Starting phenix.real_space_refine on Sat Feb 7 16:50:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oew_16838/02_2026/8oew_16838.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 1.056 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 8 6.06 5 P 77 5.49 5 Mg 1 5.21 5 S 212 5.16 5 C 21870 2.51 5 N 6151 2.21 5 O 6718 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35037 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1409, 11159 Classifications: {'peptide': 1409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1340} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 280 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 769 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1074 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 120} 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: "O" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "Q" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 83} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 69.733 99.369 57.029 1.00 55.63 S ATOM 494 SG CYS A 74 73.434 98.257 56.646 1.00 53.41 S ATOM 541 SG CYS A 81 71.478 97.206 59.783 1.00 43.12 S ATOM 776 SG CYS A 111 78.025 137.452 83.544 1.00 79.39 S ATOM 804 SG CYS A 114 80.442 138.586 81.099 1.00 78.95 S ATOM 1117 SG CYS A 154 80.950 139.353 84.771 1.00 89.81 S ATOM 1144 SG CYS A 184 78.172 141.243 82.685 1.00 87.15 S ATOM 19775 SG CYS B1196 85.699 108.766 59.849 1.00 51.07 S ATOM 19797 SG CYS B1199 83.417 109.517 62.765 1.00 50.76 S ATOM 19912 SG CYS B1214 82.034 108.961 59.277 1.00 61.29 S ATOM 19933 SG CYS B1217 83.998 112.208 60.245 1.00 68.34 S ATOM 20900 SG CYS C 88 67.316 31.592 67.669 1.00 42.39 S ATOM 20913 SG CYS C 90 64.872 34.431 66.712 1.00 53.45 S ATOM 20948 SG CYS C 94 63.905 30.874 67.660 1.00 33.19 S ATOM 20970 SG CYS C 97 65.105 33.368 70.347 1.00 29.03 S ATOM 28739 SG CYS I 86 58.841 88.610 157.312 1.00 59.16 S ATOM 28763 SG CYS I 89 55.644 86.922 158.659 1.00 61.10 S ATOM 28967 SG CYS I 114 56.521 86.683 154.962 1.00 49.30 S ATOM 29002 SG CYS I 119 55.382 89.971 156.639 1.00 53.99 S ATOM 28187 SG CYS I 17 48.086 128.522 141.160 1.00 81.19 S ATOM 28211 SG CYS I 20 47.209 128.566 137.366 1.00 82.04 S ATOM 28362 SG CYS I 39 50.584 129.681 138.381 1.00 89.78 S ATOM 28387 SG CYS I 42 47.714 131.808 139.329 1.00 94.48 S ATOM 29112 SG CYS J 7 65.198 41.314 100.489 1.00 10.76 S ATOM 29136 SG CYS J 10 67.097 38.064 99.769 1.00 14.19 S ATOM 29400 SG CYS J 44 67.751 40.228 103.012 1.00 15.14 S ATOM 29406 SG CYS J 45 64.866 37.916 102.520 1.00 16.53 S ATOM 30543 SG CYS L 19 31.661 61.763 81.008 1.00 54.09 S ATOM 30562 SG CYS L 22 29.206 58.982 80.646 1.00 61.21 S ATOM 30673 SG CYS L 36 28.996 61.716 78.238 1.00 63.51 S ATOM 30699 SG CYS L 39 28.149 62.525 81.949 1.00 64.33 S Time building chain proxies: 6.76, per 1000 atoms: 0.19 Number of scatterers: 35037 At special positions: 0 Unit cell: (157.5, 166.95, 200.55, 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 8 29.99 S 212 16.00 P 77 15.00 Mg 1 11.99 O 6718 8.00 N 6151 7.00 C 21870 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7876 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 47 sheets defined 39.4% alpha, 18.7% beta 27 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 4.62 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.638A pdb=" N LYS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.716A pdb=" N ARG A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.581A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.852A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 684 removed outlier: 7.941A pdb=" N HIS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N ASP A 663 " --> pdb=" O GLU A 659 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 664 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 removed outlier: 3.500A pdb=" N ASP A 691 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 760 removed outlier: 3.546A pdb=" N LEU A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.585A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.811A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1019 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1101 Proline residue: A1098 - end of helix removed outlier: 3.933A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.502A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.509A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.502A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.911A pdb=" N LYS A1317 " --> pdb=" O THR A1314 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A1318 " --> pdb=" O ASP A1315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1314 through 1318' Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1361 through 1370 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.913A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.667A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.549A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 114 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 354 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 385 removed outlier: 3.728A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 422 Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.768A pdb=" N LYS B 438 " --> pdb=" O CYS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.576A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.741A pdb=" N ILE B 787 " --> pdb=" O CYS B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.805A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1131 through 1135 Processing helix chain 'B' and resid 1154 through 1158 Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1242 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 removed outlier: 3.699A pdb=" N ARG C 133 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.581A pdb=" N LYS D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 Processing helix chain 'D' and resid 165 through 180 removed outlier: 4.008A pdb=" N LEU D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.730A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.516A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 111 through 122 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 142 removed outlier: 6.310A pdb=" N THR E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.604A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.686A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.566A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.550A pdb=" N GLN I 67 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.761A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 3.928A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP I 106 " --> pdb=" O ARG I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.743A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.767A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 576 through 588 Processing helix chain 'M' and resid 589 through 592 Processing helix chain 'M' and resid 599 through 609 Proline residue: M 605 - end of helix Processing helix chain 'M' and resid 611 through 622 Processing helix chain 'M' and resid 625 through 641 removed outlier: 3.695A pdb=" N ASP M 630 " --> pdb=" O ILE M 626 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN M 631 " --> pdb=" O GLU M 627 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU M 632 " --> pdb=" O GLU M 628 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 634 " --> pdb=" O ASP M 630 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL M 635 " --> pdb=" O GLN M 631 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS M 636 " --> pdb=" O LEU M 632 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 639 " --> pdb=" O VAL M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 680 removed outlier: 3.566A pdb=" N PHE M 676 " --> pdb=" O LYS M 672 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS M 678 " --> pdb=" O ILE M 674 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 44 Processing helix chain 'O' and resid 54 through 58 removed outlier: 3.731A pdb=" N THR O 57 " --> pdb=" O GLU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 84 Processing helix chain 'O' and resid 98 through 110 removed outlier: 4.252A pdb=" N GLU O 102 " --> pdb=" O GLU O 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 36 removed outlier: 3.848A pdb=" N LEU Q 27 " --> pdb=" O THR Q 23 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE Q 34 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 16 removed outlier: 4.495A pdb=" N ARG B1227 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.469A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.300A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.654A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 7.798A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.572A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.125A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.474A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.225A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.723A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1244 through 1248 removed outlier: 4.206A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 7.317A pdb=" N ARG E 172 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AC2, first strand: chain 'B' and resid 142 through 145 removed outlier: 5.431A pdb=" N TYR B 161 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE B 210 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU B 163 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 208 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 165 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 206 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 167 " --> pdb=" O ASP B 204 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ALA B 199 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 228 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 201 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 205 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLN B 222 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLN B 220 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 209 " --> pdb=" O GLN B 218 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 218 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.010A pdb=" N LYS M 688 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC5, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC6, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC7, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.771A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC9, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.513A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 6.629A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.323A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 904 through 906 removed outlier: 6.851A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 942 through 944 Processing sheet with id=AD8, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.291A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.411A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE3, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.607A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.536A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 83 through 86 removed outlier: 6.703A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 120 removed outlier: 3.620A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.443A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 60 through 61 removed outlier: 3.781A pdb=" N THR Q 13 " --> pdb=" O GLU O 28 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA Q 73 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ARG Q 8 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL Q 75 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Q 78 " --> pdb=" O ARG Q 43 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 9.80 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10277 1.33 - 1.46: 6327 1.46 - 1.58: 18766 1.58 - 1.70: 150 1.70 - 1.82: 336 Bond restraints: 35856 Sorted by residual: bond pdb=" C ILE B1049 " pdb=" N PRO B1050 " ideal model delta sigma weight residual 1.335 1.385 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" CA VAL A 521 " pdb=" CB VAL A 521 " ideal model delta sigma weight residual 1.539 1.556 -0.017 5.40e-03 3.43e+04 9.38e+00 bond pdb=" N ARG Q 9 " pdb=" CA ARG Q 9 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.21e-02 6.83e+03 5.52e+00 bond pdb=" CB VAL B 886 " pdb=" CG2 VAL B 886 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" C3' DC T 33 " pdb=" O3' DC T 33 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.10e+00 ... (remaining 35851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 47872 2.45 - 4.90: 752 4.90 - 7.35: 106 7.35 - 9.80: 26 9.80 - 12.25: 5 Bond angle restraints: 48761 Sorted by residual: angle pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta sigma weight residual 121.54 133.79 -12.25 1.91e+00 2.74e-01 4.12e+01 angle pdb=" C HIS Q 10 " pdb=" N LYS Q 11 " pdb=" CA LYS Q 11 " ideal model delta sigma weight residual 126.32 136.64 -10.32 1.74e+00 3.30e-01 3.52e+01 angle pdb=" C PHE O 52 " pdb=" N ALA O 53 " pdb=" CA ALA O 53 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 angle pdb=" N ARG Q 9 " pdb=" CA ARG Q 9 " pdb=" C ARG Q 9 " ideal model delta sigma weight residual 109.07 101.41 7.66 1.61e+00 3.86e-01 2.26e+01 angle pdb=" N GLN D 131 " pdb=" CA GLN D 131 " pdb=" CB GLN D 131 " ideal model delta sigma weight residual 110.39 118.15 -7.76 1.66e+00 3.63e-01 2.18e+01 ... (remaining 48756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 21169 35.10 - 70.21: 578 70.21 - 105.31: 36 105.31 - 140.41: 0 140.41 - 175.51: 1 Dihedral angle restraints: 21784 sinusoidal: 9616 harmonic: 12168 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 146.89 33.11 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA ASN D 144 " pdb=" C ASN D 144 " pdb=" N LEU D 145 " pdb=" CA LEU D 145 " ideal model delta harmonic sigma weight residual 180.00 147.68 32.32 0 5.00e+00 4.00e-02 4.18e+01 dihedral pdb=" CA ILE O 90 " pdb=" C ILE O 90 " pdb=" N PRO O 91 " pdb=" CA PRO O 91 " ideal model delta harmonic sigma weight residual -180.00 -151.03 -28.97 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 21781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 5132 0.103 - 0.206: 300 0.206 - 0.309: 11 0.309 - 0.412: 4 0.412 - 0.515: 1 Chirality restraints: 5448 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CG LEU A 831 " pdb=" CB LEU A 831 " pdb=" CD1 LEU A 831 " pdb=" CD2 LEU A 831 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CG LEU L 52 " pdb=" CB LEU L 52 " pdb=" CD1 LEU L 52 " pdb=" CD2 LEU L 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 5445 not shown) Planarity restraints: 6052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 539 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C GLN A 539 " -0.094 2.00e-02 2.50e+03 pdb=" O GLN A 539 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 540 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 829 " -0.028 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR B 829 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR B 829 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 829 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 829 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 829 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU M 604 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO M 605 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 605 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 605 " 0.039 5.00e-02 4.00e+02 ... (remaining 6049 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 495 2.65 - 3.21: 30318 3.21 - 3.77: 58262 3.77 - 4.34: 82304 4.34 - 4.90: 129763 Nonbonded interactions: 301142 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.087 2.170 nonbonded pdb=" O3' U P 46 " pdb="MG MG A2001 " model vdw 2.126 2.170 nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A2001 " model vdw 2.136 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.152 2.170 nonbonded pdb=" O ASN D 76 " pdb=" OG1 THR D 110 " model vdw 2.210 3.040 ... (remaining 301137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.010 Normalize map: mean=0, sd=1: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 40.710 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.005 0.069 35888 Z= 0.209 Angle : 0.795 12.253 48806 Z= 0.435 Chirality : 0.052 0.515 5448 Planarity : 0.006 0.069 6052 Dihedral : 15.704 175.515 13908 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.03 % 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: 4128 helix: -0.48 (0.13), residues: 1462 sheet: -0.34 (0.20), residues: 603 loop : -0.75 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A1153 TYR 0.059 0.002 TYR B 829 PHE 0.046 0.003 PHE A 431 TRP 0.028 0.003 TRP A 479 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00471 (35856) covalent geometry : angle 0.78470 (48761) hydrogen bonds : bond 0.15418 ( 1508) hydrogen bonds : angle 6.89423 ( 4177) metal coordination : bond 0.00630 ( 32) metal coordination : angle 4.24034 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.6793 (mtt) cc_final: 0.6583 (mtm) REVERT: I 93 GLU cc_start: 0.7971 (tt0) cc_final: 0.7716 (tt0) REVERT: K 1 MET cc_start: 0.7236 (ttm) cc_final: 0.6996 (ttm) REVERT: K 111 ASP cc_start: 0.7839 (m-30) cc_final: 0.7635 (m-30) REVERT: Q 46 LYS cc_start: 0.4745 (mmpt) cc_final: 0.4061 (pptt) REVERT: Q 52 ASP cc_start: 0.5728 (m-30) cc_final: 0.4631 (p0) REVERT: Q 65 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7580 (tm-30) REVERT: Q 79 PHE cc_start: 0.6080 (p90) cc_final: 0.4983 (m-80) outliers start: 0 outliers final: 0 residues processed: 598 average time/residue: 0.8628 time to fit residues: 602.5238 Evaluate side-chains 452 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN A 757 GLN A1303 GLN A1384 HIS B 342 GLN B 538 GLN B 818 HIS B1084 ASN B1171 GLN C 51 GLN C 111 GLN C 217 GLN G 138 GLN H 76 ASN I 41 ASN I 45 GLN M 578 HIS M 587 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114265 restraints weight = 49983.010| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.85 r_work: 0.3073 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35888 Z= 0.224 Angle : 0.647 12.622 48806 Z= 0.340 Chirality : 0.046 0.232 5448 Planarity : 0.005 0.053 6052 Dihedral : 12.644 172.440 5431 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.60 % Allowed : 10.04 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.41 (0.13), residues: 4128 helix: 0.35 (0.13), residues: 1485 sheet: -0.47 (0.20), residues: 585 loop : -0.59 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 227 TYR 0.021 0.002 TYR O 79 PHE 0.032 0.002 PHE Q 79 TRP 0.019 0.002 TRP B 104 HIS 0.011 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00514 (35856) covalent geometry : angle 0.63637 (48761) hydrogen bonds : bond 0.04861 ( 1508) hydrogen bonds : angle 5.47255 ( 4177) metal coordination : bond 0.00690 ( 32) metal coordination : angle 3.98414 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 479 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 271 ARG cc_start: 0.6656 (mtp85) cc_final: 0.6222 (mtp85) REVERT: A 290 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 317 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8035 (ttm) REVERT: A 329 MET cc_start: 0.7109 (mtt) cc_final: 0.6749 (mtm) REVERT: A 334 ARG cc_start: 0.7714 (ptm-80) cc_final: 0.7490 (ptt-90) REVERT: A 735 GLN cc_start: 0.7840 (tp-100) cc_final: 0.7429 (tp-100) REVERT: A 749 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6865 (tpt-90) REVERT: A 1246 ILE cc_start: 0.7393 (mm) cc_final: 0.7042 (pt) REVERT: A 1262 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3722 (mmm) REVERT: A 1279 MET cc_start: 0.4910 (ppp) cc_final: 0.3969 (tmm) REVERT: B 414 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7437 (mttp) REVERT: B 494 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 515 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8130 (tpp80) REVERT: B 821 MET cc_start: 0.9198 (mtt) cc_final: 0.8782 (mtm) REVERT: B 1186 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: C 228 ARG cc_start: 0.9051 (ttm110) cc_final: 0.8803 (ttm110) REVERT: D 137 PHE cc_start: 0.7464 (t80) cc_final: 0.7197 (t80) REVERT: E 116 GLN cc_start: 0.7759 (tp40) cc_final: 0.7538 (tp40) REVERT: F 100 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8370 (mtp-110) REVERT: H 147 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8792 (mttt) REVERT: I 15 ARG cc_start: 0.7226 (mmt90) cc_final: 0.6968 (mpt-90) REVERT: I 18 GLN cc_start: 0.7735 (mp10) cc_final: 0.7399 (mp10) REVERT: I 93 GLU cc_start: 0.8475 (tt0) cc_final: 0.8111 (tt0) REVERT: K 111 ASP cc_start: 0.8381 (m-30) cc_final: 0.8156 (m-30) REVERT: M 574 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5076 (ptm) REVERT: Q 65 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7824 (tm-30) outliers start: 59 outliers final: 21 residues processed: 501 average time/residue: 0.7710 time to fit residues: 455.6119 Evaluate side-chains 468 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 439 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 592 ILE Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 402 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 335 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 366 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 313 optimal weight: 0.9990 chunk 385 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN A1303 GLN B 175 HIS B 342 GLN B 727 ASN B 818 HIS B 826 HIS B1084 ASN C 111 GLN E 133 GLN H 76 ASN I 45 GLN ** M 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.115035 restraints weight = 50054.175| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.80 r_work: 0.3086 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35888 Z= 0.160 Angle : 0.590 10.755 48806 Z= 0.308 Chirality : 0.044 0.194 5448 Planarity : 0.004 0.049 6052 Dihedral : 12.559 172.535 5431 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.79 % Allowed : 12.23 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.10 (0.13), residues: 4128 helix: 0.73 (0.14), residues: 1488 sheet: -0.37 (0.21), residues: 575 loop : -0.49 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 82 TYR 0.021 0.001 TYR O 79 PHE 0.026 0.002 PHE Q 79 TRP 0.017 0.002 TRP B 104 HIS 0.010 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00363 (35856) covalent geometry : angle 0.58051 (48761) hydrogen bonds : bond 0.04257 ( 1508) hydrogen bonds : angle 5.20355 ( 4177) metal coordination : bond 0.00484 ( 32) metal coordination : angle 3.54866 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 478 time to evaluate : 1.425 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8319 (tm) cc_final: 0.8085 (tm) REVERT: A 271 ARG cc_start: 0.6747 (mtp85) cc_final: 0.6389 (mtp85) REVERT: A 290 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7722 (mt) REVERT: A 317 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7959 (ttm) REVERT: A 329 MET cc_start: 0.7124 (mtt) cc_final: 0.6771 (mtm) REVERT: A 735 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7494 (tp-100) REVERT: A 749 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6875 (tpt-90) REVERT: A 1246 ILE cc_start: 0.7449 (mm) cc_final: 0.7162 (pt) REVERT: A 1262 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.3672 (mmm) REVERT: B 515 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8144 (tpp80) REVERT: B 821 MET cc_start: 0.9164 (mtt) cc_final: 0.8677 (mtm) REVERT: B 1153 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: B 1158 ASP cc_start: 0.7948 (t0) cc_final: 0.7673 (t0) REVERT: B 1220 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8058 (mtpt) REVERT: F 100 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8364 (mtp-110) REVERT: F 125 ILE cc_start: 0.8707 (pt) cc_final: 0.8420 (mp) REVERT: G 94 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (mtmm) REVERT: G 151 ARG cc_start: 0.7469 (ttp80) cc_final: 0.7145 (tmm160) REVERT: H 21 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8603 (mtpt) REVERT: H 104 THR cc_start: 0.7749 (m) cc_final: 0.7449 (p) REVERT: H 147 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8779 (mttt) REVERT: I 18 GLN cc_start: 0.7830 (mp10) cc_final: 0.7445 (mp10) REVERT: K 111 ASP cc_start: 0.8404 (m-30) cc_final: 0.8180 (m-30) REVERT: L 52 LEU cc_start: 0.8145 (mt) cc_final: 0.7905 (mt) REVERT: M 574 MET cc_start: 0.5520 (OUTLIER) cc_final: 0.5045 (ptm) REVERT: M 593 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6745 (m-80) outliers start: 66 outliers final: 24 residues processed: 505 average time/residue: 0.8235 time to fit residues: 491.6025 Evaluate side-chains 473 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 440 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 574 MET Chi-restraints excluded: chain M residue 593 PHE Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 80 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 396 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 388 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 531 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN A1303 GLN B 175 HIS B 342 GLN B 727 ASN B 818 HIS B1084 ASN C 111 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN I 45 GLN M 578 HIS M 587 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.155237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115804 restraints weight = 49829.745| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.81 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35888 Z= 0.137 Angle : 0.563 10.196 48806 Z= 0.293 Chirality : 0.043 0.245 5448 Planarity : 0.004 0.049 6052 Dihedral : 12.490 172.519 5431 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.98 % Allowed : 13.75 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.12 (0.13), residues: 4128 helix: 1.01 (0.14), residues: 1481 sheet: -0.28 (0.21), residues: 570 loop : -0.43 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 307 TYR 0.022 0.001 TYR O 79 PHE 0.020 0.001 PHE Q 79 TRP 0.016 0.001 TRP B 104 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00311 (35856) covalent geometry : angle 0.55412 (48761) hydrogen bonds : bond 0.03877 ( 1508) hydrogen bonds : angle 4.98763 ( 4177) metal coordination : bond 0.00433 ( 32) metal coordination : angle 3.27649 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 473 time to evaluate : 1.393 Fit side-chains REVERT: A 271 ARG cc_start: 0.6780 (mtp85) cc_final: 0.6467 (mtp85) REVERT: A 290 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7858 (mt) REVERT: A 317 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8071 (ttm) REVERT: A 322 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7611 (pp) REVERT: A 329 MET cc_start: 0.7164 (mtt) cc_final: 0.6808 (mtm) REVERT: A 330 GLN cc_start: 0.6302 (mm-40) cc_final: 0.6036 (mm-40) REVERT: A 735 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7858 (tp-100) REVERT: A 749 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6898 (tpt-90) REVERT: A 849 ASP cc_start: 0.7589 (m-30) cc_final: 0.7379 (m-30) REVERT: A 1246 ILE cc_start: 0.7569 (mm) cc_final: 0.7304 (pt) REVERT: A 1262 MET cc_start: 0.4633 (OUTLIER) cc_final: 0.3859 (mpp) REVERT: A 1288 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8154 (mm) REVERT: B 414 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7585 (mttp) REVERT: B 493 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7256 (ttm110) REVERT: B 726 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 907 GLU cc_start: 0.6941 (pp20) cc_final: 0.6660 (pp20) REVERT: B 1153 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 1158 ASP cc_start: 0.7939 (t0) cc_final: 0.7727 (t0) REVERT: B 1220 LYS cc_start: 0.8483 (mmtp) cc_final: 0.8039 (mtpt) REVERT: D 137 PHE cc_start: 0.6709 (t80) cc_final: 0.6450 (t80) REVERT: F 94 MET cc_start: 0.8629 (mtm) cc_final: 0.8344 (mtp) REVERT: G 94 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: G 129 LYS cc_start: 0.7821 (ptmt) cc_final: 0.7553 (pttt) REVERT: H 70 LEU cc_start: 0.8504 (mm) cc_final: 0.8163 (mt) REVERT: H 104 THR cc_start: 0.7814 (m) cc_final: 0.7548 (p) REVERT: I 15 ARG cc_start: 0.7414 (mmt90) cc_final: 0.7201 (mpt-90) REVERT: K 111 ASP cc_start: 0.8406 (m-30) cc_final: 0.8188 (m-30) REVERT: L 52 LEU cc_start: 0.8209 (mt) cc_final: 0.8002 (mt) REVERT: M 593 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: Q 45 TYR cc_start: 0.4210 (OUTLIER) cc_final: 0.2723 (m-80) REVERT: Q 79 PHE cc_start: 0.5701 (p90) cc_final: 0.4821 (m-10) outliers start: 73 outliers final: 22 residues processed: 508 average time/residue: 0.7889 time to fit residues: 472.5104 Evaluate side-chains 471 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 437 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 593 PHE Chi-restraints excluded: chain M residue 635 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 317 optimal weight: 0.9980 chunk 402 optimal weight: 2.9990 chunk 187 optimal weight: 0.3980 chunk 151 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 300 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 396 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 189 optimal weight: 0.0970 chunk 179 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 ASN A1303 GLN B 175 HIS B 342 GLN B 389 GLN B 818 HIS ** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN H 76 ASN I 45 GLN M 578 HIS M 587 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115985 restraints weight = 50526.397| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.84 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35888 Z= 0.124 Angle : 0.556 11.636 48806 Z= 0.287 Chirality : 0.043 0.249 5448 Planarity : 0.004 0.047 6052 Dihedral : 12.446 172.624 5431 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.98 % Allowed : 15.05 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.26 (0.13), residues: 4128 helix: 1.18 (0.14), residues: 1471 sheet: -0.28 (0.21), residues: 559 loop : -0.36 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 307 TYR 0.022 0.001 TYR M 600 PHE 0.025 0.001 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.019 0.001 HIS M 578 Details of bonding type rmsd covalent geometry : bond 0.00281 (35856) covalent geometry : angle 0.54848 (48761) hydrogen bonds : bond 0.03700 ( 1508) hydrogen bonds : angle 4.89497 ( 4177) metal coordination : bond 0.00382 ( 32) metal coordination : angle 3.07654 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 464 time to evaluate : 1.139 Fit side-chains REVERT: A 271 ARG cc_start: 0.6761 (mtp85) cc_final: 0.6205 (mtp85) REVERT: A 290 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7825 (mt) REVERT: A 317 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: A 329 MET cc_start: 0.7119 (mtt) cc_final: 0.6778 (mtm) REVERT: A 330 GLN cc_start: 0.6132 (mm-40) cc_final: 0.5851 (mm-40) REVERT: A 735 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7873 (tp-100) REVERT: A 749 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6941 (tpt-90) REVERT: A 849 ASP cc_start: 0.7593 (m-30) cc_final: 0.7381 (m-30) REVERT: A 955 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: A 1133 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8563 (mtmt) REVERT: A 1221 MET cc_start: 0.7891 (mmm) cc_final: 0.7598 (mmm) REVERT: A 1246 ILE cc_start: 0.7654 (mm) cc_final: 0.7428 (pt) REVERT: A 1262 MET cc_start: 0.4642 (OUTLIER) cc_final: 0.3866 (mpp) REVERT: B 332 ARG cc_start: 0.7503 (mtm-85) cc_final: 0.7302 (mtm-85) REVERT: B 414 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7411 (mttp) REVERT: B 726 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8074 (p0) REVERT: B 743 ASP cc_start: 0.8530 (p0) cc_final: 0.8311 (p0) REVERT: B 907 GLU cc_start: 0.6827 (pp20) cc_final: 0.6546 (pp20) REVERT: B 991 GLU cc_start: 0.8384 (pm20) cc_final: 0.8130 (pm20) REVERT: B 1153 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: B 1158 ASP cc_start: 0.7973 (t0) cc_final: 0.7764 (t0) REVERT: B 1220 LYS cc_start: 0.8475 (mmtp) cc_final: 0.8036 (mtpt) REVERT: D 137 PHE cc_start: 0.6543 (t80) cc_final: 0.6264 (t80) REVERT: F 94 MET cc_start: 0.8659 (mtm) cc_final: 0.8393 (mtp) REVERT: G 129 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7491 (pttt) REVERT: H 70 LEU cc_start: 0.8474 (mm) cc_final: 0.8149 (mt) REVERT: H 104 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7627 (p) REVERT: I 18 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: I 58 ILE cc_start: 0.7565 (mm) cc_final: 0.7339 (mt) REVERT: K 111 ASP cc_start: 0.8437 (m-30) cc_final: 0.8214 (m-30) REVERT: L 52 LEU cc_start: 0.8241 (mt) cc_final: 0.8038 (mt) REVERT: Q 45 TYR cc_start: 0.4188 (OUTLIER) cc_final: 0.2830 (m-80) REVERT: Q 79 PHE cc_start: 0.5700 (p90) cc_final: 0.4795 (m-10) outliers start: 73 outliers final: 28 residues processed: 499 average time/residue: 0.7318 time to fit residues: 433.8079 Evaluate side-chains 477 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 436 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 787 ILE Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 635 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 77 PHE Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 374 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 330 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 378 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 459 ASN A 671 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN A1291 ASN B 222 GLN ** B 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 818 HIS B1084 ASN C 217 GLN D 135 HIS E 169 GLN H 76 ASN I 45 GLN M 578 HIS M 587 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116936 restraints weight = 49941.345| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.83 r_work: 0.3053 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 35888 Z= 0.258 Angle : 0.645 11.731 48806 Z= 0.333 Chirality : 0.047 0.244 5448 Planarity : 0.005 0.050 6052 Dihedral : 12.583 170.493 5431 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.38 % Allowed : 15.43 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.09 (0.13), residues: 4128 helix: 0.93 (0.14), residues: 1485 sheet: -0.38 (0.20), residues: 609 loop : -0.37 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 307 TYR 0.023 0.002 TYR M 600 PHE 0.027 0.002 PHE Q 62 TRP 0.017 0.002 TRP B 104 HIS 0.009 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00605 (35856) covalent geometry : angle 0.63453 (48761) hydrogen bonds : bond 0.04529 ( 1508) hydrogen bonds : angle 5.10927 ( 4177) metal coordination : bond 0.00793 ( 32) metal coordination : angle 3.87491 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 445 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 317 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8065 (ttm) REVERT: A 329 MET cc_start: 0.7059 (mtt) cc_final: 0.6712 (mtt) REVERT: A 701 ASP cc_start: 0.8109 (m-30) cc_final: 0.7894 (t0) REVERT: A 735 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7746 (tp-100) REVERT: A 749 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6765 (tpt-90) REVERT: A 1133 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8550 (mtmt) REVERT: A 1246 ILE cc_start: 0.7563 (mm) cc_final: 0.7329 (pt) REVERT: A 1262 MET cc_start: 0.4626 (OUTLIER) cc_final: 0.3709 (mpp) REVERT: A 1288 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7902 (tt) REVERT: B 220 GLN cc_start: 0.8585 (tp40) cc_final: 0.8226 (mm110) REVERT: B 414 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7510 (mttp) REVERT: B 726 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8097 (p0) REVERT: B 991 GLU cc_start: 0.8323 (pm20) cc_final: 0.8008 (pm20) REVERT: B 1153 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: B 1158 ASP cc_start: 0.7998 (t0) cc_final: 0.7748 (t0) REVERT: B 1220 LYS cc_start: 0.8444 (mmtp) cc_final: 0.7986 (mtpt) REVERT: D 137 PHE cc_start: 0.6756 (t80) cc_final: 0.6485 (t80) REVERT: F 94 MET cc_start: 0.8652 (mtm) cc_final: 0.8372 (mtp) REVERT: I 15 ARG cc_start: 0.7427 (mmt90) cc_final: 0.7223 (mpt-90) REVERT: I 58 ILE cc_start: 0.7558 (mm) cc_final: 0.7309 (mt) REVERT: K 111 ASP cc_start: 0.8408 (m-30) cc_final: 0.8193 (m-30) REVERT: Q 45 TYR cc_start: 0.4342 (OUTLIER) cc_final: 0.3135 (m-80) REVERT: Q 79 PHE cc_start: 0.6138 (p90) cc_final: 0.4946 (m-10) REVERT: Q 86 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.4279 (pm20) outliers start: 88 outliers final: 39 residues processed: 493 average time/residue: 0.7399 time to fit residues: 431.7581 Evaluate side-chains 474 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 424 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 726 ASN Chi-restraints excluded: chain B residue 805 MET Chi-restraints excluded: chain B residue 1153 GLU Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain M residue 661 ASP Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Chi-restraints excluded: chain Q residue 86 GLU Chi-restraints excluded: chain Q residue 88 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 327 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 671 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 389 GLN B 726 ASN B 818 HIS B1084 ASN C 51 GLN C 217 GLN G 122 ASN H 76 ASN I 22 ASN I 45 GLN I 67 GLN J 61 ASN ** M 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114532 restraints weight = 50021.578| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.84 r_work: 0.3074 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35888 Z= 0.163 Angle : 0.596 11.776 48806 Z= 0.308 Chirality : 0.044 0.195 5448 Planarity : 0.004 0.053 6052 Dihedral : 12.541 172.110 5431 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.03 % Allowed : 16.16 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.17 (0.13), residues: 4128 helix: 1.03 (0.14), residues: 1485 sheet: -0.32 (0.20), residues: 594 loop : -0.36 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 82 TYR 0.030 0.001 TYR M 600 PHE 0.027 0.002 PHE A 112 TRP 0.016 0.002 TRP B 104 HIS 0.023 0.001 HIS M 578 Details of bonding type rmsd covalent geometry : bond 0.00378 (35856) covalent geometry : angle 0.58736 (48761) hydrogen bonds : bond 0.03992 ( 1508) hydrogen bonds : angle 5.00768 ( 4177) metal coordination : bond 0.00525 ( 32) metal coordination : angle 3.47400 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 443 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 290 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (mt) REVERT: A 317 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8060 (ttm) REVERT: A 329 MET cc_start: 0.7115 (mtt) cc_final: 0.6822 (mtm) REVERT: A 555 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9240 (mt) REVERT: A 735 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7784 (tp-100) REVERT: A 749 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6856 (tpt-90) REVERT: A 1133 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: A 1246 ILE cc_start: 0.7586 (mm) cc_final: 0.7369 (pt) REVERT: A 1262 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3710 (mpp) REVERT: B 220 GLN cc_start: 0.8515 (tp40) cc_final: 0.8188 (mm110) REVERT: B 991 GLU cc_start: 0.8354 (pm20) cc_final: 0.8045 (pm20) REVERT: B 1158 ASP cc_start: 0.7987 (t0) cc_final: 0.7766 (t0) REVERT: B 1220 LYS cc_start: 0.8435 (mmtp) cc_final: 0.8014 (mtpt) REVERT: D 137 PHE cc_start: 0.6516 (t80) cc_final: 0.6251 (t80) REVERT: F 94 MET cc_start: 0.8689 (mtm) cc_final: 0.8444 (mtp) REVERT: H 70 LEU cc_start: 0.8461 (mm) cc_final: 0.8138 (mt) REVERT: H 104 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7737 (p) REVERT: I 18 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: K 111 ASP cc_start: 0.8452 (m-30) cc_final: 0.8235 (m-30) REVERT: L 27 GLU cc_start: 0.6744 (tp30) cc_final: 0.6473 (tp30) REVERT: Q 45 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.3489 (m-80) outliers start: 75 outliers final: 36 residues processed: 483 average time/residue: 0.7353 time to fit residues: 423.0348 Evaluate side-chains 472 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 427 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 512 ILE Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 1186 GLU Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 691 PHE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 81 VAL Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 111 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 214 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 400 optimal weight: 4.9990 chunk 181 optimal weight: 0.8980 chunk 106 optimal weight: 0.0980 chunk 250 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 175 HIS B 818 HIS B 832 GLN B1084 ASN C 51 GLN C 217 GLN H 76 ASN I 45 GLN J 52 HIS M 578 HIS M 587 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.155563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116187 restraints weight = 50368.505| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.84 r_work: 0.3107 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 35888 Z= 0.119 Angle : 0.563 11.063 48806 Z= 0.290 Chirality : 0.042 0.195 5448 Planarity : 0.004 0.056 6052 Dihedral : 12.453 172.783 5431 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.84 % Allowed : 16.89 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.35 (0.13), residues: 4128 helix: 1.23 (0.14), residues: 1477 sheet: -0.17 (0.21), residues: 579 loop : -0.30 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1153 TYR 0.039 0.001 TYR M 600 PHE 0.031 0.001 PHE Q 62 TRP 0.014 0.001 TRP B 104 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00270 (35856) covalent geometry : angle 0.55580 (48761) hydrogen bonds : bond 0.03578 ( 1508) hydrogen bonds : angle 4.84276 ( 4177) metal coordination : bond 0.00361 ( 32) metal coordination : angle 2.96982 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 458 time to evaluate : 1.421 Fit side-chains REVERT: A 291 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6836 (ttm170) REVERT: A 317 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: A 329 MET cc_start: 0.7082 (mtt) cc_final: 0.6828 (mtm) REVERT: A 735 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7786 (tp-100) REVERT: A 749 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6967 (tpt-90) REVERT: A 849 ASP cc_start: 0.7649 (m-30) cc_final: 0.7448 (m-30) REVERT: A 1133 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8593 (mtmt) REVERT: A 1246 ILE cc_start: 0.7649 (mm) cc_final: 0.7442 (pt) REVERT: A 1262 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.3774 (mpp) REVERT: A 1288 ILE cc_start: 0.8165 (mm) cc_final: 0.7579 (mp) REVERT: B 220 GLN cc_start: 0.8512 (tp40) cc_final: 0.8177 (mm110) REVERT: B 412 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5843 (mtm110) REVERT: B 941 ASP cc_start: 0.7126 (m-30) cc_final: 0.6891 (m-30) REVERT: B 1158 ASP cc_start: 0.8002 (t0) cc_final: 0.7784 (t0) REVERT: B 1220 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8029 (mtpt) REVERT: C 265 HIS cc_start: 0.8259 (t70) cc_final: 0.8043 (t70) REVERT: D 137 PHE cc_start: 0.6269 (t80) cc_final: 0.5988 (t80) REVERT: F 94 MET cc_start: 0.8706 (mtm) cc_final: 0.8421 (mtp) REVERT: G 129 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (pttt) REVERT: H 70 LEU cc_start: 0.8433 (mm) cc_final: 0.8120 (mt) REVERT: H 104 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7730 (p) REVERT: I 18 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: I 125 GLU cc_start: 0.7597 (pt0) cc_final: 0.7391 (pm20) REVERT: K 111 ASP cc_start: 0.8437 (m-30) cc_final: 0.8218 (m-30) REVERT: M 645 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6163 (mmt180) REVERT: Q 45 TYR cc_start: 0.4394 (OUTLIER) cc_final: 0.3309 (m-80) outliers start: 68 outliers final: 27 residues processed: 496 average time/residue: 0.7335 time to fit residues: 432.9335 Evaluate side-chains 468 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 431 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 691 PHE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 108 ASN Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 230 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 406 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 356 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 405 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 175 HIS B 389 GLN B 818 HIS B1084 ASN C 217 GLN G 138 GLN H 76 ASN I 22 ASN J 61 ASN M 578 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116004 restraints weight = 50122.308| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.81 r_work: 0.3105 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35888 Z= 0.136 Angle : 0.587 12.167 48806 Z= 0.300 Chirality : 0.043 0.250 5448 Planarity : 0.004 0.063 6052 Dihedral : 12.437 172.317 5431 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.30 % Allowed : 18.05 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.37 (0.13), residues: 4128 helix: 1.24 (0.14), residues: 1487 sheet: -0.19 (0.21), residues: 587 loop : -0.29 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 307 TYR 0.022 0.001 TYR O 79 PHE 0.024 0.001 PHE A 112 TRP 0.015 0.001 TRP B 104 HIS 0.020 0.001 HIS M 578 Details of bonding type rmsd covalent geometry : bond 0.00316 (35856) covalent geometry : angle 0.57980 (48761) hydrogen bonds : bond 0.03683 ( 1508) hydrogen bonds : angle 4.82165 ( 4177) metal coordination : bond 0.00402 ( 32) metal coordination : angle 3.03697 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 441 time to evaluate : 1.360 Fit side-chains REVERT: A 291 ARG cc_start: 0.7077 (ttm170) cc_final: 0.6790 (ttm170) REVERT: A 317 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7978 (ttm) REVERT: A 735 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7702 (tp-100) REVERT: A 749 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.6835 (tpt-90) REVERT: A 1133 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8578 (mtmt) REVERT: A 1228 MET cc_start: 0.8124 (mtm) cc_final: 0.7891 (mtm) REVERT: A 1246 ILE cc_start: 0.7573 (mm) cc_final: 0.7349 (pt) REVERT: A 1262 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.3713 (mpp) REVERT: A 1288 ILE cc_start: 0.8004 (mm) cc_final: 0.7373 (mp) REVERT: B 220 GLN cc_start: 0.8520 (tp40) cc_final: 0.8172 (mm110) REVERT: B 412 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5819 (mtm110) REVERT: B 941 ASP cc_start: 0.7080 (m-30) cc_final: 0.6836 (m-30) REVERT: B 1158 ASP cc_start: 0.7949 (t0) cc_final: 0.7687 (t0) REVERT: B 1220 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7995 (mtpt) REVERT: C 265 HIS cc_start: 0.8220 (t70) cc_final: 0.8010 (t70) REVERT: D 137 PHE cc_start: 0.6219 (t80) cc_final: 0.5984 (t80) REVERT: F 94 MET cc_start: 0.8708 (mtm) cc_final: 0.8415 (mtp) REVERT: G 129 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7480 (pttt) REVERT: G 170 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7815 (mt) REVERT: H 70 LEU cc_start: 0.8434 (mm) cc_final: 0.8131 (mt) REVERT: H 104 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7725 (p) REVERT: I 15 ARG cc_start: 0.7386 (mmt90) cc_final: 0.7165 (mmt90) REVERT: I 18 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: I 22 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7683 (t0) REVERT: I 125 GLU cc_start: 0.7570 (pt0) cc_final: 0.7271 (pm20) REVERT: K 111 ASP cc_start: 0.8395 (m-30) cc_final: 0.8176 (m-30) REVERT: M 645 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6158 (mmt180) REVERT: Q 36 LYS cc_start: 0.6436 (mppt) cc_final: 0.5729 (pptt) REVERT: Q 45 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.3186 (m-80) REVERT: Q 86 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6085 (pp20) outliers start: 48 outliers final: 26 residues processed: 463 average time/residue: 0.7358 time to fit residues: 405.1579 Evaluate side-chains 467 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 428 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 691 PHE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Chi-restraints excluded: chain Q residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 91 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 260 optimal weight: 0.9990 chunk 379 optimal weight: 20.0000 chunk 389 optimal weight: 0.5980 chunk 401 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 410 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 175 HIS B 389 GLN B 818 HIS B1084 ASN C 217 GLN E 129 GLN G 138 GLN H 76 ASN I 22 ASN J 61 ASN M 578 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116189 restraints weight = 50614.945| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.84 r_work: 0.3111 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35888 Z= 0.133 Angle : 0.584 10.147 48806 Z= 0.299 Chirality : 0.043 0.227 5448 Planarity : 0.004 0.065 6052 Dihedral : 12.427 172.234 5431 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.43 % Allowed : 18.38 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.39 (0.13), residues: 4128 helix: 1.26 (0.14), residues: 1488 sheet: -0.17 (0.21), residues: 583 loop : -0.28 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 307 TYR 0.022 0.001 TYR B 237 PHE 0.033 0.001 PHE Q 62 TRP 0.016 0.001 TRP B 104 HIS 0.017 0.001 HIS M 578 Details of bonding type rmsd covalent geometry : bond 0.00308 (35856) covalent geometry : angle 0.57666 (48761) hydrogen bonds : bond 0.03669 ( 1508) hydrogen bonds : angle 4.80311 ( 4177) metal coordination : bond 0.00426 ( 32) metal coordination : angle 3.03817 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 443 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 291 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6782 (ttm170) REVERT: A 317 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7997 (ttm) REVERT: A 329 MET cc_start: 0.7051 (mtt) cc_final: 0.6801 (mtt) REVERT: A 735 GLN cc_start: 0.8120 (tp-100) cc_final: 0.7678 (tp-100) REVERT: A 749 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.6790 (tpt-90) REVERT: A 1054 MET cc_start: 0.9309 (tpp) cc_final: 0.9071 (mmt) REVERT: A 1133 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8360 (ttpp) REVERT: A 1228 MET cc_start: 0.8100 (mtm) cc_final: 0.7857 (mtm) REVERT: A 1246 ILE cc_start: 0.7550 (mm) cc_final: 0.7323 (pt) REVERT: A 1262 MET cc_start: 0.4727 (OUTLIER) cc_final: 0.3726 (mpp) REVERT: A 1288 ILE cc_start: 0.7969 (mm) cc_final: 0.7338 (mp) REVERT: B 220 GLN cc_start: 0.8530 (tp40) cc_final: 0.8175 (mm110) REVERT: B 412 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5812 (mtm110) REVERT: B 941 ASP cc_start: 0.7068 (m-30) cc_final: 0.6825 (m-30) REVERT: B 1153 GLU cc_start: 0.8038 (tt0) cc_final: 0.7759 (tt0) REVERT: B 1220 LYS cc_start: 0.8449 (mmtp) cc_final: 0.7982 (mtpt) REVERT: C 265 HIS cc_start: 0.8198 (t70) cc_final: 0.7989 (t70) REVERT: D 137 PHE cc_start: 0.6181 (t80) cc_final: 0.5973 (t80) REVERT: F 94 MET cc_start: 0.8676 (mtm) cc_final: 0.8374 (mtp) REVERT: G 129 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7470 (pttt) REVERT: G 170 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (mt) REVERT: H 70 LEU cc_start: 0.8426 (mm) cc_final: 0.8128 (mt) REVERT: H 104 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7721 (p) REVERT: I 18 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: I 22 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7728 (t0) REVERT: I 93 GLU cc_start: 0.8561 (tt0) cc_final: 0.8264 (tt0) REVERT: I 125 GLU cc_start: 0.7557 (pt0) cc_final: 0.7238 (pm20) REVERT: K 111 ASP cc_start: 0.8367 (m-30) cc_final: 0.8150 (m-30) REVERT: M 573 LYS cc_start: 0.6158 (mmtt) cc_final: 0.5523 (tmtt) REVERT: M 645 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6169 (mmt180) REVERT: O 46 LEU cc_start: 0.2122 (OUTLIER) cc_final: 0.1853 (tp) REVERT: O 82 ARG cc_start: 0.6313 (ptp-110) cc_final: 0.5685 (tpt-90) REVERT: Q 36 LYS cc_start: 0.6545 (mppt) cc_final: 0.5832 (pptt) REVERT: Q 45 TYR cc_start: 0.4235 (OUTLIER) cc_final: 0.3267 (m-80) outliers start: 53 outliers final: 30 residues processed: 471 average time/residue: 0.7576 time to fit residues: 422.2692 Evaluate side-chains 470 residues out of total 3704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 427 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 412 ARG Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 CYS Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 18 GLN Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain M residue 578 HIS Chi-restraints excluded: chain M residue 645 ARG Chi-restraints excluded: chain M residue 669 VAL Chi-restraints excluded: chain M residue 691 PHE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 79 TYR Chi-restraints excluded: chain O residue 109 PHE Chi-restraints excluded: chain Q residue 45 TYR Chi-restraints excluded: chain Q residue 86 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 415 random chunks: chunk 9 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 chunk 402 optimal weight: 0.9980 chunk 280 optimal weight: 0.6980 chunk 168 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 118 optimal weight: 30.0000 chunk 336 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 439 HIS A 671 ASN A 723 ASN ** A 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN B 389 GLN B 818 HIS B 832 GLN B1084 ASN C 217 GLN G 138 GLN H 76 ASN I 22 ASN I 67 GLN J 61 ASN M 578 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117003 restraints weight = 49230.165| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.89 r_work: 0.3080 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 35888 Z= 0.240 Angle : 0.652 11.807 48806 Z= 0.333 Chirality : 0.046 0.250 5448 Planarity : 0.005 0.065 6052 Dihedral : 12.520 170.657 5431 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.60 % Allowed : 18.32 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: 0.24 (0.13), residues: 4128 helix: 1.07 (0.14), residues: 1487 sheet: -0.27 (0.21), residues: 592 loop : -0.31 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 307 TYR 0.030 0.002 TYR B 237 PHE 0.025 0.002 PHE A 112 TRP 0.018 0.002 TRP A1210 HIS 0.010 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00565 (35856) covalent geometry : angle 0.64383 (48761) hydrogen bonds : bond 0.04283 ( 1508) hydrogen bonds : angle 4.97331 ( 4177) metal coordination : bond 0.00768 ( 32) metal coordination : angle 3.47931 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15668.20 seconds wall clock time: 266 minutes 50.89 seconds (16010.89 seconds total)