start: 0.7093 (tptp) cc_final: 0.6876 (ttmt) REVERT: O 629 MET cc_start: 0.6756 (mmp) cc_final: 0.6431 (mpp) REVERT: P 308 GLU cc_start: 0.7497 (mp0) cc_final: 0.7100 (mm-30) REVERT: Q 65 VAL cc_start: 0.8153 (t) cc_final: 0.7939 (t) outliers start: 96 outliers final: 31 residues processed: 554 average time/residue: 1.7103 time to fit residues: 1152.8507 Evaluate side-chains 541 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 492 time to evaluate : 5.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 ARG Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 353 GLU Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain Q residue 134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 369 optimal weight: 8.9990 chunk 204 optimal weight: 0.6980 chunk 423 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 253 optimal weight: 0.5980 chunk 445 optimal weight: 3.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1262 GLN B1077 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 61 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43278 Z= 0.180 Angle : 0.487 8.512 58733 Z= 0.255 Chirality : 0.041 0.229 6636 Planarity : 0.004 0.058 7320 Dihedral : 11.376 140.198 6489 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.98 % Allowed : 12.84 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.12), residues: 5092 helix: 1.74 (0.12), residues: 1895 sheet: 0.36 (0.19), residues: 745 loop : -0.08 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 197 HIS 0.006 0.001 HIS A 427 PHE 0.019 0.001 PHE O 217 TYR 0.014 0.001 TYR J 44 ARG 0.009 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 508 time to evaluate : 4.818 Fit side-chains REVERT: A 361 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7663 (mm-40) REVERT: A 658 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.6929 (mm110) REVERT: A 784 GLU cc_start: 0.7011 (tp30) cc_final: 0.6661 (tp30) REVERT: A 819 SER cc_start: 0.8466 (t) cc_final: 0.8150 (m) REVERT: A 909 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.7950 (t0) REVERT: A 1210 THR cc_start: 0.8085 (m) cc_final: 0.7869 (m) REVERT: A 1264 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7479 (ttt180) REVERT: A 1294 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7519 (pp) REVERT: B 171 MET cc_start: 0.7648 (mmt) cc_final: 0.7325 (mtp) REVERT: B 239 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7858 (mtpt) REVERT: B 250 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 281 ASP cc_start: 0.7215 (m-30) cc_final: 0.6772 (m-30) REVERT: B 628 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7159 (ttm-80) REVERT: B 631 LEU cc_start: 0.8070 (mt) cc_final: 0.7863 (mt) REVERT: B 639 ASP cc_start: 0.7004 (t70) cc_final: 0.6750 (t0) REVERT: B 882 ASP cc_start: 0.7016 (t0) cc_final: 0.6677 (t0) REVERT: B 958 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: C 9 TYR cc_start: 0.8632 (p90) cc_final: 0.8289 (p90) REVERT: C 38 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7903 (ttpp) REVERT: E 169 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7577 (mtt180) REVERT: G 167 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5619 (mp0) REVERT: H 55 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7513 (pp) REVERT: M 133 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: M 261 LYS cc_start: 0.7537 (tmmt) cc_final: 0.7199 (tppt) REVERT: M 282 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7263 (t) REVERT: O 183 MET cc_start: 0.7256 (tpp) cc_final: 0.6884 (mmp) REVERT: O 317 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7120 (mpt-90) REVERT: O 343 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7143 (mppt) REVERT: O 542 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6848 (mmm160) REVERT: O 629 MET cc_start: 0.6762 (mmp) cc_final: 0.6453 (mpp) REVERT: P 308 GLU cc_start: 0.7507 (mp0) cc_final: 0.7114 (mm-30) REVERT: P 309 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (t) REVERT: P 314 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6241 (mt-10) outliers start: 90 outliers final: 34 residues processed: 555 average time/residue: 1.6848 time to fit residues: 1142.4494 Evaluate side-chains 537 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 485 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 958 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 353 GLU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain P residue 309 VAL Chi-restraints excluded: chain P residue 314 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 3.9990 chunk 446 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 496 optimal weight: 3.9990 chunk 412 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 8 ASN D 61 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43278 Z= 0.265 Angle : 0.522 10.998 58733 Z= 0.271 Chirality : 0.043 0.232 6636 Planarity : 0.004 0.052 7320 Dihedral : 11.406 140.226 6489 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.33 % Allowed : 13.25 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 5092 helix: 1.72 (0.12), residues: 1893 sheet: 0.27 (0.19), residues: 757 loop : -0.08 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.021 0.001 PHE A 610 TYR 0.018 0.001 TYR J 44 ARG 0.010 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 508 time to evaluate : 4.961 Fit side-chains REVERT: A 361 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7681 (mm-40) REVERT: A 658 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.6965 (mm110) REVERT: A 714 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 784 GLU cc_start: 0.6991 (tp30) cc_final: 0.6605 (tp30) REVERT: A 819 SER cc_start: 0.8480 (t) cc_final: 0.8156 (m) REVERT: A 843 GLN cc_start: 0.7956 (pm20) cc_final: 0.7517 (pm20) REVERT: A 890 MET cc_start: 0.7663 (tpp) cc_final: 0.7420 (tpp) REVERT: A 909 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.7942 (t0) REVERT: A 1155 ARG cc_start: 0.7124 (tpp80) cc_final: 0.6877 (mtp85) REVERT: A 1173 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7409 (t) REVERT: A 1187 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6961 (ttt-90) REVERT: A 1189 ASP cc_start: 0.6691 (t0) cc_final: 0.6415 (t0) REVERT: A 1210 THR cc_start: 0.8107 (m) cc_final: 0.7889 (m) REVERT: A 1264 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7499 (ttt180) REVERT: A 1294 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7560 (pp) REVERT: B 109 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7290 (mtmm) REVERT: B 171 MET cc_start: 0.7680 (mmt) cc_final: 0.7288 (mmt) REVERT: B 239 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7877 (mtpt) REVERT: B 250 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: B 281 ASP cc_start: 0.7227 (m-30) cc_final: 0.6763 (m-30) REVERT: B 470 MET cc_start: 0.7932 (mpp) cc_final: 0.7725 (mmm) REVERT: B 628 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.7164 (ttm-80) REVERT: B 639 ASP cc_start: 0.7012 (t70) cc_final: 0.6768 (t0) REVERT: B 882 ASP cc_start: 0.7040 (t0) cc_final: 0.6690 (t0) REVERT: C 9 TYR cc_start: 0.8653 (p90) cc_final: 0.8279 (p90) REVERT: C 38 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7911 (ttpp) REVERT: E 169 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7621 (mtt180) REVERT: G 84 ILE cc_start: 0.8503 (pt) cc_final: 0.8265 (pp) REVERT: G 114 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.7015 (pmm) REVERT: G 167 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5694 (mp0) REVERT: H 55 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7475 (pp) REVERT: M 133 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7302 (mptt) REVERT: M 261 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7224 (tppt) REVERT: M 280 ASN cc_start: 0.7112 (m110) cc_final: 0.6885 (p0) REVERT: M 282 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7276 (t) REVERT: N 312 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6691 (ttp-170) REVERT: O 183 MET cc_start: 0.7283 (tpp) cc_final: 0.6910 (mmp) REVERT: O 317 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7097 (mpt-90) REVERT: O 343 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7169 (mppt) REVERT: O 542 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6874 (mmm160) REVERT: O 629 MET cc_start: 0.6736 (mmp) cc_final: 0.6429 (mpp) REVERT: P 308 GLU cc_start: 0.7515 (mp0) cc_final: 0.7127 (mm-30) REVERT: P 309 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8061 (t) REVERT: P 314 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6429 (tt0) outliers start: 106 outliers final: 48 residues processed: 560 average time/residue: 1.7180 time to fit residues: 1174.5280 Evaluate side-chains 572 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 501 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 309 VAL Chi-restraints excluded: chain P residue 314 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 494 optimal weight: 9.9990 chunk 309 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 8 ASN D 61 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 43278 Z= 0.273 Angle : 0.519 9.309 58733 Z= 0.270 Chirality : 0.043 0.234 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.403 140.205 6489 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.40 % Allowed : 13.91 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 5092 helix: 1.67 (0.12), residues: 1905 sheet: 0.28 (0.19), residues: 752 loop : -0.08 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.021 0.001 PHE A 610 TYR 0.017 0.001 TYR J 44 ARG 0.010 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 506 time to evaluate : 5.117 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7685 (mm-40) REVERT: A 658 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6987 (mm110) REVERT: A 714 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 784 GLU cc_start: 0.7009 (tp30) cc_final: 0.6621 (tp30) REVERT: A 819 SER cc_start: 0.8472 (t) cc_final: 0.8162 (m) REVERT: A 843 GLN cc_start: 0.7960 (pm20) cc_final: 0.7547 (pm20) REVERT: A 1155 ARG cc_start: 0.7115 (tpp80) cc_final: 0.6878 (mtp85) REVERT: A 1173 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7402 (t) REVERT: A 1187 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6961 (ttt-90) REVERT: A 1189 ASP cc_start: 0.6689 (t0) cc_final: 0.6383 (t0) REVERT: A 1210 THR cc_start: 0.8094 (m) cc_final: 0.7880 (m) REVERT: A 1264 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7394 (ttt180) REVERT: A 1294 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7556 (pp) REVERT: A 1380 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7787 (mtp-110) REVERT: B 109 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7313 (mtmm) REVERT: B 171 MET cc_start: 0.7663 (mmt) cc_final: 0.7261 (mmt) REVERT: B 239 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7883 (mtpt) REVERT: B 250 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: B 281 ASP cc_start: 0.7229 (m-30) cc_final: 0.6772 (m-30) REVERT: B 470 MET cc_start: 0.7891 (mpp) cc_final: 0.7648 (mmm) REVERT: B 628 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.7168 (ttm-80) REVERT: B 639 ASP cc_start: 0.6923 (t70) cc_final: 0.6687 (t0) REVERT: B 882 ASP cc_start: 0.7045 (t0) cc_final: 0.6691 (t0) REVERT: C 9 TYR cc_start: 0.8666 (p90) cc_final: 0.8280 (p90) REVERT: C 38 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7913 (ttpp) REVERT: C 128 ASP cc_start: 0.7459 (p0) cc_final: 0.7131 (p0) REVERT: D 107 MET cc_start: 0.6687 (mmp) cc_final: 0.6467 (tpp) REVERT: E 169 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7597 (mtt180) REVERT: G 84 ILE cc_start: 0.8493 (pt) cc_final: 0.8240 (pp) REVERT: G 101 LEU cc_start: 0.7579 (mt) cc_final: 0.7372 (mp) REVERT: G 114 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6893 (pmm) REVERT: G 167 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5691 (mp0) REVERT: H 55 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7491 (pp) REVERT: M 261 LYS cc_start: 0.7506 (tmmt) cc_final: 0.7178 (tppt) REVERT: M 280 ASN cc_start: 0.7113 (m110) cc_final: 0.6901 (p0) REVERT: M 282 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7255 (t) REVERT: N 312 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6687 (ttp-170) REVERT: O 183 MET cc_start: 0.7311 (tpp) cc_final: 0.6933 (mmp) REVERT: O 317 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7249 (mpt-90) REVERT: O 343 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7172 (mppt) REVERT: O 542 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6894 (mmm160) REVERT: O 629 MET cc_start: 0.6728 (mmp) cc_final: 0.6425 (mpp) REVERT: P 308 GLU cc_start: 0.7494 (mp0) cc_final: 0.7089 (mm-30) REVERT: P 309 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8061 (t) outliers start: 109 outliers final: 53 residues processed: 563 average time/residue: 1.7373 time to fit residues: 1198.0501 Evaluate side-chains 573 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 500 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 239 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 722 ASP Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain K residue 142 MET Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 353 GLU Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 336 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 388 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 8 ASN D 61 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 43278 Z= 0.476 Angle : 0.599 10.027 58733 Z= 0.308 Chirality : 0.047 0.239 6636 Planarity : 0.005 0.063 7320 Dihedral : 11.498 140.390 6489 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.35 % Allowed : 14.13 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.12), residues: 5092 helix: 1.42 (0.12), residues: 1916 sheet: 0.16 (0.19), residues: 769 loop : -0.19 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 201 HIS 0.010 0.001 HIS A 427 PHE 0.029 0.002 PHE A 610 TYR 0.021 0.002 TYR J 44 ARG 0.012 0.001 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 512 time to evaluate : 4.792 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: A 784 GLU cc_start: 0.7072 (tp30) cc_final: 0.6648 (tp30) REVERT: A 819 SER cc_start: 0.8465 (t) cc_final: 0.8151 (m) REVERT: A 1155 ARG cc_start: 0.7181 (tpp80) cc_final: 0.6928 (mtp85) REVERT: A 1173 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7550 (t) REVERT: A 1187 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6986 (ttt-90) REVERT: A 1189 ASP cc_start: 0.6822 (t0) cc_final: 0.6518 (t0) REVERT: A 1210 THR cc_start: 0.8115 (m) cc_final: 0.7894 (m) REVERT: A 1264 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7526 (ttt180) REVERT: A 1294 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7646 (pp) REVERT: B 109 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7363 (mtmm) REVERT: B 250 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: B 281 ASP cc_start: 0.7299 (m-30) cc_final: 0.6819 (m-30) REVERT: B 470 MET cc_start: 0.8014 (mpp) cc_final: 0.7744 (mmm) REVERT: B 628 ARG cc_start: 0.7341 (ttp-110) cc_final: 0.7127 (ttm-80) REVERT: B 639 ASP cc_start: 0.7085 (t70) cc_final: 0.6834 (t0) REVERT: B 882 ASP cc_start: 0.7066 (t0) cc_final: 0.6705 (t0) REVERT: C 9 TYR cc_start: 0.8711 (p90) cc_final: 0.8369 (p90) REVERT: C 38 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7927 (ttpp) REVERT: C 128 ASP cc_start: 0.7400 (p0) cc_final: 0.7121 (p0) REVERT: E 169 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7706 (mtt180) REVERT: G 84 ILE cc_start: 0.8570 (pt) cc_final: 0.8306 (pp) REVERT: G 114 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6891 (pmm) REVERT: G 167 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5705 (mp0) REVERT: H 55 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7516 (pp) REVERT: J 66 LEU cc_start: 0.8567 (mp) cc_final: 0.8316 (mp) REVERT: M 261 LYS cc_start: 0.7524 (tmmt) cc_final: 0.7197 (tppt) REVERT: M 280 ASN cc_start: 0.7225 (m110) cc_final: 0.6958 (p0) REVERT: M 282 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7315 (t) REVERT: N 312 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6686 (ttp-170) REVERT: O 183 MET cc_start: 0.7387 (tpp) cc_final: 0.6999 (mmp) REVERT: O 317 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7171 (mpt-90) REVERT: O 343 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7193 (mppt) REVERT: O 542 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.6903 (mmm160) REVERT: O 629 MET cc_start: 0.6713 (mmp) cc_final: 0.6404 (mpp) REVERT: O 653 MET cc_start: 0.7211 (mmt) cc_final: 0.4830 (mmt) REVERT: P 308 GLU cc_start: 0.7482 (mp0) cc_final: 0.7092 (mm-30) outliers start: 107 outliers final: 56 residues processed: 570 average time/residue: 1.7100 time to fit residues: 1196.0831 Evaluate side-chains 576 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 504 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 381 LEU Chi-restraints excluded: chain O residue 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain P residue 216 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 0.0970 chunk 473 optimal weight: 3.9990 chunk 432 optimal weight: 0.8980 chunk 460 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 361 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 416 optimal weight: 5.9990 chunk 435 optimal weight: 0.4980 chunk 459 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 61 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43278 Z= 0.193 Angle : 0.510 11.970 58733 Z= 0.266 Chirality : 0.042 0.221 6636 Planarity : 0.004 0.060 7320 Dihedral : 11.379 139.949 6489 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.76 % Allowed : 14.90 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.12), residues: 5092 helix: 1.69 (0.12), residues: 1905 sheet: 0.18 (0.19), residues: 754 loop : -0.11 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 201 HIS 0.005 0.001 HIS A 427 PHE 0.020 0.001 PHE O 217 TYR 0.014 0.001 TYR J 44 ARG 0.013 0.000 ARG O 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 497 time to evaluate : 4.579 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7669 (mm-40) REVERT: A 784 GLU cc_start: 0.7072 (tp30) cc_final: 0.6665 (tp30) REVERT: A 819 SER cc_start: 0.8467 (t) cc_final: 0.8146 (m) REVERT: A 885 MET cc_start: 0.7525 (ttm) cc_final: 0.7235 (ttp) REVERT: A 1039 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.4614 (mt) REVERT: A 1155 ARG cc_start: 0.7099 (tpp80) cc_final: 0.6863 (mtp85) REVERT: A 1173 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7422 (t) REVERT: A 1189 ASP cc_start: 0.6692 (t0) cc_final: 0.6379 (t0) REVERT: A 1210 THR cc_start: 0.8090 (m) cc_final: 0.7877 (m) REVERT: A 1264 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: A 1294 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7541 (pp) REVERT: A 1337 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7503 (mtm180) REVERT: B 250 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 281 ASP cc_start: 0.7228 (m-30) cc_final: 0.6769 (m-30) REVERT: B 628 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.7099 (ttm-80) REVERT: B 639 ASP cc_start: 0.6922 (t70) cc_final: 0.6685 (t0) REVERT: B 882 ASP cc_start: 0.6989 (t0) cc_final: 0.6631 (t0) REVERT: C 9 TYR cc_start: 0.8677 (p90) cc_final: 0.8282 (p90) REVERT: C 38 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7914 (ttpp) REVERT: C 128 ASP cc_start: 0.7410 (p0) cc_final: 0.7168 (p0) REVERT: D 131 MET cc_start: 0.6747 (tpt) cc_final: 0.6227 (tpt) REVERT: E 36 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7265 (mp0) REVERT: E 169 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7601 (mtt180) REVERT: G 84 ILE cc_start: 0.8512 (pt) cc_final: 0.8269 (pp) REVERT: G 114 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6647 (pmm) REVERT: G 167 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5609 (mp0) REVERT: M 132 ASN cc_start: 0.7233 (t0) cc_final: 0.6971 (t0) REVERT: M 261 LYS cc_start: 0.7537 (tmmt) cc_final: 0.7237 (tppt) REVERT: M 280 ASN cc_start: 0.7095 (m110) cc_final: 0.6872 (m110) REVERT: M 282 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7334 (t) REVERT: N 312 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6696 (ttp-170) REVERT: O 183 MET cc_start: 0.7300 (tpp) cc_final: 0.6925 (mmp) REVERT: O 317 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7377 (mpt-90) REVERT: O 343 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7100 (mppt) REVERT: O 542 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6854 (mmm160) REVERT: O 629 MET cc_start: 0.6716 (mmp) cc_final: 0.6423 (mpp) REVERT: P 308 GLU cc_start: 0.7435 (mp0) cc_final: 0.7030 (mm-30) outliers start: 80 outliers final: 41 residues processed: 543 average time/residue: 1.7212 time to fit residues: 1155.4529 Evaluate side-chains 547 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 492 time to evaluate : 5.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 204 SER Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 353 GLU Chi-restraints excluded: chain O residue 542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 3.9990 chunk 487 optimal weight: 7.9990 chunk 297 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 338 optimal weight: 0.8980 chunk 511 optimal weight: 4.9990 chunk 470 optimal weight: 0.8980 chunk 406 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 314 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN D 8 ASN D 61 ASN G 32 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43278 Z= 0.224 Angle : 0.523 12.779 58733 Z= 0.271 Chirality : 0.042 0.223 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.360 139.613 6489 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.47 % Allowed : 15.36 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.12), residues: 5092 helix: 1.71 (0.12), residues: 1912 sheet: 0.21 (0.19), residues: 752 loop : -0.08 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 201 HIS 0.008 0.001 HIS O 152 PHE 0.023 0.001 PHE O 217 TYR 0.015 0.001 TYR J 44 ARG 0.015 0.000 ARG A 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10184 Ramachandran restraints generated. 5092 Oldfield, 0 Emsley, 5092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 506 time to evaluate : 4.874 Fit side-chains REVERT: A 361 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7670 (mm-40) REVERT: A 784 GLU cc_start: 0.7087 (tp30) cc_final: 0.6673 (tp30) REVERT: A 819 SER cc_start: 0.8474 (t) cc_final: 0.8153 (m) REVERT: A 885 MET cc_start: 0.7511 (ttm) cc_final: 0.7273 (ttp) REVERT: A 1039 LEU cc_start: 0.5680 (OUTLIER) cc_final: 0.4601 (mt) REVERT: A 1155 ARG cc_start: 0.7102 (tpp80) cc_final: 0.6862 (mtp85) REVERT: A 1173 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7415 (t) REVERT: A 1189 ASP cc_start: 0.6731 (t0) cc_final: 0.6416 (t0) REVERT: A 1210 THR cc_start: 0.8104 (m) cc_final: 0.7885 (m) REVERT: A 1264 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7393 (ttt180) REVERT: A 1294 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7543 (pp) REVERT: B 250 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: B 281 ASP cc_start: 0.7223 (m-30) cc_final: 0.6762 (m-30) REVERT: B 628 ARG cc_start: 0.7320 (ttp-110) cc_final: 0.7084 (ttm-80) REVERT: B 639 ASP cc_start: 0.6927 (t70) cc_final: 0.6688 (t0) REVERT: B 882 ASP cc_start: 0.7016 (t0) cc_final: 0.6662 (t0) REVERT: C 9 TYR cc_start: 0.8674 (p90) cc_final: 0.8278 (p90) REVERT: C 38 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7913 (ttpp) REVERT: C 77 SER cc_start: 0.8158 (t) cc_final: 0.7951 (m) REVERT: C 128 ASP cc_start: 0.7367 (p0) cc_final: 0.7155 (p0) REVERT: C 174 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6556 (ptt90) REVERT: D 131 MET cc_start: 0.6620 (tpt) cc_final: 0.6165 (tpt) REVERT: E 36 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7270 (mp0) REVERT: E 169 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7569 (mtt180) REVERT: G 84 ILE cc_start: 0.8497 (pt) cc_final: 0.8254 (pp) REVERT: G 114 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6681 (pmm) REVERT: G 167 GLU cc_start: 0.5903 (OUTLIER) cc_final: 0.5610 (mp0) REVERT: H 78 SER cc_start: 0.8348 (t) cc_final: 0.8127 (m) REVERT: M 132 ASN cc_start: 0.7233 (t0) cc_final: 0.6976 (t0) REVERT: M 261 LYS cc_start: 0.7545 (tmmt) cc_final: 0.7232 (tppt) REVERT: M 280 ASN cc_start: 0.7193 (m110) cc_final: 0.6981 (m110) REVERT: M 282 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7337 (t) REVERT: N 312 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6704 (ttp-170) REVERT: O 183 MET cc_start: 0.7285 (tpp) cc_final: 0.6907 (mmp) REVERT: O 317 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7268 (mpt-90) REVERT: O 343 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7161 (mppt) REVERT: O 542 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6920 (mmm160) REVERT: O 629 MET cc_start: 0.6709 (mmp) cc_final: 0.6420 (mpp) REVERT: P 308 GLU cc_start: 0.7441 (mp0) cc_final: 0.7033 (mm-30) outliers start: 67 outliers final: 42 residues processed: 542 average time/residue: 1.6882 time to fit residues: 1118.0322 Evaluate side-chains 555 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 498 time to evaluate : 4.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 449 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 135 TYR Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 169 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 282 VAL Chi-restraints excluded: chain N residue 205 VAL Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 317 ARG Chi-restraints excluded: chain O residue 343 LYS Chi-restraints excluded: chain O residue 542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 0.9990 chunk 433 optimal weight: 1.9990 chunk 124 optimal weight: 0.0000 chunk 375 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 407 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 418 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN G 32 ASN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107623 restraints weight = 56501.738| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.92 r_work: 0.3328 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43278 Z= 0.179 Angle : 0.514 12.011 58733 Z= 0.265 Chirality : 0.041 0.220 6636 Planarity : 0.004 0.061 7320 Dihedral : 11.316 139.455 6489 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.56 % Allowed : 15.49 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 5092 helix: 1.80 (0.12), residues: 1906 sheet: 0.20 (0.19), residues: 760 loop : -0.04 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 201 HIS 0.008 0.001 HIS O 152 PHE 0.022 0.001 PHE O 217 TYR 0.014 0.001 TYR J 44 ARG 0.014 0.000 ARG A 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16529.14 seconds wall clock time: 297 minutes 32.65 seconds (17852.65 seconds total)