Starting phenix.real_space_refine on Tue Sep 15 17:28:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z1o_14451/09_2026/7z1o_14451.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'GLU:plan': 2} 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: {'RNAv2': 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: 9 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: 9 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: 9.06, per 1000 atoms: 0.21 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: 3.79 Conformation dependent library (CDL) restraints added in 1.6 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: 5.61 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: 12.47 Time building geometry restraints manager: 4.78 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=" C3' DT S 40 " pdb=" C2' DT S 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA S 20 " pdb=" C2' DA S 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT S 27 " pdb=" C2' DT S 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+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 ... (remaining 43273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 57881 2.34 - 4.68: 732 4.68 - 7.03: 93 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=" N3 DT T 26 " pdb=" C4 DT T 26 " pdb=" O4 DT T 26 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 58728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 25204 27.48 - 54.95: 1029 54.95 - 82.43: 102 82.43 - 109.91: 2 109.91 - 137.39: 2 Dihedral angle restraints: 26339 sinusoidal: 11316 harmonic: 15023 Sorted by residual: dihedral pdb=" C4' A R 20 " pdb=" C3' A R 20 " pdb=" C2' A R 20 " pdb=" C1' A R 20 " ideal model delta sinusoidal sigma weight residual 36.34 -35.66 72.01 1 3.10e+00 1.04e-01 6.90e+02 dihedral pdb=" O4' A R 20 " pdb=" C4' A R 20 " pdb=" C3' A R 20 " pdb=" C2' A R 20 " ideal model delta sinusoidal sigma weight residual -35.15 24.91 -60.05 1 4.00e+00 6.25e-02 3.00e+02 dihedral pdb=" O4' A R 20 " pdb=" C2' A R 20 " pdb=" C1' A R 20 " pdb=" C3' A R 20 " ideal model delta sinusoidal sigma weight residual -94.41 -35.07 -59.33 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 26336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5678 0.068 - 0.135: 904 0.135 - 0.203: 30 0.203 - 0.270: 18 0.270 - 0.338: 6 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 51.450 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 43305 Z= 0.204 Angle : 0.673 11.709 58766 Z= 0.381 Chirality : 0.048 0.338 6636 Planarity : 0.005 0.132 7320 Dihedral : 14.107 137.386 16619 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (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 ARG 0.015 0.000 ARG B 915 TYR 0.017 0.001 TYR B 416 PHE 0.027 0.001 PHE B1018 TRP 0.016 0.001 TRP A 185 HIS 0.007 0.001 HIS L 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (43278) covalent geometry : angle 0.66890 / 0.38 (58733) hydrogen bonds : bond 0.15788 / 10.80 ( 1721) hydrogen bonds : angle 6.05614 / 4.33 ( 4755) metal coordination : bond 0.00374 / 0.22 ( 27) metal coordination : angle 3.06264 / 1.59 ( 33) *********************** 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 : 1.852 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: 0.8802 time to fit residues: 630.5596 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 : 1.732 ------------------------------------------------------------------------------- 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 394 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 0.0980 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 7.9990 chunk 223 optimal weight: 0.8980 chunk 142 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 ASN A 808 GLN A 821 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN B 80 ASN B 237 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107380 restraints weight = 56976.907| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.92 r_work: 0.3334 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43305 Z= 0.190 Angle : 0.572 12.954 58766 Z= 0.297 Chirality : 0.045 0.315 6636 Planarity : 0.005 0.076 7320 Dihedral : 11.011 142.578 6322 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.25 % Allowed : 7.85 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 5092 helix: 1.25 (0.12), residues: 1898 sheet: 0.33 (0.19), residues: 718 loop : -0.27 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 915 TYR 0.016 0.001 TYR J 44 PHE 0.021 0.001 PHE B1018 TRP 0.010 0.001 TRP A 197 HIS 0.011 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (43278) covalent geometry : angle 0.56570 / 0.30 (58733) hydrogen bonds : bond 0.04441 / 3.03 ( 1721) hydrogen bonds : angle 4.67936 / 3.31 ( 4755) metal coordination : bond 0.00597 / 0.37 ( 27) metal coordination : angle 3.73119 / 1.93 ( 33) *********************** 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 586 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 529 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: A 213 ARG cc_start: 0.8296 (ttp-110) cc_final: 0.7880 (ptm-80) REVERT: A 312 MET cc_start: 0.7172 (tmm) cc_final: 0.6918 (ttt) REVERT: A 361 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: A 556 ASP cc_start: 0.7336 (t0) cc_final: 0.7123 (t0) REVERT: A 583 MET cc_start: 0.8832 (ptp) cc_final: 0.8364 (ptp) REVERT: A 658 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7869 (mm110) REVERT: A 759 GLU cc_start: 0.7607 (tp30) cc_final: 0.7395 (tp30) REVERT: A 775 GLU cc_start: 0.7341 (tp30) cc_final: 0.7030 (mm-30) REVERT: A 909 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8084 (t0) REVERT: A 915 THR cc_start: 0.8283 (m) cc_final: 0.8060 (t) REVERT: A 1210 THR cc_start: 0.7873 (m) cc_final: 0.7648 (m) REVERT: A 1409 GLU cc_start: 0.7111 (pt0) cc_final: 0.6827 (mt-10) REVERT: B 171 MET cc_start: 0.8011 (mmt) cc_final: 0.7656 (mmt) REVERT: B 250 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: B 470 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.6921 (mtm) REVERT: B 628 ARG cc_start: 0.7547 (ttp-110) cc_final: 0.7341 (ttm-80) REVERT: B 631 LEU cc_start: 0.7736 (mt) cc_final: 0.7521 (mt) REVERT: B 665 ASP cc_start: 0.8024 (t0) cc_final: 0.7731 (m-30) REVERT: B 958 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.8022 (mtt) REVERT: B 1068 ASP cc_start: 0.7199 (m-30) cc_final: 0.6995 (m-30) REVERT: C 9 TYR cc_start: 0.8849 (p90) cc_final: 0.8525 (p90) REVERT: D 51 ASN cc_start: 0.7702 (t0) cc_final: 0.7459 (t0) REVERT: E 73 PRO cc_start: 0.8350 (Cg_endo) cc_final: 0.8136 (Cg_exo) REVERT: G 75 VAL cc_start: 0.7800 (t) cc_final: 0.7492 (m) REVERT: G 114 MET cc_start: 0.7046 (mpp) cc_final: 0.6766 (ptp) REVERT: I 1 MET cc_start: 0.8037 (tpp) cc_final: 0.7785 (tpp) REVERT: K 52 GLN cc_start: 0.8373 (pp30) cc_final: 0.8001 (tm-30) REVERT: M 133 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6605 (mppt) REVERT: O 86 MET cc_start: 0.8915 (mtt) cc_final: 0.8619 (mtt) REVERT: O 144 MET cc_start: 0.6938 (ptp) cc_final: 0.6648 (ptp) REVERT: O 183 MET cc_start: 0.6879 (tpp) cc_final: 0.6571 (mmp) REVERT: O 343 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.6968 (mppt) REVERT: O 542 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7248 (mmm160) REVERT: O 554 THR cc_start: 0.8608 (p) cc_final: 0.8326 (p) REVERT: O 629 MET cc_start: 0.6956 (mmp) cc_final: 0.6635 (mpp) outliers start: 57 outliers final: 22 residues processed: 552 average time/residue: 0.8410 time to fit residues: 564.4058 Evaluate side-chains 528 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 497 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 658 GLN Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1165 LEU 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 324 ILE Chi-restraints excluded: chain B residue 470 MET 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 796 LYS Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 958 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 K residue 139 ILE Chi-restraints excluded: chain M residue 116 SER Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain O residue 204 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 289 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 293 optimal weight: 0.0570 chunk 417 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 324 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 434 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN B 550 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 71 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.139003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108376 restraints weight = 56805.374| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.87 r_work: 0.3344 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43305 Z= 0.135 Angle : 0.521 12.096 58766 Z= 0.270 Chirality : 0.043 0.296 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.014 141.721 6319 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.34 % Allowed : 10.13 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.12), residues: 5092 helix: 1.55 (0.12), residues: 1889 sheet: 0.39 (0.19), residues: 728 loop : -0.19 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 874 TYR 0.016 0.001 TYR J 44 PHE 0.020 0.001 PHE B 678 TRP 0.011 0.001 TRP A 197 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (43278) covalent geometry : angle 0.51461 / 0.27 (58733) hydrogen bonds : bond 0.03929 / 2.66 ( 1721) hydrogen bonds : angle 4.47734 / 3.16 ( 4755) metal coordination : bond 0.00508 / 0.31 ( 27) metal coordination : angle 3.37217 / 1.72 ( 33) *********************** 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 555 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 494 time to evaluate : 1.686 Fit side-chains REVERT: A 216 LYS cc_start: 0.7806 (pttm) cc_final: 0.7557 (mtmm) REVERT: A 312 MET cc_start: 0.7142 (tmm) cc_final: 0.6900 (ttt) REVERT: A 556 ASP cc_start: 0.7384 (t0) cc_final: 0.7134 (t0) REVERT: A 583 MET cc_start: 0.8848 (ptp) cc_final: 0.8640 (ptp) REVERT: A 658 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7794 (mm110) REVERT: A 759 GLU cc_start: 0.7573 (tp30) cc_final: 0.7306 (tp30) REVERT: A 763 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 775 GLU cc_start: 0.7269 (tp30) cc_final: 0.6957 (mm-30) REVERT: A 784 GLU cc_start: 0.7604 (tp30) cc_final: 0.7359 (tp30) REVERT: A 909 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8062 (t0) REVERT: A 915 THR cc_start: 0.8298 (m) cc_final: 0.8074 (t) REVERT: A 1210 THR cc_start: 0.7734 (m) cc_final: 0.7530 (m) REVERT: A 1337 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7875 (mtm180) REVERT: B 171 MET cc_start: 0.7906 (mmt) cc_final: 0.7562 (mmt) REVERT: B 250 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: B 628 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7190 (ttm-80) REVERT: B 665 ASP cc_start: 0.7979 (t0) cc_final: 0.7685 (m-30) REVERT: B 882 ASP cc_start: 0.7902 (t0) cc_final: 0.7593 (t0) REVERT: C 9 TYR cc_start: 0.8827 (p90) cc_final: 0.8477 (p90) REVERT: D 51 ASN cc_start: 0.7659 (t0) cc_final: 0.7414 (t0) REVERT: E 73 PRO cc_start: 0.8440 (Cg_endo) cc_final: 0.8233 (Cg_exo) REVERT: E 169 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8141 (mtt180) REVERT: G 75 VAL cc_start: 0.7751 (t) cc_final: 0.7416 (m) REVERT: G 114 MET cc_start: 0.7100 (mpp) cc_final: 0.6776 (ptp) REVERT: G 167 GLU cc_start: 0.5771 (OUTLIER) cc_final: 0.5421 (mp0) REVERT: I 1 MET cc_start: 0.8049 (tpp) cc_final: 0.7742 (tpp) REVERT: M 166 MET cc_start: 0.7396 (tpt) cc_final: 0.7169 (mmm) REVERT: O 144 MET cc_start: 0.6868 (ptp) cc_final: 0.6579 (ptp) REVERT: O 343 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.6912 (mppt) REVERT: O 542 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7195 (mmm160) REVERT: O 554 THR cc_start: 0.8566 (p) cc_final: 0.8251 (p) REVERT: O 628 LYS cc_start: 0.7054 (tptp) cc_final: 0.6757 (ttmm) REVERT: O 629 MET cc_start: 0.6903 (mmp) cc_final: 0.6507 (mpp) REVERT: P 308 GLU cc_start: 0.7922 (mp0) cc_final: 0.7273 (mm-30) outliers start: 61 outliers final: 20 residues processed: 519 average time/residue: 0.8261 time to fit residues: 522.4369 Evaluate side-chains 506 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 479 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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 658 GLN Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1413 GLU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 886 MET Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1119 MET Chi-restraints excluded: chain C residue 77 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 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 233 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 435 optimal weight: 0.7980 chunk 354 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 503 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** D 71 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108455 restraints weight = 56625.464| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.86 r_work: 0.3345 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43305 Z= 0.129 Angle : 0.509 11.594 58766 Z= 0.263 Chirality : 0.042 0.283 6636 Planarity : 0.004 0.058 7320 Dihedral : 11.026 139.344 6317 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 11.21 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 5092 helix: 1.68 (0.12), residues: 1891 sheet: 0.41 (0.19), residues: 725 loop : -0.12 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.016 0.001 TYR J 44 PHE 0.019 0.001 PHE B 678 TRP 0.011 0.001 TRP A 197 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (43278) covalent geometry : angle 0.50277 / 0.26 (58733) hydrogen bonds : bond 0.03671 / 2.48 ( 1721) hydrogen bonds : angle 4.35385 / 3.07 ( 4755) metal coordination : bond 0.00487 / 0.30 ( 27) metal coordination : angle 3.29685 / 1.71 ( 33) *********************** 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 582 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 510 time to evaluate : 1.656 Fit side-chains REVERT: A 312 MET cc_start: 0.7104 (tmm) cc_final: 0.6893 (ttt) REVERT: A 361 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7998 (mm-40) REVERT: A 556 ASP cc_start: 0.7370 (t0) cc_final: 0.7119 (t0) REVERT: A 697 MET cc_start: 0.8437 (tmm) cc_final: 0.8192 (ttp) REVERT: A 759 GLU cc_start: 0.7534 (tp30) cc_final: 0.7251 (tp30) REVERT: A 763 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6941 (mm-30) REVERT: A 775 GLU cc_start: 0.7240 (tp30) cc_final: 0.6934 (mm-30) REVERT: A 784 GLU cc_start: 0.7606 (tp30) cc_final: 0.7317 (tp30) REVERT: A 819 SER cc_start: 0.8617 (t) cc_final: 0.8324 (m) REVERT: A 909 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8060 (t0) REVERT: A 915 THR cc_start: 0.8336 (m) cc_final: 0.8121 (t) REVERT: A 1158 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7330 (ttmm) REVERT: B 250 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 281 ASP cc_start: 0.7512 (m-30) cc_final: 0.7060 (m-30) REVERT: B 628 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.7197 (ttm-80) REVERT: B 639 ASP cc_start: 0.7391 (t70) cc_final: 0.7008 (t0) REVERT: B 665 ASP cc_start: 0.7984 (t0) cc_final: 0.7666 (m-30) REVERT: B 882 ASP cc_start: 0.7884 (t0) cc_final: 0.7570 (t0) REVERT: C 9 TYR cc_start: 0.8824 (p90) cc_final: 0.8515 (p90) REVERT: D 51 ASN cc_start: 0.7646 (t0) cc_final: 0.7405 (t0) REVERT: E 66 GLU cc_start: 0.6740 (mp0) cc_final: 0.6215 (mp0) REVERT: E 73 PRO cc_start: 0.8405 (Cg_endo) cc_final: 0.8197 (Cg_exo) REVERT: E 169 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8082 (mtt180) REVERT: G 16 ASP cc_start: 0.8200 (p0) cc_final: 0.7962 (p0) REVERT: G 75 VAL cc_start: 0.7774 (t) cc_final: 0.7424 (m) REVERT: G 114 MET cc_start: 0.7128 (mpp) cc_final: 0.6803 (ptp) REVERT: G 167 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5364 (mp0) REVERT: H 25 ARG cc_start: 0.8567 (ttp-170) cc_final: 0.8155 (ttm-80) REVERT: I 1 MET cc_start: 0.8062 (tpp) cc_final: 0.7685 (tpp) REVERT: M 261 LYS cc_start: 0.7353 (tmmm) cc_final: 0.6990 (tppt) REVERT: O 144 MET cc_start: 0.6926 (ptp) cc_final: 0.6603 (ptp) REVERT: O 343 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.6958 (mppt) REVERT: O 542 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7212 (mmm160) REVERT: O 554 THR cc_start: 0.8558 (p) cc_final: 0.8234 (p) REVERT: O 628 LYS cc_start: 0.7045 (tptp) cc_final: 0.6755 (ttmm) REVERT: O 629 MET cc_start: 0.6948 (mmp) cc_final: 0.6566 (mpp) REVERT: P 308 GLU cc_start: 0.7893 (mp0) cc_final: 0.7247 (mm-30) outliers start: 72 outliers final: 28 residues processed: 545 average time/residue: 0.7809 time to fit residues: 520.1116 Evaluate side-chains 524 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 488 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1295 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 215 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 562 ILE 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 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 G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 8 ASP 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 Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain P residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 414 optimal weight: 9.9990 chunk 450 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 340 optimal weight: 0.0970 chunk 139 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 400 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 81 optimal weight: 0.0010 chunk 328 optimal weight: 1.9990 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1262 GLN B 837 GLN C 200 GLN D 61 ASN J 64 ASN O 143 GLN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106725 restraints weight = 56453.478| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.97 r_work: 0.3323 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43305 Z= 0.182 Angle : 0.539 12.311 58766 Z= 0.277 Chirality : 0.044 0.287 6636 Planarity : 0.004 0.066 7320 Dihedral : 11.082 139.172 6317 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.07 % Allowed : 12.15 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 5092 helix: 1.65 (0.12), residues: 1893 sheet: 0.37 (0.19), residues: 743 loop : -0.10 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 213 TYR 0.018 0.001 TYR J 44 PHE 0.021 0.001 PHE A 610 TRP 0.010 0.001 TRP A 197 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (43278) covalent geometry : angle 0.53177 / 0.28 (58733) hydrogen bonds : bond 0.03963 / 2.68 ( 1721) hydrogen bonds : angle 4.36859 / 3.08 ( 4755) metal coordination : bond 0.00677 / 0.43 ( 27) metal coordination : angle 3.74954 / 1.95 ( 33) *********************** 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 604 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 510 time to evaluate : 1.657 Fit side-chains REVERT: A 361 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: A 556 ASP cc_start: 0.7411 (t0) cc_final: 0.7154 (t0) REVERT: A 759 GLU cc_start: 0.7602 (tp30) cc_final: 0.7322 (tp30) REVERT: A 775 GLU cc_start: 0.7294 (tp30) cc_final: 0.6994 (mm-30) REVERT: A 784 GLU cc_start: 0.7672 (tp30) cc_final: 0.7335 (tp30) REVERT: A 843 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 909 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8067 (t0) REVERT: A 915 THR cc_start: 0.8404 (m) cc_final: 0.8174 (t) REVERT: A 1158 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7447 (ttmm) REVERT: A 1173 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7588 (t) REVERT: A 1380 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7039 (mmp-170) REVERT: B 109 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7184 (mtmm) REVERT: B 239 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7989 (mtpt) REVERT: B 250 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: B 281 ASP cc_start: 0.7598 (m-30) cc_final: 0.7135 (m-30) REVERT: B 628 ARG cc_start: 0.7524 (ttp-110) cc_final: 0.7261 (ttm-80) REVERT: B 631 LEU cc_start: 0.7814 (mt) cc_final: 0.7603 (mt) REVERT: B 639 ASP cc_start: 0.7513 (t70) cc_final: 0.7134 (t0) REVERT: B 665 ASP cc_start: 0.8047 (t0) cc_final: 0.7763 (m-30) REVERT: B 882 ASP cc_start: 0.7886 (t0) cc_final: 0.7549 (t0) REVERT: C 9 TYR cc_start: 0.8855 (p90) cc_final: 0.8527 (p90) REVERT: C 77 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (m) REVERT: C 201 GLU cc_start: 0.7846 (tt0) cc_final: 0.7573 (tt0) REVERT: D 51 ASN cc_start: 0.7656 (t0) cc_final: 0.7420 (t0) REVERT: E 66 GLU cc_start: 0.6684 (mp0) cc_final: 0.6287 (mp0) REVERT: E 73 PRO cc_start: 0.8436 (Cg_endo) cc_final: 0.8226 (Cg_exo) REVERT: E 169 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8085 (mtt180) REVERT: G 16 ASP cc_start: 0.8175 (p0) cc_final: 0.7962 (p0) REVERT: G 101 LEU cc_start: 0.7558 (mt) cc_final: 0.7355 (mt) REVERT: G 114 MET cc_start: 0.7191 (mpp) cc_final: 0.6877 (ptp) REVERT: G 167 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5349 (mp0) REVERT: H 25 ARG cc_start: 0.8619 (ttp-170) cc_final: 0.8236 (ttm-80) REVERT: H 55 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7515 (pp) REVERT: I 1 MET cc_start: 0.8222 (tpp) cc_final: 0.7842 (tpp) REVERT: M 261 LYS cc_start: 0.7405 (tmmm) cc_final: 0.7015 (tppt) REVERT: N 367 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7939 (pmmt) REVERT: O 86 MET cc_start: 0.8873 (mtm) cc_final: 0.8662 (mtt) REVERT: O 144 MET cc_start: 0.6993 (ptp) cc_final: 0.6626 (ptp) REVERT: O 153 LYS cc_start: 0.6922 (tptt) cc_final: 0.6665 (tptt) REVERT: O 317 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7001 (mpt-90) REVERT: O 343 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7046 (mppt) REVERT: O 542 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7273 (mmm160) REVERT: O 554 THR cc_start: 0.8558 (p) cc_final: 0.8223 (p) REVERT: O 628 LYS cc_start: 0.7126 (tptp) cc_final: 0.6878 (ttmt) REVERT: O 629 MET cc_start: 0.7053 (mmp) cc_final: 0.6715 (mpp) REVERT: P 308 GLU cc_start: 0.7968 (mp0) cc_final: 0.7382 (mm-30) outliers start: 94 outliers final: 36 residues processed: 549 average time/residue: 0.7942 time to fit residues: 532.5490 Evaluate side-chains 546 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 494 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1158 LYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1361 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 A residue 1413 GLU Chi-restraints excluded: chain B residue 78 LYS 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 324 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 562 ILE 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 C residue 77 SER Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 92 LYS 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 G residue 85 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 167 GLU 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 N residue 311 THR 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 507 LEU Chi-restraints excluded: chain O residue 542 ARG Chi-restraints excluded: chain O residue 596 LYS Chi-restraints excluded: chain Q residue 134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 395 optimal weight: 1.9990 chunk 229 optimal weight: 0.0770 chunk 466 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 397 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 324 optimal weight: 0.9980 chunk 448 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 478 optimal weight: 10.0000 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 = 0.3865 r_free = 0.3865 target = 0.137320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106636 restraints weight = 56794.986| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.88 r_work: 0.3324 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43305 Z= 0.175 Angle : 0.537 12.427 58766 Z= 0.275 Chirality : 0.043 0.286 6636 Planarity : 0.004 0.057 7320 Dihedral : 11.079 139.029 6317 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.96 % Allowed : 13.10 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 5092 helix: 1.67 (0.12), residues: 1892 sheet: 0.31 (0.19), residues: 751 loop : -0.10 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 213 TYR 0.016 0.001 TYR J 44 PHE 0.021 0.001 PHE A 610 TRP 0.010 0.001 TRP A 197 HIS 0.008 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (43278) covalent geometry : angle 0.52995 / 0.28 (58733) hydrogen bonds : bond 0.03884 / 2.62 ( 1721) hydrogen bonds : angle 4.35672 / 3.07 ( 4755) metal coordination : bond 0.00638 / 0.40 ( 27) metal coordination : angle 3.79461 / 1.97 ( 33) *********************** 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 597 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 508 time to evaluate : 1.662 Fit side-chains REVERT: A 361 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: A 556 ASP cc_start: 0.7377 (t0) cc_final: 0.7149 (t0) REVERT: A 697 MET cc_start: 0.8492 (tmm) cc_final: 0.8194 (ttp) REVERT: A 759 GLU cc_start: 0.7601 (tp30) cc_final: 0.7336 (tp30) REVERT: A 784 GLU cc_start: 0.7653 (tp30) cc_final: 0.7299 (tp30) REVERT: A 843 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: A 915 THR cc_start: 0.8409 (m) cc_final: 0.8188 (t) REVERT: A 1155 ARG cc_start: 0.7321 (tpp80) cc_final: 0.7085 (mtp85) REVERT: A 1264 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7700 (ttt180) REVERT: A 1380 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7062 (mmp-170) REVERT: B 171 MET cc_start: 0.7949 (mmt) cc_final: 0.7648 (mtp) REVERT: B 239 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7929 (mtpt) REVERT: B 250 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: B 269 MET cc_start: 0.7907 (tpp) cc_final: 0.7620 (ttm) REVERT: B 281 ASP cc_start: 0.7610 (m-30) cc_final: 0.7144 (m-30) REVERT: B 628 ARG cc_start: 0.7545 (ttp-110) cc_final: 0.7279 (ttm-80) REVERT: B 631 LEU cc_start: 0.7837 (mt) cc_final: 0.7628 (mt) REVERT: B 639 ASP cc_start: 0.7531 (t70) cc_final: 0.7168 (t0) REVERT: B 665 ASP cc_start: 0.8069 (t0) cc_final: 0.7805 (m-30) REVERT: B 882 ASP cc_start: 0.7843 (t0) cc_final: 0.7510 (t0) REVERT: C 9 TYR cc_start: 0.8863 (p90) cc_final: 0.8526 (p90) REVERT: C 176 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7715 (p) REVERT: C 201 GLU cc_start: 0.7837 (tt0) cc_final: 0.7577 (tt0) REVERT: D 51 ASN cc_start: 0.7634 (t0) cc_final: 0.7404 (t0) REVERT: E 66 GLU cc_start: 0.6758 (mp0) cc_final: 0.6340 (mp0) REVERT: E 73 PRO cc_start: 0.8444 (Cg_endo) cc_final: 0.8229 (Cg_exo) REVERT: E 169 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8059 (mtt180) REVERT: G 16 ASP cc_start: 0.8161 (p0) cc_final: 0.7946 (p0) REVERT: G 84 ILE cc_start: 0.8497 (pt) cc_final: 0.8270 (pp) REVERT: G 101 LEU cc_start: 0.7621 (mt) cc_final: 0.7412 (mt) REVERT: G 114 MET cc_start: 0.7260 (mpp) cc_final: 0.6952 (ptp) REVERT: G 167 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5389 (mp0) REVERT: H 25 ARG cc_start: 0.8614 (ttp-170) cc_final: 0.8224 (ttm-80) REVERT: H 55 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7510 (pp) REVERT: I 1 MET cc_start: 0.8274 (tpp) cc_final: 0.7828 (tpp) REVERT: M 261 LYS cc_start: 0.7450 (tmmm) cc_final: 0.7053 (tppt) REVERT: M 282 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7391 (t) REVERT: O 144 MET cc_start: 0.7058 (ptp) cc_final: 0.6670 (ptp) REVERT: O 317 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6981 (mpt-90) REVERT: O 343 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7076 (mppt) REVERT: O 542 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7269 (mmm160) REVERT: O 554 THR cc_start: 0.8573 (p) cc_final: 0.8278 (p) REVERT: O 628 LYS cc_start: 0.7157 (tptp) cc_final: 0.6925 (ttmt) REVERT: O 629 MET cc_start: 0.7066 (mmp) cc_final: 0.6737 (mpp) REVERT: P 308 GLU cc_start: 0.7929 (mp0) cc_final: 0.7410 (mm-30) REVERT: P 309 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8069 (t) REVERT: P 314 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6390 (mt-10) outliers start: 89 outliers final: 41 residues processed: 553 average time/residue: 0.7954 time to fit residues: 538.4469 Evaluate side-chains 551 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 494 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1264 ARG 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 71 THR 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 511 VAL Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 722 ASP 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 C residue 240 LYS Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain E residue 22 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 G residue 65 SER Chi-restraints excluded: chain G residue 76 VAL 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 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 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 238 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 490 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 482 optimal weight: 0.0030 chunk 344 optimal weight: 8.9990 chunk 319 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 419 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 61 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 = 0.3874 r_free = 0.3874 target = 0.138068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107461 restraints weight = 56538.619| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.87 r_work: 0.3337 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43305 Z= 0.124 Angle : 0.517 12.047 58766 Z= 0.266 Chirality : 0.042 0.281 6636 Planarity : 0.004 0.064 7320 Dihedral : 11.046 138.763 6317 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.00 % Allowed : 13.27 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.12), residues: 5092 helix: 1.76 (0.12), residues: 1892 sheet: 0.30 (0.19), residues: 752 loop : -0.06 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 327 TYR 0.015 0.001 TYR J 44 PHE 0.020 0.001 PHE O 217 TRP 0.012 0.001 TRP A 201 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (43278) covalent geometry : angle 0.51013 / 0.27 (58733) hydrogen bonds : bond 0.03599 / 2.43 ( 1721) hydrogen bonds : angle 4.30599 / 3.04 ( 4755) metal coordination : bond 0.00494 / 0.31 ( 27) metal coordination : angle 3.53422 / 1.83 ( 33) *********************** 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 597 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 506 time to evaluate : 1.749 Fit side-chains REVERT: A 361 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7989 (mm-40) REVERT: A 556 ASP cc_start: 0.7314 (t0) cc_final: 0.7095 (t0) REVERT: A 759 GLU cc_start: 0.7589 (tp30) cc_final: 0.7318 (tp30) REVERT: A 784 GLU cc_start: 0.7656 (tp30) cc_final: 0.7301 (tp30) REVERT: A 819 SER cc_start: 0.8632 (t) cc_final: 0.8355 (m) REVERT: A 843 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: A 915 THR cc_start: 0.8369 (m) cc_final: 0.8162 (t) REVERT: A 1155 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7028 (mtp85) REVERT: A 1173 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7571 (t) REVERT: A 1189 ASP cc_start: 0.6927 (t0) cc_final: 0.6668 (t0) REVERT: A 1210 THR cc_start: 0.7869 (m) cc_final: 0.7662 (m) REVERT: A 1264 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (ttt180) REVERT: B 171 MET cc_start: 0.7930 (mmt) cc_final: 0.7620 (mtp) REVERT: B 239 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7924 (mtpt) REVERT: B 250 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: B 281 ASP cc_start: 0.7598 (m-30) cc_final: 0.7120 (m-30) REVERT: B 628 ARG cc_start: 0.7555 (ttp-110) cc_final: 0.7297 (ttm-80) REVERT: B 631 LEU cc_start: 0.7851 (mt) cc_final: 0.7642 (mt) REVERT: B 639 ASP cc_start: 0.7509 (t70) cc_final: 0.7175 (t0) REVERT: B 665 ASP cc_start: 0.8055 (t0) cc_final: 0.7795 (m-30) REVERT: B 882 ASP cc_start: 0.7828 (t0) cc_final: 0.7492 (t0) REVERT: C 9 TYR cc_start: 0.8852 (p90) cc_final: 0.8511 (p90) REVERT: C 176 SER cc_start: 0.7941 (OUTLIER) cc_final: 0.7736 (p) REVERT: C 201 GLU cc_start: 0.7831 (tt0) cc_final: 0.7526 (tt0) REVERT: D 51 ASN cc_start: 0.7604 (t0) cc_final: 0.7371 (t0) REVERT: D 106 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4937 (tp) REVERT: E 73 PRO cc_start: 0.8437 (Cg_endo) cc_final: 0.8220 (Cg_exo) REVERT: E 78 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7613 (tp) REVERT: E 169 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: G 16 ASP cc_start: 0.8136 (p0) cc_final: 0.7925 (p0) REVERT: G 84 ILE cc_start: 0.8470 (pt) cc_final: 0.8252 (pp) REVERT: G 101 LEU cc_start: 0.7588 (mt) cc_final: 0.7383 (mt) REVERT: G 114 MET cc_start: 0.7280 (mpp) cc_final: 0.6979 (ptp) REVERT: G 167 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5346 (mp0) REVERT: H 25 ARG cc_start: 0.8616 (ttp-170) cc_final: 0.8237 (ttm-80) REVERT: I 1 MET cc_start: 0.8302 (tpp) cc_final: 0.7891 (tpp) REVERT: M 261 LYS cc_start: 0.7464 (tmmm) cc_final: 0.7067 (tppt) REVERT: M 282 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7383 (t) REVERT: O 183 MET cc_start: 0.6844 (tpp) cc_final: 0.6551 (mmp) REVERT: O 317 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7159 (mpt-90) REVERT: O 343 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7068 (mppt) REVERT: O 542 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7225 (mmm160) REVERT: O 554 THR cc_start: 0.8580 (p) cc_final: 0.8254 (p) REVERT: O 628 LYS cc_start: 0.6978 (tptp) cc_final: 0.6760 (ttmt) REVERT: O 629 MET cc_start: 0.7050 (mmp) cc_final: 0.6718 (mpp) REVERT: P 308 GLU cc_start: 0.7930 (mp0) cc_final: 0.7407 (mm-30) REVERT: P 309 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8062 (t) REVERT: P 314 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6392 (mt-10) outliers start: 91 outliers final: 45 residues processed: 551 average time/residue: 0.7925 time to fit residues: 533.0573 Evaluate side-chains 563 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 501 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 870 GLU 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 1264 ARG 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 71 THR 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 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 C residue 249 LYS Chi-restraints excluded: chain C residue 268 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 22 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 G residue 65 SER Chi-restraints excluded: chain G residue 70 VAL 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 H residue 8 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 O residue 26 VAL Chi-restraints excluded: chain O residue 172 GLU 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 Chi-restraints excluded: chain P residue 309 VAL Chi-restraints excluded: chain P residue 314 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 466 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 511 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 251 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN 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 61 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106452 restraints weight = 56943.466| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.96 r_work: 0.3310 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43305 Z= 0.200 Angle : 0.563 12.901 58766 Z= 0.287 Chirality : 0.044 0.288 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.102 138.506 6317 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.26 % Allowed : 13.45 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 5092 helix: 1.62 (0.12), residues: 1900 sheet: 0.17 (0.19), residues: 770 loop : -0.09 (0.13), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 327 TYR 0.019 0.001 TYR J 44 PHE 0.024 0.001 PHE A 610 TRP 0.017 0.001 TRP A 201 HIS 0.010 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.20 (43278) covalent geometry : angle 0.55541 / 0.29 (58733) hydrogen bonds : bond 0.04028 / 2.72 ( 1721) hydrogen bonds : angle 4.35458 / 3.07 ( 4755) metal coordination : bond 0.00738 / 0.47 ( 27) metal coordination : angle 4.04187 / 2.09 ( 33) *********************** 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 614 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 511 time to evaluate : 1.714 Fit side-chains REVERT: A 361 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8028 (mm-40) REVERT: A 759 GLU cc_start: 0.7608 (tp30) cc_final: 0.7343 (tp30) REVERT: A 784 GLU cc_start: 0.7708 (tp30) cc_final: 0.7330 (tp30) REVERT: A 843 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: A 915 THR cc_start: 0.8440 (m) cc_final: 0.8224 (t) REVERT: A 1151 GLU cc_start: 0.6745 (tp30) cc_final: 0.6510 (tp30) REVERT: A 1155 ARG cc_start: 0.7273 (tpp80) cc_final: 0.7022 (mtp85) REVERT: A 1173 VAL cc_start: 0.7946 (OUTLIER) cc_final: 0.7620 (t) REVERT: A 1189 ASP cc_start: 0.6974 (t0) cc_final: 0.6665 (t0) REVERT: A 1210 THR cc_start: 0.7868 (m) cc_final: 0.7656 (m) REVERT: A 1264 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7705 (ttt180) REVERT: A 1292 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 1348 MET cc_start: 0.7082 (mmm) cc_final: 0.6837 (mmm) REVERT: B 109 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7236 (mtmm) REVERT: B 171 MET cc_start: 0.7942 (mmt) cc_final: 0.7579 (mmt) REVERT: B 250 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: B 269 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7588 (ttm) REVERT: B 281 ASP cc_start: 0.7624 (m-30) cc_final: 0.7157 (m-30) REVERT: B 628 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7237 (ttm-80) REVERT: B 631 LEU cc_start: 0.7879 (mt) cc_final: 0.7677 (mt) REVERT: B 639 ASP cc_start: 0.7543 (t70) cc_final: 0.7201 (t0) REVERT: B 665 ASP cc_start: 0.8108 (t0) cc_final: 0.7820 (m-30) REVERT: B 882 ASP cc_start: 0.7857 (t0) cc_final: 0.7512 (t0) REVERT: C 9 TYR cc_start: 0.8876 (p90) cc_final: 0.8508 (p90) REVERT: C 176 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7753 (p) REVERT: C 201 GLU cc_start: 0.7847 (tt0) cc_final: 0.7575 (tt0) REVERT: D 51 ASN cc_start: 0.7632 (t0) cc_final: 0.7405 (t0) REVERT: E 73 PRO cc_start: 0.8427 (Cg_endo) cc_final: 0.8197 (Cg_exo) REVERT: E 78 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7622 (tp) REVERT: E 169 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8105 (mtt180) REVERT: G 16 ASP cc_start: 0.8188 (p0) cc_final: 0.7977 (p0) REVERT: G 84 ILE cc_start: 0.8523 (pt) cc_final: 0.8290 (pp) REVERT: G 114 MET cc_start: 0.7314 (mpp) cc_final: 0.6978 (ptp) REVERT: G 167 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5414 (mp0) REVERT: H 25 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8262 (ttm-80) REVERT: H 55 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7515 (pp) REVERT: I 1 MET cc_start: 0.8321 (tpp) cc_final: 0.7954 (tpp) REVERT: M 261 LYS cc_start: 0.7480 (tmmm) cc_final: 0.7043 (tppt) REVERT: M 280 ASN cc_start: 0.7274 (m110) cc_final: 0.6759 (p0) REVERT: M 282 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7388 (t) REVERT: N 312 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6726 (ttp-170) REVERT: N 367 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7889 (pmmt) REVERT: O 59 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7386 (mt-10) REVERT: O 86 MET cc_start: 0.8394 (mtt) cc_final: 0.8085 (mmm) REVERT: O 183 MET cc_start: 0.6894 (tpp) cc_final: 0.6596 (mmp) REVERT: O 317 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7102 (mpt-90) REVERT: O 343 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7100 (mppt) REVERT: O 542 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7278 (mmm160) REVERT: O 554 THR cc_start: 0.8596 (p) cc_final: 0.8290 (p) REVERT: O 628 LYS cc_start: 0.7128 (tptp) cc_final: 0.6890 (ttmt) REVERT: O 629 MET cc_start: 0.7045 (mmp) cc_final: 0.6716 (mpp) REVERT: P 308 GLU cc_start: 0.7932 (mp0) cc_final: 0.7400 (mm-30) REVERT: P 309 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.8068 (t) REVERT: P 314 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6491 (mt-10) outliers start: 103 outliers final: 52 residues processed: 564 average time/residue: 0.7824 time to fit residues: 540.7113 Evaluate side-chains 569 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 498 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 511 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 1022 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1264 ARG Chi-restraints excluded: chain A residue 1282 VAL 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 1382 SER Chi-restraints excluded: chain B residue 71 THR 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 263 LEU Chi-restraints excluded: chain B residue 269 MET 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 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 176 SER Chi-restraints excluded: chain C residue 240 LYS Chi-restraints excluded: chain C residue 249 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 106 LEU 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 85 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 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 305 MET Chi-restraints excluded: chain N residue 312 ARG Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 172 GLU 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 216 SER Chi-restraints excluded: chain P residue 309 VAL Chi-restraints excluded: chain P residue 314 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 65 optimal weight: 0.6980 chunk 234 optimal weight: 0.5980 chunk 346 optimal weight: 6.9990 chunk 240 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 407 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 125 optimal weight: 0.0470 chunk 145 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 B1077 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** M 242 ASN O 225 ASN O 332 GLN Q 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108282 restraints weight = 56430.102| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.89 r_work: 0.3343 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 43305 Z= 0.108 Angle : 0.509 11.488 58766 Z= 0.263 Chirality : 0.042 0.279 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.016 138.487 6317 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.65 % Allowed : 14.46 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.12), residues: 5092 helix: 1.81 (0.12), residues: 1902 sheet: 0.24 (0.19), residues: 749 loop : -0.03 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 327 TYR 0.013 0.001 TYR J 44 PHE 0.020 0.001 PHE O 217 TRP 0.018 0.001 TRP A 201 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (43278) covalent geometry : angle 0.50290 / 0.26 (58733) hydrogen bonds : bond 0.03409 / 2.29 ( 1721) hydrogen bonds : angle 4.25837 / 3.01 ( 4755) metal coordination : bond 0.00398 / 0.25 ( 27) metal coordination : angle 3.35513 / 1.75 ( 33) *********************** 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 586 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 511 time to evaluate : 1.703 Fit side-chains REVERT: A 213 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.7687 (ptm-80) REVERT: A 361 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8020 (mm-40) REVERT: A 556 ASP cc_start: 0.7261 (t0) cc_final: 0.7046 (t0) REVERT: A 658 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7483 (mm110) REVERT: A 759 GLU cc_start: 0.7605 (tp30) cc_final: 0.7332 (tp30) REVERT: A 784 GLU cc_start: 0.7690 (tp30) cc_final: 0.7327 (tp30) REVERT: A 819 SER cc_start: 0.8632 (t) cc_final: 0.8359 (m) REVERT: A 843 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: A 885 MET cc_start: 0.7945 (ttm) cc_final: 0.7655 (ttp) REVERT: A 915 THR cc_start: 0.8377 (m) cc_final: 0.8173 (t) REVERT: A 1039 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4197 (mt) REVERT: A 1155 ARG cc_start: 0.7246 (tpp80) cc_final: 0.6997 (mtp85) REVERT: A 1173 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7519 (t) REVERT: A 1189 ASP cc_start: 0.6907 (t0) cc_final: 0.6608 (t0) REVERT: A 1210 THR cc_start: 0.7870 (m) cc_final: 0.7661 (m) REVERT: A 1264 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7597 (ttt180) REVERT: A 1292 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7279 (mt-10) REVERT: B 171 MET cc_start: 0.7956 (mmt) cc_final: 0.7646 (mtp) REVERT: B 250 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7685 (mt-10) REVERT: B 269 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7620 (ttm) REVERT: B 281 ASP cc_start: 0.7585 (m-30) cc_final: 0.7107 (m-30) REVERT: B 628 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7339 (ttm-80) REVERT: B 631 LEU cc_start: 0.7897 (mt) cc_final: 0.7687 (mt) REVERT: B 639 ASP cc_start: 0.7513 (t70) cc_final: 0.7152 (t0) REVERT: B 665 ASP cc_start: 0.8054 (t0) cc_final: 0.7845 (m-30) REVERT: B 882 ASP cc_start: 0.7832 (t0) cc_final: 0.7486 (t0) REVERT: C 9 TYR cc_start: 0.8861 (p90) cc_final: 0.8506 (p90) REVERT: C 176 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7777 (p) REVERT: C 201 GLU cc_start: 0.7824 (tt0) cc_final: 0.7544 (tt0) REVERT: D 51 ASN cc_start: 0.7598 (t0) cc_final: 0.7367 (t0) REVERT: D 106 LEU cc_start: 0.5218 (OUTLIER) cc_final: 0.4965 (tp) REVERT: D 131 MET cc_start: 0.6817 (tpt) cc_final: 0.6332 (tpt) REVERT: E 73 PRO cc_start: 0.8433 (Cg_endo) cc_final: 0.8209 (Cg_exo) REVERT: E 78 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7667 (tp) REVERT: E 169 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7983 (mtt180) REVERT: G 84 ILE cc_start: 0.8503 (pt) cc_final: 0.8292 (pp) REVERT: G 114 MET cc_start: 0.7271 (mpp) cc_final: 0.7009 (ptp) REVERT: G 167 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5345 (mp0) REVERT: H 8 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7280 (t70) REVERT: H 25 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8256 (ttm-80) REVERT: H 55 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7494 (pp) REVERT: I 1 MET cc_start: 0.8241 (tpp) cc_final: 0.7894 (tpp) REVERT: M 261 LYS cc_start: 0.7445 (tmmm) cc_final: 0.7036 (tppt) REVERT: M 280 ASN cc_start: 0.7258 (m110) cc_final: 0.6776 (p0) REVERT: M 282 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7375 (t) REVERT: N 312 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6743 (ttp-170) REVERT: N 367 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7852 (pmmt) REVERT: O 86 MET cc_start: 0.8391 (mtt) cc_final: 0.8106 (mmm) REVERT: O 183 MET cc_start: 0.6854 (tpp) cc_final: 0.6563 (mmp) REVERT: O 343 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7081 (mppt) REVERT: O 542 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7247 (mmm160) REVERT: O 554 THR cc_start: 0.8574 (p) cc_final: 0.8281 (p) REVERT: O 628 LYS cc_start: 0.6976 (tptp) cc_final: 0.6762 (ttmt) REVERT: O 629 MET cc_start: 0.7049 (mmp) cc_final: 0.6722 (mpp) REVERT: P 308 GLU cc_start: 0.7922 (mp0) cc_final: 0.7393 (mm-30) REVERT: P 309 VAL cc_start: 0.8355 (OUTLIER) cc_final: 0.8084 (t) REVERT: P 314 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6442 (mt-10) outliers start: 75 outliers final: 30 residues processed: 555 average time/residue: 0.7863 time to fit residues: 534.6204 Evaluate side-chains 541 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 490 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 511 ASP Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 843 GLN 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 1295 VAL Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1369 LEU 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 269 MET Chi-restraints excluded: chain B residue 562 ILE 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 176 SER Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 135 TYR 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 70 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 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 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 343 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 66 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 438 optimal weight: 4.9990 chunk 189 optimal weight: 0.1980 chunk 459 optimal weight: 3.9990 chunk 490 optimal weight: 0.8980 chunk 377 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 325 optimal weight: 0.7980 chunk 356 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 61 ASN ** G 36 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.138236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107674 restraints weight = 56527.308| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.88 r_work: 0.3334 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43305 Z= 0.138 Angle : 0.526 12.395 58766 Z= 0.270 Chirality : 0.043 0.283 6636 Planarity : 0.004 0.062 7320 Dihedral : 11.010 138.014 6317 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.32 % Allowed : 15.03 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 5092 helix: 1.80 (0.12), residues: 1902 sheet: 0.26 (0.19), residues: 750 loop : -0.04 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 327 TYR 0.014 0.001 TYR J 44 PHE 0.020 0.001 PHE O 217 TRP 0.016 0.001 TRP A 201 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (43278) covalent geometry : angle 0.51992 / 0.27 (58733) hydrogen bonds : bond 0.03561 / 2.40 ( 1721) hydrogen bonds : angle 4.24906 / 3.00 ( 4755) metal coordination : bond 0.00503 / 0.31 ( 27) metal coordination : angle 3.45003 / 1.81 ( 33) ********************** 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 559 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 499 time to evaluate : 1.718 Fit side-chains REVERT: A 361 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: A 556 ASP cc_start: 0.7303 (t0) cc_final: 0.7079 (t0) REVERT: A 658 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7475 (mm110) REVERT: A 759 GLU cc_start: 0.7578 (tp30) cc_final: 0.7300 (tp30) REVERT: A 784 GLU cc_start: 0.7713 (tp30) cc_final: 0.7347 (tp30) REVERT: A 819 SER cc_start: 0.8632 (t) cc_final: 0.8355 (m) REVERT: A 843 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: A 915 THR cc_start: 0.8387 (m) cc_final: 0.8181 (t) REVERT: A 1151 GLU cc_start: 0.6694 (tp30) cc_final: 0.6484 (tp30) REVERT: A 1155 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6971 (mtp85) REVERT: A 1173 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7513 (t) REVERT: A 1189 ASP cc_start: 0.6963 (t0) cc_final: 0.6630 (t0) REVERT: A 1210 THR cc_start: 0.7868 (m) cc_final: 0.7654 (m) REVERT: A 1264 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7596 (ttt180) REVERT: A 1292 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 250 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: B 269 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7580 (ttm) REVERT: B 281 ASP cc_start: 0.7580 (m-30) cc_final: 0.7100 (m-30) REVERT: B 628 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.7236 (ttm-80) REVERT: B 631 LEU cc_start: 0.7883 (mt) cc_final: 0.7675 (mt) REVERT: B 639 ASP cc_start: 0.7514 (t70) cc_final: 0.7154 (t0) REVERT: B 665 ASP cc_start: 0.8061 (t0) cc_final: 0.7845 (m-30) REVERT: B 882 ASP cc_start: 0.7839 (t0) cc_final: 0.7492 (t0) REVERT: C 9 TYR cc_start: 0.8861 (p90) cc_final: 0.8505 (p90) REVERT: C 77 SER cc_start: 0.8572 (t) cc_final: 0.8339 (m) REVERT: C 176 SER cc_start: 0.7986 (OUTLIER) cc_final: 0.7781 (p) REVERT: C 201 GLU cc_start: 0.7858 (tt0) cc_final: 0.7562 (tt0) REVERT: D 51 ASN cc_start: 0.7603 (t0) cc_final: 0.7364 (t0) REVERT: E 73 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8105 (Cg_exo) REVERT: E 78 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7644 (tp) REVERT: E 169 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7980 (mtt180) REVERT: G 84 ILE cc_start: 0.8494 (pt) cc_final: 0.8277 (pp) REVERT: G 101 LEU cc_start: 0.7531 (mt) cc_final: 0.7301 (mt) REVERT: G 114 MET cc_start: 0.7245 (mpp) cc_final: 0.6948 (ptp) REVERT: G 167 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.5336 (mp0) REVERT: H 25 ARG cc_start: 0.8610 (ttp-170) cc_final: 0.8259 (ttm-80) REVERT: H 55 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7494 (pp) REVERT: I 1 MET cc_start: 0.8231 (tpp) cc_final: 0.7909 (tpp) REVERT: M 261 LYS cc_start: 0.7435 (tmmm) cc_final: 0.7016 (tppt) REVERT: M 280 ASN cc_start: 0.7244 (m110) cc_final: 0.6760 (p0) REVERT: M 282 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7398 (t) REVERT: N 312 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6731 (ttp-170) REVERT: N 367 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7853 (pmmt) REVERT: O 86 MET cc_start: 0.8392 (mtt) cc_final: 0.8119 (mmm) REVERT: O 183 MET cc_start: 0.6835 (tpp) cc_final: 0.6545 (mmp) REVERT: O 343 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7072 (mppt) REVERT: O 542 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7216 (mmm160) REVERT: O 554 THR cc_start: 0.8572 (p) cc_final: 0.8282 (p) REVERT: O 628 LYS cc_start: 0.6951 (tptp) cc_final: 0.6741 (ttmt) REVERT: O 629 MET cc_start: 0.7024 (mmp) cc_final: 0.6693 (mpp) REVERT: P 308 GLU cc_start: 0.7921 (mp0) cc_final: 0.7382 (mm-30) REVERT: P 309 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (t) REVERT: P 314 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6455 (mt-10) outliers start: 60 outliers final: 35 residues processed: 535 average time/residue: 0.8022 time to fit residues: 524.7173 Evaluate side-chains 547 residues out of total 4557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 494 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 652 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 843 GLN Chi-restraints excluded: chain A residue 849 ARG Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1264 ARG 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 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 269 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 597 MET 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 176 SER Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 135 TYR 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 70 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 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 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 343 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 85 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 248 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 450 optimal weight: 8.9990 chunk 377 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 325 optimal weight: 2.9990 chunk 367 optimal weight: 30.0000 chunk 236 optimal weight: 0.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 61 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 ASN O 225 ASN O 332 GLN O 652 GLN Q 138 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107072 restraints weight = 56886.417| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.89 r_work: 0.3329 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43305 Z= 0.148 Angle : 0.531 12.397 58766 Z= 0.271 Chirality : 0.043 0.286 6636 Planarity : 0.004 0.061 7320 Dihedral : 11.012 138.089 6317 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.23 % Allowed : 15.12 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 5092 helix: 1.80 (0.12), residues: 1897 sheet: 0.22 (0.19), residues: 757 loop : -0.04 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 327 TYR 0.017 0.001 TYR J 44 PHE 0.022 0.001 PHE O 217 TRP 0.016 0.001 TRP A 201 HIS 0.007 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (43278) covalent geometry : angle 0.52461 / 0.27 (58733) hydrogen bonds : bond 0.03612 / 2.43 ( 1721) hydrogen bonds : angle 4.25970 / 3.01 ( 4755) metal coordination : bond 0.00539 / 0.33 ( 27) metal coordination : angle 3.53029 / 1.85 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18403.41 seconds wall clock time: 313 minutes 35.08 seconds (18815.08 seconds total)