Starting phenix.real_space_refine on Mon Aug 10 02:52:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4e_17407/08_2026/8p4e_17407.cif" } resolution = 3.9 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= 0.001 sd= 0.005 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 84 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 25812 2.51 5 N 7192 2.21 5 O 7866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 146 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41213 Number of models: 1 Model: "" Number of chains: 24 Chain: "Z" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 397 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "M" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2649 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "A" Number of atoms: 11142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11142 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 8928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8928 Classifications: {'peptide': 1116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1062} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2071 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} 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: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 76} 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: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 950 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} 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: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 389 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "D" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 998 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "O" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5643 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 27, 'TRANS': 663} Chain: "P" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 462 Unusual residues: {'MGT': 1} Classifications: {'RNAv2': 20, 'undetermined': 1} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 14, None: 1} Not linked: pdbres="MGT P 101 " pdbres=" G P 31 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "N" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "T" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 714 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} 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 3814 SG CYS A 111 79.820 13.495 79.663 1.00 52.15 S ATOM 3842 SG CYS A 114 80.492 9.649 81.560 1.00 60.58 S ATOM 3510 SG CYS A 71 65.908 44.656 112.718 1.00 41.25 S ATOM 3532 SG CYS A 74 69.610 46.534 113.136 1.00 35.32 S ATOM 3579 SG CYS A 81 67.422 47.926 110.442 1.00 35.83 S ATOM 22685 SG CYS B1119 82.293 39.715 107.622 1.00 32.24 S ATOM 22707 SG CYS B1122 81.599 37.103 105.178 1.00 35.98 S ATOM 22822 SG CYS B1137 79.363 37.773 108.243 1.00 48.78 S ATOM 23810 SG CYS C 88 52.916 112.776 114.184 1.00 27.25 S ATOM 23823 SG CYS C 90 50.781 109.558 114.461 1.00 37.75 S ATOM 23858 SG CYS C 94 49.382 112.758 113.325 1.00 23.11 S ATOM 23880 SG CYS C 97 50.804 110.919 110.565 1.00 16.65 S ATOM 28821 SG CYS I 17 45.228 27.392 24.003 1.00 39.89 S ATOM 28845 SG CYS I 20 45.045 26.576 27.518 1.00 41.99 S ATOM 29006 SG CYS I 39 48.625 25.952 27.380 1.00 38.99 S ATOM 29031 SG CYS I 42 46.030 23.999 25.030 1.00 43.23 S ATOM 29383 SG CYS I 86 49.026 70.546 15.137 1.00 32.07 S ATOM 29407 SG CYS I 89 45.624 71.910 14.579 1.00 31.64 S ATOM 29646 SG CYS I 119 44.390 69.710 17.205 1.00 38.63 S ATOM 29757 SG CYS J 7 50.945 108.090 79.517 1.00 28.01 S ATOM 29781 SG CYS J 10 53.852 111.855 79.476 1.00 23.57 S ATOM 30045 SG CYS J 44 53.469 109.588 76.811 1.00 23.69 S ATOM 30051 SG CYS J 45 50.077 111.463 78.259 1.00 21.59 S ATOM 31232 SG CYS L 22 18.898 79.732 95.306 1.00 35.66 S ATOM 31349 SG CYS L 36 19.130 78.109 98.513 1.00 37.97 S Time building chain proxies: 8.13, per 1000 atoms: 0.20 Number of scatterers: 41213 At special positions: 0 Unit cell: (148.05, 149.1, 215.25, 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 250 16.00 P 84 15.00 Mg 1 11.99 O 7866 8.00 N 7192 7.00 C 25812 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " 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 119 " 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 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 21 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 57 sheets defined 36.3% alpha, 19.4% beta 29 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'M' and resid 246 through 262 Processing helix chain 'M' and resid 279 through 286 removed outlier: 3.517A pdb=" N LYS M 282 " --> pdb=" O GLN M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 389 Processing helix chain 'M' and resid 389 through 398 Processing helix chain 'M' and resid 402 through 406 Processing helix chain 'M' and resid 419 through 421 No H-bonds generated for 'chain 'M' and resid 419 through 421' Processing helix chain 'M' and resid 461 through 464 Processing helix chain 'M' and resid 507 through 511 Processing helix chain 'M' and resid 538 through 551 removed outlier: 3.686A pdb=" N SER M 548 " --> pdb=" O ALA M 544 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN M 551 " --> pdb=" O ASN M 547 " (cutoff:3.500A) Processing helix chain 'M' and resid 554 through 566 removed outlier: 3.617A pdb=" N PHE M 559 " --> pdb=" O LYS M 555 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS M 565 " --> pdb=" O PHE M 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.601A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.696A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.499A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.326A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.714A pdb=" N ASP A 437 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for '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 488 through 493 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 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 659 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.069A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 693 removed outlier: 3.844A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 removed outlier: 3.625A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 757 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.637A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.556A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.105A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 removed outlier: 3.531A pdb=" N ASP A 894 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 removed outlier: 3.892A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 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 1102 Proline residue: A1098 - end of helix removed outlier: 4.156A 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 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.835A pdb=" N TRP A1192 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A1194 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.785A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.534A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1294 removed outlier: 3.994A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.852A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.751A 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 1431 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.648A pdb=" N LEU A1439 " --> pdb=" O THR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1460 Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.323A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.270A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.742A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 335 through 346 Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.687A pdb=" N VAL B 351 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.935A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.195A pdb=" N GLY B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 583 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.655A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 removed outlier: 3.605A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 removed outlier: 3.646A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 671' Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.503A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.513A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 762 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 968 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.968A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.863A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1059 Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.645A pdb=" N ARG B1080 " --> pdb=" O GLY B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 173 through 177 removed outlier: 3.709A pdb=" N ASN C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.924A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.566A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 97 removed outlier: 4.421A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.615A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.812A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.525A pdb=" N GLY F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.948A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.201A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.826A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.550A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.966A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 4.132A 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 9 removed outlier: 3.781A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 5.812A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 removed outlier: 3.726A pdb=" N THR K 92 " --> pdb=" O THR K 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 removed outlier: 3.515A pdb=" N GLN D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 16 through 20' Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.627A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.931A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'O' and resid 169 through 174 removed outlier: 4.400A pdb=" N ASP O 173 " --> pdb=" O GLU O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 205 Processing helix chain 'O' and resid 210 through 222 Processing helix chain 'O' and resid 224 through 228 Processing helix chain 'O' and resid 234 through 247 removed outlier: 4.220A pdb=" N MET O 238 " --> pdb=" O ASN O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 292 Processing helix chain 'O' and resid 309 through 313 Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'O' and resid 328 through 332 removed outlier: 3.662A pdb=" N GLY O 332 " --> pdb=" O GLY O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 352 Processing helix chain 'O' and resid 372 through 374 No H-bonds generated for 'chain 'O' and resid 372 through 374' Processing helix chain 'O' and resid 375 through 394 removed outlier: 5.275A pdb=" N GLN O 382 " --> pdb=" O ILE O 378 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU O 383 " --> pdb=" O LEU O 379 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 423 Processing helix chain 'O' and resid 453 through 471 Processing helix chain 'O' and resid 482 through 489 Processing helix chain 'O' and resid 489 through 520 Processing helix chain 'O' and resid 527 through 540 Processing helix chain 'O' and resid 553 through 563 Processing helix chain 'O' and resid 566 through 572 removed outlier: 3.830A pdb=" N TYR O 572 " --> pdb=" O ILE O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 581 through 586 Processing helix chain 'O' and resid 587 through 589 No H-bonds generated for 'chain 'O' and resid 587 through 589' Processing helix chain 'O' and resid 648 through 652 Processing helix chain 'O' and resid 675 through 690 removed outlier: 3.528A pdb=" N LYS O 688 " --> pdb=" O GLU O 684 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 717 removed outlier: 3.815A pdb=" N PHE O 716 " --> pdb=" O MET O 712 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL O 717 " --> pdb=" O GLU O 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 712 through 717' Processing helix chain 'O' and resid 784 through 788 Processing helix chain 'O' and resid 790 through 797 Processing helix chain 'O' and resid 822 through 833 Processing sheet with id=AA1, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.789A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 242 through 243 removed outlier: 6.238A pdb=" N LEU M 341 " --> pdb=" O ILE M 365 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU M 345 " --> pdb=" O ILE M 361 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE M 361 " --> pdb=" O GLU M 345 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE M 347 " --> pdb=" O TYR M 359 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TYR M 359 " --> pdb=" O ILE M 347 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP M 349 " --> pdb=" O PRO M 357 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 271 through 275 removed outlier: 3.868A pdb=" N VAL M 274 " --> pdb=" O CYS M 453 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP M 455 " --> pdb=" O VAL M 274 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY M 439 " --> pdb=" O LYS M 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 499 through 501 removed outlier: 3.582A pdb=" N ALA M 499 " --> pdb=" O LEU M 489 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE M 514 " --> pdb=" O GLN M 529 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN M 529 " --> pdb=" O ILE M 514 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.554A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 362 through 369 removed outlier: 8.133A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.722A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB4, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.549A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.223A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL B 794 " --> pdb=" O CYS B 945 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B 947 " --> pdb=" O VAL B 794 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 685 through 686 removed outlier: 4.223A pdb=" N HIS A 685 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.955A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AC1, first strand: chain 'A' and resid 1139 through 1140 removed outlier: 3.707A pdb=" N THR A1140 " --> pdb=" O THR A1358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1243 through 1246 removed outlier: 4.000A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1308 through 1310 Processing sheet with id=AC4, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC5, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.715A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.715A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.735A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.541A pdb=" N SER B 106 " --> pdb=" O HIS B 98 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.350A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 205 through 208 removed outlier: 3.796A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD4, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AD5, first strand: chain 'B' and resid 551 through 552 removed outlier: 7.175A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.683A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD9, first strand: chain 'B' and resid 827 through 829 removed outlier: 7.344A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.526A pdb=" N ILE B 866 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AE3, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AE4, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.827A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.332A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AE7, first strand: chain 'E' and resid 102 through 105 Processing sheet with id=AE8, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE9, first strand: chain 'H' and resid 139 through 142 removed outlier: 3.848A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF4, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.525A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF6, first strand: chain 'O' and resid 176 through 179 removed outlier: 6.726A pdb=" N VAL O 176 " --> pdb=" O ASN O 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 321 through 323 removed outlier: 7.910A pdb=" N TYR O 272 " --> pdb=" O HIS O 359 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU O 361 " --> pdb=" O TYR O 272 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA O 274 " --> pdb=" O LEU O 361 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA O 363 " --> pdb=" O ALA O 274 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL O 276 " --> pdb=" O ALA O 363 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL O 358 " --> pdb=" O ARG O 396 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY O 398 " --> pdb=" O VAL O 358 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE O 360 " --> pdb=" O GLY O 398 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS O 400 " --> pdb=" O PHE O 360 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET O 362 " --> pdb=" O HIS O 400 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE O 402 " --> pdb=" O MET O 362 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLY O 399 " --> pdb=" O GLY O 448 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU O 449 " --> pdb=" O PHE O 424 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE O 424 " --> pdb=" O LEU O 449 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 575 through 576 removed outlier: 6.217A pdb=" N THR O 575 " --> pdb=" O PHE O 800 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU O 802 " --> pdb=" O THR O 575 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY O 747 " --> pdb=" O SER O 596 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'O' and resid 623 through 624 removed outlier: 7.971A pdb=" N LEU O 636 " --> pdb=" O VAL O 663 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL O 663 " --> pdb=" O LEU O 636 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER O 638 " --> pdb=" O LEU O 661 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 623 through 624 removed outlier: 7.971A pdb=" N LEU O 636 " --> pdb=" O VAL O 663 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL O 663 " --> pdb=" O LEU O 636 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER O 638 " --> pdb=" O LEU O 661 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 719 through 723 Processing sheet with id=AG3, first strand: chain 'O' and resid 758 through 763 removed outlier: 3.548A pdb=" N LYS O 768 " --> pdb=" O SER O 763 " (cutoff:3.500A) 1657 hydrogen bonds defined for protein. 4557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 11.97 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.47: 22728 1.47 - 1.73: 19062 1.73 - 2.00: 394 2.00 - 2.26: 2 2.26 - 2.53: 1 Bond restraints: 42187 Sorted by residual: bond pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.321 2.526 -1.205 1.00e-02 1.00e+04 1.45e+04 bond pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " ideal model delta sigma weight residual 1.321 2.154 -0.833 1.00e-02 1.00e+04 6.94e+03 bond pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.374 2.142 -0.768 1.10e-02 8.26e+03 4.88e+03 bond pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 1.332 1.660 -0.328 1.37e-02 5.33e+03 5.73e+02 bond pdb=" C6 MGT P 101 " pdb=" O6 MGT P 101 " ideal model delta sigma weight residual 1.228 1.409 -0.181 2.00e-02 2.50e+03 8.17e+01 ... (remaining 42182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.52: 57322 10.52 - 21.04: 13 21.04 - 31.56: 3 31.56 - 42.09: 0 42.09 - 52.61: 5 Bond angle restraints: 57343 Sorted by residual: angle pdb=" CA PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 115.71 65.18 50.53 1.19e+00 7.06e-01 1.80e+03 angle pdb=" O PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 122.98 165.65 -42.67 1.09e+00 8.42e-01 1.53e+03 angle pdb=" C PRO O 549 " pdb=" N SER O 550 " pdb=" CA SER O 550 " ideal model delta sigma weight residual 121.31 76.05 45.26 1.49e+00 4.50e-01 9.23e+02 angle pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 108.40 84.97 23.43 1.00e+00 1.00e+00 5.49e+02 angle pdb=" CG HIS O 659 " pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 107.20 128.79 -21.59 1.00e+00 1.00e+00 4.66e+02 ... (remaining 57338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 24903 35.51 - 71.01: 612 71.01 - 106.52: 38 106.52 - 142.03: 1 142.03 - 177.53: 3 Dihedral angle restraints: 25557 sinusoidal: 11198 harmonic: 14359 Sorted by residual: dihedral pdb=" C4' A P 38 " pdb=" C3' A P 38 " pdb=" C2' A P 38 " pdb=" C1' A P 38 " ideal model delta sinusoidal sigma weight residual 36.35 -38.24 74.59 1 3.10e+00 1.04e-01 7.33e+02 dihedral pdb=" C4' C P 37 " pdb=" C3' C P 37 " pdb=" C2' C P 37 " pdb=" C1' C P 37 " ideal model delta sinusoidal sigma weight residual 36.35 -36.12 72.47 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' A P 40 " pdb=" C3' A P 40 " pdb=" C2' A P 40 " pdb=" C1' A P 40 " ideal model delta sinusoidal sigma weight residual 36.35 -35.61 71.96 1 3.10e+00 1.04e-01 6.90e+02 ... (remaining 25554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.885: 6382 0.885 - 1.770: 0 1.770 - 2.656: 1 2.656 - 3.541: 0 3.541 - 4.426: 1 Chirality restraints: 6384 Sorted by residual: chirality pdb=" C4' A P 40 " pdb=" C5' A P 40 " pdb=" O4' A P 40 " pdb=" C3' A P 40 " both_signs ideal model delta sigma weight residual False -2.49 1.93 -4.43 2.00e-01 2.50e+01 4.90e+02 chirality pdb=" P A P 34 " pdb=" OP1 A P 34 " pdb=" OP2 A P 34 " pdb=" O5' A P 34 " both_signs ideal model delta sigma weight residual True 2.17 0.08 2.09 2.00e-01 2.50e+01 1.10e+02 chirality pdb=" CA ASN M 521 " pdb=" N ASN M 521 " pdb=" C ASN M 521 " pdb=" CB ASN M 521 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 6381 not shown) Planarity restraints: 7139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 314 " -0.113 2.00e-02 2.50e+03 7.19e-02 1.03e+02 pdb=" CG TYR O 314 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR O 314 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR O 314 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR O 314 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR O 314 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR O 314 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR O 314 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 443 " -0.102 2.00e-02 2.50e+03 5.80e-02 6.72e+01 pdb=" CG TYR O 443 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR O 443 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR O 443 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR O 443 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR O 443 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 791 " 0.086 2.00e-02 2.50e+03 5.35e-02 5.01e+01 pdb=" CG PHE O 791 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE O 791 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE O 791 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE O 791 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE O 791 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE O 791 " 0.058 2.00e-02 2.50e+03 ... (remaining 7136 not shown) Histogram of nonbonded interaction distances: 0.35 - 1.26: 8 1.26 - 2.17: 52 2.17 - 3.08: 26916 3.08 - 3.99: 110725 3.99 - 4.90: 206583 Warning: very small nonbonded interaction distances. Nonbonded interactions: 344284 Sorted by model distance: nonbonded pdb=" CE LYS A 331 " pdb=" C7 DT N 14 " model vdw 0.354 3.860 nonbonded pdb=" CD LYS A 331 " pdb=" C4 DT N 14 " model vdw 0.949 3.660 nonbonded pdb=" OE2 GLU M 495 " pdb=" CB SER A 436 " model vdw 1.038 3.440 nonbonded pdb=" CD LYS A 331 " pdb=" C5 DT N 14 " model vdw 1.169 3.660 nonbonded pdb=" NH1 ARG A 358 " pdb=" OP1 DC T 23 " model vdw 1.186 3.120 ... (remaining 344279 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 48.930 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 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 : 0.014 1.205 42215 Z= 0.999 Angle : 1.359 53.487 57364 Z= 0.808 Chirality : 0.097 4.426 6384 Planarity : 0.009 0.123 7139 Dihedral : 14.266 177.532 16269 Min Nonbonded Distance : 0.354 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 1.72 % Allowed : 5.58 % Favored : 92.70 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.11 % 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: -2.95 (0.10), residues: 4884 helix: -2.10 (0.10), residues: 1630 sheet: -1.66 (0.17), residues: 794 loop : -1.89 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG O 702 TYR 0.127 0.006 TYR O 314 PHE 0.086 0.006 PHE O 791 TRP 0.064 0.007 TRP O 622 HIS 0.037 0.003 HIS O 659 Details of bonding type rmsd/Z covalent geometry : bond 0.01282 / 0.94 (42187) covalent geometry : angle 1.30504 / 0.81 (57343) hydrogen bonds : bond 0.16109 / 10.68 ( 1669) hydrogen bonds : angle 7.57729 / 5.27 ( 4687) metal coordination : bond 0.21622 / 12.66 ( 26) metal coordination : angle 19.81092 / 13.86 ( 21) Misc. bond : bond 0.39690 / 18.90 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 746 ASP cc_start: 0.9246 (m-30) cc_final: 0.8932 (p0) REVERT: Z 749 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8889 (mtt-85) REVERT: M 396 MET cc_start: -0.0494 (mtm) cc_final: -0.0963 (mtm) REVERT: M 474 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (p) REVERT: O 182 MET cc_start: -0.0361 (mmm) cc_final: -0.2632 (mtm) REVERT: O 645 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.3634 (mp) outliers start: 75 outliers final: 12 residues processed: 434 average time/residue: 0.2400 time to fit residues: 169.6883 Evaluate side-chains 235 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 366 LYS Chi-restraints excluded: chain M residue 390 SER Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 474 THR Chi-restraints excluded: chain M residue 475 ARG Chi-restraints excluded: chain M residue 485 ASN Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain O residue 645 LEU Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 653 ARG Chi-restraints excluded: chain O residue 655 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 470 optimal weight: 40.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 368 ASN M 378 ASN A 72 GLN A 123 ASN A 152 ASN A 272 ASN A 273 GLN A 278 HIS A 311 GLN A 341 GLN A 387 ASN A 403 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 507 GLN A 576 GLN A 609 HIS A 654 HIS A 662 HIS A 780 ASN ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 905 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN A1093 GLN A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 ASN A1248 ASN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1332 GLN A1384 HIS A1457 ASN B 111 ASN B 315 ASN B 486 ASN B 503 ASN B 518 HIS B 552 ASN B 577 HIS B 639 HIS B 650 ASN B 683 GLN B 699 HIS B 842 HIS B 980 HIS B1003 ASN B1021 HIS B1129 ASN B1133 HIS B1145 GLN C 55 ASN C 232 ASN E 132 GLN E 168 ASN H 44 ASN H 76 ASN H 87 GLN I 22 ASN I 32 ASN I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN D 135 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 352 ASN O 515 HIS ** O 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 667 ASN ** O 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.057369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036542 restraints weight = 301748.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036744 restraints weight = 166669.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037307 restraints weight = 106924.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.037577 restraints weight = 80005.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037798 restraints weight = 68260.271| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 42215 Z= 0.209 Angle : 0.824 19.272 57364 Z= 0.404 Chirality : 0.055 1.240 6384 Planarity : 0.005 0.086 7139 Dihedral : 14.323 177.610 6345 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 1.90 % Allowed : 8.54 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.11), residues: 4884 helix: -0.34 (0.12), residues: 1666 sheet: -1.65 (0.17), residues: 801 loop : -1.37 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 711 TYR 0.018 0.002 TYR O 421 PHE 0.027 0.002 PHE E 73 TRP 0.024 0.002 TRP A 988 HIS 0.015 0.001 HIS O 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (42187) covalent geometry : angle 0.81165 / 0.40 (57343) hydrogen bonds : bond 0.04867 / 3.22 ( 1669) hydrogen bonds : angle 5.61405 / 3.88 ( 4687) metal coordination : bond 0.01078 / 0.63 ( 26) metal coordination : angle 7.45480 / 4.87 ( 21) Misc. bond : bond 0.01177 / 0.56 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 232 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 746 ASP cc_start: 0.9545 (m-30) cc_final: 0.9032 (p0) REVERT: Z 748 GLN cc_start: 0.9298 (mp10) cc_final: 0.9074 (pm20) REVERT: M 346 MET cc_start: 0.0604 (tpt) cc_final: -0.0146 (tpt) REVERT: M 476 MET cc_start: 0.9287 (mmm) cc_final: 0.9028 (mmm) REVERT: A 78 MET cc_start: 0.8204 (ttm) cc_final: 0.7637 (ttm) REVERT: A 216 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9024 (tt) REVERT: A 248 MET cc_start: 0.9266 (mtp) cc_final: 0.9065 (mtp) REVERT: A 561 MET cc_start: 0.9055 (mtt) cc_final: 0.8799 (mtt) REVERT: A 769 MET cc_start: 0.9165 (mtt) cc_final: 0.8798 (mtt) REVERT: A 959 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9082 (mmp) REVERT: A 1228 MET cc_start: 0.8579 (mmm) cc_final: 0.8168 (mtt) REVERT: A 1440 MET cc_start: 0.9153 (mmm) cc_final: 0.8583 (ttt) REVERT: B 200 MET cc_start: 0.8023 (mmm) cc_final: 0.7711 (mmt) REVERT: B 298 MET cc_start: 0.9448 (mtt) cc_final: 0.8749 (mpp) REVERT: B 347 MET cc_start: 0.8581 (ptm) cc_final: 0.7868 (ppp) REVERT: B 508 MET cc_start: 0.9041 (mmm) cc_final: 0.8838 (mmm) REVERT: B 675 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9390 (tp) REVERT: B 677 MET cc_start: 0.8906 (mmm) cc_final: 0.8529 (tpp) REVERT: B 702 MET cc_start: 0.9124 (mmp) cc_final: 0.8847 (mmm) REVERT: B 908 MET cc_start: 0.8037 (tmm) cc_final: 0.7812 (tmm) REVERT: B 1075 MET cc_start: 0.9101 (mmm) cc_final: 0.8694 (mmm) REVERT: B 1163 MET cc_start: 0.9662 (mtm) cc_final: 0.9299 (mtm) REVERT: E 18 MET cc_start: 0.8718 (mmm) cc_final: 0.7336 (mpp) REVERT: J 66 GLU cc_start: 0.7648 (pm20) cc_final: 0.7346 (pp20) REVERT: L 15 MET cc_start: 0.7620 (mmm) cc_final: 0.7366 (mtp) REVERT: O 182 MET cc_start: -0.0689 (mmm) cc_final: -0.1066 (mpp) REVERT: O 300 MET cc_start: 0.1020 (ttp) cc_final: 0.0368 (tpp) REVERT: O 650 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8878 (mtpt) outliers start: 83 outliers final: 18 residues processed: 302 average time/residue: 0.2585 time to fit residues: 131.2290 Evaluate side-chains 230 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 298 THR Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 366 LYS Chi-restraints excluded: chain M residue 475 ARG Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 435 optimal weight: 9.9990 chunk 351 optimal weight: 0.3980 chunk 236 optimal weight: 0.1980 chunk 395 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 chunk 463 optimal weight: 50.0000 chunk 380 optimal weight: 9.9990 chunk 384 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 18 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 643 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.057247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.036252 restraints weight = 302008.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.036780 restraints weight = 169437.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037162 restraints weight = 113349.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037437 restraints weight = 84326.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.038237 restraints weight = 67756.015| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 42215 Z= 0.147 Angle : 0.700 17.303 57364 Z= 0.345 Chirality : 0.049 0.814 6384 Planarity : 0.004 0.075 7139 Dihedral : 13.956 177.593 6329 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Rotamer: Outliers : 1.54 % Allowed : 9.06 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.12), residues: 4884 helix: 0.45 (0.13), residues: 1646 sheet: -1.43 (0.17), residues: 822 loop : -1.09 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG O 653 TYR 0.015 0.001 TYR B 766 PHE 0.026 0.001 PHE E 73 TRP 0.017 0.002 TRP A 988 HIS 0.010 0.001 HIS O 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (42187) covalent geometry : angle 0.69254 / 0.34 (57343) hydrogen bonds : bond 0.03860 / 2.57 ( 1669) hydrogen bonds : angle 5.12898 / 3.54 ( 4687) metal coordination : bond 0.00589 / 0.39 ( 26) metal coordination : angle 5.52839 / 3.40 ( 21) Misc. bond : bond 0.01322 / 0.64 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9313 (mmmm) cc_final: 0.9112 (mmmm) REVERT: Z 726 ASP cc_start: 0.8440 (t0) cc_final: 0.8208 (t0) REVERT: Z 746 ASP cc_start: 0.9454 (m-30) cc_final: 0.9104 (p0) REVERT: Z 748 GLN cc_start: 0.9317 (mp10) cc_final: 0.9084 (mp10) REVERT: M 346 MET cc_start: 0.0267 (tpt) cc_final: -0.0694 (mmt) REVERT: M 437 MET cc_start: 0.3391 (ttt) cc_final: 0.2462 (tpp) REVERT: A 78 MET cc_start: 0.8159 (ttm) cc_final: 0.7647 (ttm) REVERT: A 104 MET cc_start: 0.9607 (mtp) cc_final: 0.8792 (tmm) REVERT: A 216 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.9019 (tt) REVERT: A 388 MET cc_start: 0.9246 (mtp) cc_final: 0.8974 (mmt) REVERT: A 467 MET cc_start: 0.9054 (mpp) cc_final: 0.8660 (mpp) REVERT: A 524 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: A 561 MET cc_start: 0.9062 (mtt) cc_final: 0.8807 (mtt) REVERT: A 769 MET cc_start: 0.9228 (mtt) cc_final: 0.8883 (mtt) REVERT: A 959 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9125 (mmp) REVERT: A 1228 MET cc_start: 0.8537 (mmm) cc_final: 0.8028 (mtt) REVERT: A 1440 MET cc_start: 0.9230 (mmm) cc_final: 0.8766 (mmm) REVERT: B 297 MET cc_start: 0.9056 (tpp) cc_final: 0.8764 (tpp) REVERT: B 298 MET cc_start: 0.9451 (mtt) cc_final: 0.8747 (mpp) REVERT: B 347 MET cc_start: 0.8594 (ptm) cc_final: 0.8316 (ppp) REVERT: B 361 LYS cc_start: 0.9671 (OUTLIER) cc_final: 0.9247 (mttt) REVERT: B 614 ILE cc_start: 0.9733 (mt) cc_final: 0.9479 (tp) REVERT: B 677 MET cc_start: 0.8910 (mmm) cc_final: 0.8488 (tpp) REVERT: B 908 MET cc_start: 0.8224 (tmm) cc_final: 0.7810 (tmm) REVERT: B 1075 MET cc_start: 0.9144 (mmm) cc_final: 0.8688 (mmm) REVERT: B 1163 MET cc_start: 0.9675 (mtm) cc_final: 0.9304 (mtm) REVERT: B 1165 MET cc_start: 0.9047 (mmm) cc_final: 0.8672 (mmm) REVERT: C 15 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9262 (p) REVERT: F 75 MET cc_start: 0.9111 (mtp) cc_final: 0.8885 (mtp) REVERT: L 15 MET cc_start: 0.7572 (mmm) cc_final: 0.7370 (mtp) REVERT: L 44 MET cc_start: 0.8575 (mmt) cc_final: 0.8119 (mmm) REVERT: G 164 MET cc_start: 0.7830 (mtt) cc_final: 0.7543 (mmm) REVERT: O 182 MET cc_start: -0.0646 (mmm) cc_final: -0.0943 (mpp) REVERT: O 300 MET cc_start: 0.0716 (ttp) cc_final: 0.0017 (tpp) REVERT: O 654 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8056 (mmtm) outliers start: 67 outliers final: 19 residues processed: 289 average time/residue: 0.2560 time to fit residues: 124.9635 Evaluate side-chains 233 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 745 VAL Chi-restraints excluded: chain M residue 263 TRP Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 329 optimal weight: 9.9990 chunk 463 optimal weight: 50.0000 chunk 300 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 369 optimal weight: 1.9990 chunk 264 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 401 optimal weight: 0.9980 chunk 278 optimal weight: 5.9990 chunk 442 optimal weight: 50.0000 chunk 47 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 481 HIS B 585 ASN B 649 ASN ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN I 41 ASN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.056291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035284 restraints weight = 304567.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.035902 restraints weight = 172565.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036264 restraints weight = 111231.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036497 restraints weight = 82336.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036651 restraints weight = 68420.293| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 42215 Z= 0.185 Angle : 0.677 16.020 57364 Z= 0.334 Chirality : 0.047 0.674 6384 Planarity : 0.004 0.060 7139 Dihedral : 13.791 178.075 6321 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 1.51 % Allowed : 9.78 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.12), residues: 4884 helix: 0.87 (0.13), residues: 1662 sheet: -1.24 (0.17), residues: 826 loop : -0.91 (0.13), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 749 TYR 0.029 0.001 TYR I 25 PHE 0.027 0.001 PHE E 73 TRP 0.013 0.001 TRP C 203 HIS 0.006 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 (42187) covalent geometry : angle 0.66838 / 0.33 (57343) hydrogen bonds : bond 0.03712 / 2.47 ( 1669) hydrogen bonds : angle 4.94734 / 3.41 ( 4687) metal coordination : bond 0.00784 / 0.47 ( 26) metal coordination : angle 5.72794 / 3.60 ( 21) Misc. bond : bond 0.00458 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9310 (mmmm) cc_final: 0.9088 (mmmm) REVERT: Z 726 ASP cc_start: 0.8490 (t0) cc_final: 0.8241 (t0) REVERT: Z 746 ASP cc_start: 0.9504 (m-30) cc_final: 0.9081 (p0) REVERT: Z 748 GLN cc_start: 0.9317 (mp10) cc_final: 0.9051 (mp10) REVERT: Z 751 THR cc_start: 0.9315 (m) cc_final: 0.9072 (p) REVERT: M 437 MET cc_start: 0.3295 (ttt) cc_final: 0.2557 (tpp) REVERT: A 78 MET cc_start: 0.8306 (ttm) cc_final: 0.7855 (ttm) REVERT: A 104 MET cc_start: 0.9584 (mtp) cc_final: 0.8816 (tmm) REVERT: A 329 MET cc_start: 0.8943 (tpp) cc_final: 0.8584 (tpp) REVERT: A 469 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8814 (ttp) REVERT: A 561 MET cc_start: 0.9076 (mtt) cc_final: 0.8848 (mtt) REVERT: A 660 MET cc_start: 0.8898 (mmp) cc_final: 0.8637 (mmp) REVERT: A 769 MET cc_start: 0.9196 (mtt) cc_final: 0.8895 (mtt) REVERT: A 959 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.9124 (mmp) REVERT: A 1228 MET cc_start: 0.8582 (mmm) cc_final: 0.7988 (mtt) REVERT: A 1344 MET cc_start: 0.8521 (ppp) cc_final: 0.8238 (ppp) REVERT: A 1440 MET cc_start: 0.9274 (mmm) cc_final: 0.8697 (mmm) REVERT: B 108 MET cc_start: 0.8435 (ppp) cc_final: 0.8065 (ppp) REVERT: B 109 MET cc_start: 0.8762 (mmm) cc_final: 0.7943 (mmp) REVERT: B 155 MET cc_start: 0.8616 (ptt) cc_final: 0.8140 (ptt) REVERT: B 297 MET cc_start: 0.9125 (tpp) cc_final: 0.8822 (tpp) REVERT: B 298 MET cc_start: 0.9482 (mtt) cc_final: 0.8785 (mpp) REVERT: B 347 MET cc_start: 0.8622 (ptm) cc_final: 0.8275 (ppp) REVERT: B 361 LYS cc_start: 0.9698 (OUTLIER) cc_final: 0.9250 (mttt) REVERT: B 675 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9403 (tp) REVERT: B 677 MET cc_start: 0.9001 (mmm) cc_final: 0.8546 (tpp) REVERT: B 908 MET cc_start: 0.8453 (tmm) cc_final: 0.7964 (tmm) REVERT: B 1075 MET cc_start: 0.9182 (mmm) cc_final: 0.8697 (mmm) REVERT: B 1163 MET cc_start: 0.9640 (mtm) cc_final: 0.9277 (mtm) REVERT: C 15 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9268 (p) REVERT: E 72 MET cc_start: 0.8730 (tpp) cc_final: 0.8477 (tpp) REVERT: F 75 MET cc_start: 0.9094 (mtp) cc_final: 0.8830 (mtp) REVERT: L 44 MET cc_start: 0.8452 (mmt) cc_final: 0.8098 (mmm) REVERT: G 164 MET cc_start: 0.7869 (mtt) cc_final: 0.7565 (mmt) REVERT: O 175 MET cc_start: 0.6250 (pmm) cc_final: 0.6037 (pmm) REVERT: O 182 MET cc_start: -0.0619 (mmm) cc_final: -0.0956 (mpp) REVERT: O 300 MET cc_start: 0.0330 (ttp) cc_final: -0.0210 (tpp) REVERT: O 594 MET cc_start: 0.3605 (pmm) cc_final: 0.3348 (pmm) REVERT: O 654 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7944 (mmtm) outliers start: 66 outliers final: 27 residues processed: 264 average time/residue: 0.2482 time to fit residues: 111.5854 Evaluate side-chains 233 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain M residue 263 TRP Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 306 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 416 optimal weight: 9.9990 chunk 482 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 477 optimal weight: 0.0270 overall best weight: 2.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 91 GLN O 833 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.056550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035579 restraints weight = 302242.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036178 restraints weight = 170399.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036618 restraints weight = 109756.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036865 restraints weight = 79158.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037018 restraints weight = 68323.778| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42215 Z= 0.129 Angle : 0.640 14.474 57364 Z= 0.315 Chirality : 0.046 0.566 6384 Planarity : 0.004 0.053 7139 Dihedral : 13.682 179.107 6321 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.80 % Rotamer: Outliers : 1.35 % Allowed : 10.14 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 4884 helix: 1.06 (0.13), residues: 1661 sheet: -1.09 (0.17), residues: 846 loop : -0.80 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 166 TYR 0.013 0.001 TYR B 766 PHE 0.021 0.001 PHE E 73 TRP 0.012 0.001 TRP A 679 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (42187) covalent geometry : angle 0.63369 / 0.31 (57343) hydrogen bonds : bond 0.03398 / 2.27 ( 1669) hydrogen bonds : angle 4.77673 / 3.30 ( 4687) metal coordination : bond 0.00458 / 0.29 ( 26) metal coordination : angle 4.84646 / 2.98 ( 21) Misc. bond : bond 0.00426 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9094 (mmmm) REVERT: Z 726 ASP cc_start: 0.8479 (t0) cc_final: 0.8190 (t0) REVERT: Z 746 ASP cc_start: 0.9474 (m-30) cc_final: 0.8992 (p0) REVERT: Z 747 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8697 (ttm110) REVERT: Z 751 THR cc_start: 0.9356 (m) cc_final: 0.9143 (p) REVERT: M 346 MET cc_start: 0.0010 (tpt) cc_final: -0.0979 (mmt) REVERT: M 437 MET cc_start: 0.3483 (ttt) cc_final: 0.3042 (tmm) REVERT: A 78 MET cc_start: 0.8319 (ttm) cc_final: 0.7852 (ttm) REVERT: A 104 MET cc_start: 0.9577 (mtp) cc_final: 0.8821 (tmm) REVERT: A 248 MET cc_start: 0.9128 (mtp) cc_final: 0.8238 (ttm) REVERT: A 329 MET cc_start: 0.9066 (tpp) cc_final: 0.8735 (tpp) REVERT: A 470 MET cc_start: 0.7911 (mtp) cc_final: 0.7701 (mtp) REVERT: A 524 MET cc_start: 0.8628 (mtp) cc_final: 0.8385 (mtp) REVERT: A 660 MET cc_start: 0.8953 (mmp) cc_final: 0.8693 (mmp) REVERT: A 769 MET cc_start: 0.9209 (mtt) cc_final: 0.8922 (mtt) REVERT: A 868 MET cc_start: 0.8801 (ptp) cc_final: 0.8584 (ptp) REVERT: A 959 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9124 (mmp) REVERT: A 1102 MET cc_start: 0.9196 (tmm) cc_final: 0.8814 (ppp) REVERT: A 1228 MET cc_start: 0.8614 (mmm) cc_final: 0.7929 (mtt) REVERT: A 1344 MET cc_start: 0.8520 (ppp) cc_final: 0.8232 (ppp) REVERT: A 1440 MET cc_start: 0.9265 (mmm) cc_final: 0.8530 (mmm) REVERT: A 1451 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7959 (mtp) REVERT: B 108 MET cc_start: 0.8575 (ppp) cc_final: 0.8131 (ppp) REVERT: B 109 MET cc_start: 0.8805 (mmm) cc_final: 0.8023 (mmm) REVERT: B 155 MET cc_start: 0.8686 (ptt) cc_final: 0.8202 (ptt) REVERT: B 297 MET cc_start: 0.9121 (tpp) cc_final: 0.8786 (tpp) REVERT: B 298 MET cc_start: 0.9433 (mtt) cc_final: 0.8727 (mpp) REVERT: B 361 LYS cc_start: 0.9702 (OUTLIER) cc_final: 0.8998 (mttt) REVERT: B 508 MET cc_start: 0.9250 (mmm) cc_final: 0.8485 (mmm) REVERT: B 529 MET cc_start: 0.8998 (mmm) cc_final: 0.8528 (mmm) REVERT: B 603 MET cc_start: 0.8631 (mpp) cc_final: 0.8363 (pmm) REVERT: B 675 LEU cc_start: 0.9670 (OUTLIER) cc_final: 0.9384 (tp) REVERT: B 702 MET cc_start: 0.9129 (mmm) cc_final: 0.8878 (mmm) REVERT: B 908 MET cc_start: 0.8579 (tmm) cc_final: 0.8107 (tmm) REVERT: B 1075 MET cc_start: 0.9197 (mmm) cc_final: 0.8859 (mmm) REVERT: B 1163 MET cc_start: 0.9642 (mtm) cc_final: 0.9289 (mtm) REVERT: C 15 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9308 (p) REVERT: E 18 MET cc_start: 0.8417 (mmm) cc_final: 0.8101 (mmm) REVERT: F 75 MET cc_start: 0.9124 (mtp) cc_final: 0.8842 (mtp) REVERT: L 44 MET cc_start: 0.8430 (mmt) cc_final: 0.8107 (mmm) REVERT: G 164 MET cc_start: 0.7906 (mtt) cc_final: 0.7617 (mmm) REVERT: O 300 MET cc_start: 0.0258 (ttp) cc_final: -0.0208 (tpp) REVERT: O 654 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7915 (mmtm) outliers start: 59 outliers final: 24 residues processed: 260 average time/residue: 0.2504 time to fit residues: 110.3228 Evaluate side-chains 235 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 747 ARG Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 342 ILE Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 92 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 293 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.055054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.034320 restraints weight = 310326.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034523 restraints weight = 179191.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035160 restraints weight = 122169.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.035482 restraints weight = 83849.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035508 restraints weight = 69670.368| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 42215 Z= 0.226 Angle : 0.686 15.613 57364 Z= 0.338 Chirality : 0.045 0.445 6384 Planarity : 0.004 0.050 7139 Dihedral : 13.636 176.884 6321 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.27 % Rotamer: Outliers : 1.42 % Allowed : 10.37 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4884 helix: 1.28 (0.13), residues: 1649 sheet: -1.05 (0.17), residues: 847 loop : -0.59 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 695 TYR 0.017 0.001 TYR B 766 PHE 0.021 0.002 PHE G 44 TRP 0.014 0.002 TRP C 203 HIS 0.005 0.001 HIS K 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (42187) covalent geometry : angle 0.67724 / 0.34 (57343) hydrogen bonds : bond 0.03727 / 2.48 ( 1669) hydrogen bonds : angle 4.78086 / 3.31 ( 4687) metal coordination : bond 0.01038 / 0.59 ( 26) metal coordination : angle 5.76241 / 3.63 ( 21) Misc. bond : bond 0.00424 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9108 (mmmm) REVERT: Z 726 ASP cc_start: 0.8428 (t0) cc_final: 0.8104 (t0) REVERT: Z 746 ASP cc_start: 0.9488 (m-30) cc_final: 0.9214 (p0) REVERT: Z 747 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8636 (ttm110) REVERT: Z 751 THR cc_start: 0.9326 (m) cc_final: 0.9074 (p) REVERT: M 346 MET cc_start: 0.0444 (tpt) cc_final: -0.0560 (mmt) REVERT: M 437 MET cc_start: 0.3786 (ttt) cc_final: 0.3332 (tmm) REVERT: A 78 MET cc_start: 0.8445 (ttm) cc_final: 0.8227 (ttm) REVERT: A 104 MET cc_start: 0.9579 (mtp) cc_final: 0.8861 (tmm) REVERT: A 248 MET cc_start: 0.9288 (mtp) cc_final: 0.8404 (ttm) REVERT: A 329 MET cc_start: 0.9295 (tpp) cc_final: 0.8981 (tpp) REVERT: A 470 MET cc_start: 0.7936 (mtp) cc_final: 0.7662 (mtp) REVERT: A 524 MET cc_start: 0.8727 (mtp) cc_final: 0.8456 (mtp) REVERT: A 769 MET cc_start: 0.9250 (mtt) cc_final: 0.9008 (mtt) REVERT: A 959 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9181 (mmp) REVERT: A 1228 MET cc_start: 0.8665 (mmm) cc_final: 0.8007 (mtt) REVERT: A 1344 MET cc_start: 0.8589 (ppp) cc_final: 0.8259 (ppp) REVERT: A 1440 MET cc_start: 0.9289 (mmm) cc_final: 0.8527 (mmm) REVERT: B 108 MET cc_start: 0.8698 (ppp) cc_final: 0.8254 (ppp) REVERT: B 109 MET cc_start: 0.9049 (mmm) cc_final: 0.8412 (mmm) REVERT: B 155 MET cc_start: 0.8946 (ptt) cc_final: 0.8469 (ptt) REVERT: B 298 MET cc_start: 0.9516 (mtt) cc_final: 0.8808 (mpp) REVERT: B 529 MET cc_start: 0.9051 (mmm) cc_final: 0.8813 (mmm) REVERT: B 675 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9375 (tp) REVERT: B 677 MET cc_start: 0.8996 (mmm) cc_final: 0.8714 (mmm) REVERT: B 702 MET cc_start: 0.9207 (mmm) cc_final: 0.8883 (mmm) REVERT: B 908 MET cc_start: 0.8725 (tmm) cc_final: 0.8276 (tmm) REVERT: B 1075 MET cc_start: 0.9182 (mmm) cc_final: 0.8772 (mmm) REVERT: B 1163 MET cc_start: 0.9665 (mtm) cc_final: 0.9306 (mtm) REVERT: C 15 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9280 (p) REVERT: J 48 MET cc_start: 0.9615 (mmm) cc_final: 0.9405 (mmm) REVERT: L 44 MET cc_start: 0.8512 (mmt) cc_final: 0.8222 (mmm) REVERT: G 104 MET cc_start: 0.7727 (mmm) cc_final: 0.7189 (mmm) REVERT: G 164 MET cc_start: 0.7916 (mtt) cc_final: 0.7610 (mmm) REVERT: O 300 MET cc_start: 0.0410 (ttp) cc_final: -0.0054 (tpp) REVERT: O 654 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8078 (mmtm) outliers start: 62 outliers final: 36 residues processed: 254 average time/residue: 0.2483 time to fit residues: 108.0478 Evaluate side-chains 234 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 747 ARG Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain O residue 171 MET Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 342 ILE Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 417 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 chunk 445 optimal weight: 8.9990 chunk 461 optimal weight: 50.0000 chunk 70 optimal weight: 5.9990 chunk 443 optimal weight: 50.0000 chunk 247 optimal weight: 0.9990 chunk 453 optimal weight: 40.0000 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 50.0000 chunk 435 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 ASN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.054692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.033871 restraints weight = 313002.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034341 restraints weight = 177039.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034596 restraints weight = 117637.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.034875 restraints weight = 91886.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035088 restraints weight = 73457.993| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 42215 Z= 0.226 Angle : 0.677 16.821 57364 Z= 0.334 Chirality : 0.045 0.391 6384 Planarity : 0.004 0.050 7139 Dihedral : 13.582 175.288 6321 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.50 % Favored : 95.48 % Rotamer: Outliers : 1.26 % Allowed : 10.88 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.12), residues: 4884 helix: 1.32 (0.13), residues: 1658 sheet: -0.92 (0.17), residues: 829 loop : -0.57 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 528 TYR 0.017 0.001 TYR B 766 PHE 0.021 0.001 PHE E 73 TRP 0.013 0.001 TRP C 203 HIS 0.014 0.001 HIS O 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (42187) covalent geometry : angle 0.66738 / 0.33 (57343) hydrogen bonds : bond 0.03585 / 2.39 ( 1669) hydrogen bonds : angle 4.74548 / 3.28 ( 4687) metal coordination : bond 0.01070 / 0.59 ( 26) metal coordination : angle 5.85603 / 3.63 ( 21) Misc. bond : bond 0.00450 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9101 (mmmm) REVERT: Z 726 ASP cc_start: 0.8378 (t0) cc_final: 0.8051 (t0) REVERT: Z 746 ASP cc_start: 0.9428 (m-30) cc_final: 0.9180 (p0) REVERT: Z 747 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8608 (ttm110) REVERT: M 346 MET cc_start: 0.0503 (tpt) cc_final: -0.0450 (mmt) REVERT: A 78 MET cc_start: 0.8430 (ttm) cc_final: 0.8198 (ttm) REVERT: A 104 MET cc_start: 0.9575 (mtp) cc_final: 0.8888 (tmm) REVERT: A 248 MET cc_start: 0.9314 (mtp) cc_final: 0.8361 (ttm) REVERT: A 329 MET cc_start: 0.9374 (tpp) cc_final: 0.9068 (tpp) REVERT: A 355 MET cc_start: 0.9404 (mmm) cc_final: 0.8442 (mmm) REVERT: A 388 MET cc_start: 0.9343 (mmt) cc_final: 0.8643 (mmt) REVERT: A 470 MET cc_start: 0.7872 (mtp) cc_final: 0.7631 (mtp) REVERT: A 501 MET cc_start: 0.9269 (mmm) cc_final: 0.8631 (mmm) REVERT: A 561 MET cc_start: 0.9037 (mmm) cc_final: 0.8815 (tpp) REVERT: A 769 MET cc_start: 0.9268 (mtt) cc_final: 0.9036 (mtt) REVERT: A 1228 MET cc_start: 0.8725 (mmm) cc_final: 0.8029 (mtt) REVERT: A 1344 MET cc_start: 0.8581 (ppp) cc_final: 0.8246 (ppp) REVERT: A 1412 MET cc_start: 0.8861 (tpp) cc_final: 0.8334 (tpp) REVERT: A 1440 MET cc_start: 0.9332 (mmm) cc_final: 0.8546 (mmm) REVERT: B 108 MET cc_start: 0.8723 (ppp) cc_final: 0.8357 (ppp) REVERT: B 109 MET cc_start: 0.9060 (mmm) cc_final: 0.8552 (mmm) REVERT: B 155 MET cc_start: 0.8897 (ptt) cc_final: 0.8404 (ptt) REVERT: B 298 MET cc_start: 0.9529 (mtt) cc_final: 0.8867 (mpp) REVERT: B 508 MET cc_start: 0.9387 (mmm) cc_final: 0.8894 (mmm) REVERT: B 529 MET cc_start: 0.9029 (mmm) cc_final: 0.8816 (mmm) REVERT: B 603 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8311 (pmm) REVERT: B 675 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9348 (tp) REVERT: B 677 MET cc_start: 0.9000 (mmm) cc_final: 0.8357 (tpp) REVERT: B 702 MET cc_start: 0.9227 (mmm) cc_final: 0.8957 (mmm) REVERT: B 840 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.4698 (tmm) REVERT: B 908 MET cc_start: 0.8766 (tmm) cc_final: 0.8235 (tmm) REVERT: B 1075 MET cc_start: 0.9178 (mmm) cc_final: 0.8692 (mmm) REVERT: B 1163 MET cc_start: 0.9650 (mtm) cc_final: 0.9302 (mtm) REVERT: C 15 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9294 (p) REVERT: J 48 MET cc_start: 0.9632 (mmm) cc_final: 0.9365 (mmm) REVERT: L 44 MET cc_start: 0.8384 (mmt) cc_final: 0.8160 (mmm) REVERT: G 164 MET cc_start: 0.7900 (mtt) cc_final: 0.7595 (mmm) REVERT: O 240 MET cc_start: 0.8060 (ptm) cc_final: 0.6907 (tpt) REVERT: O 300 MET cc_start: 0.1850 (ttp) cc_final: 0.0947 (tpp) REVERT: O 594 MET cc_start: 0.3647 (pmm) cc_final: 0.3307 (pmm) REVERT: O 654 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8085 (mmtm) REVERT: O 698 MET cc_start: 0.1965 (pmm) cc_final: 0.1718 (pmm) outliers start: 55 outliers final: 35 residues processed: 244 average time/residue: 0.2507 time to fit residues: 104.2476 Evaluate side-chains 237 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 736 LEU Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 747 ARG Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 342 ILE Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 47 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 276 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 347 optimal weight: 9.9990 chunk 417 optimal weight: 40.0000 chunk 23 optimal weight: 50.0000 chunk 482 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.053899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033078 restraints weight = 311477.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.033378 restraints weight = 172089.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033692 restraints weight = 114801.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034185 restraints weight = 90589.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034446 restraints weight = 74967.945| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 42215 Z= 0.273 Angle : 0.724 18.446 57364 Z= 0.355 Chirality : 0.045 0.334 6384 Planarity : 0.004 0.055 7139 Dihedral : 13.591 175.597 6321 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 1.28 % Allowed : 11.11 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4884 helix: 1.31 (0.13), residues: 1666 sheet: -0.86 (0.18), residues: 814 loop : -0.55 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 960 TYR 0.017 0.002 TYR B 766 PHE 0.030 0.002 PHE M 311 TRP 0.016 0.002 TRP M 293 HIS 0.007 0.001 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.27 (42187) covalent geometry : angle 0.71284 / 0.35 (57343) hydrogen bonds : bond 0.03881 / 2.60 ( 1669) hydrogen bonds : angle 4.80624 / 3.32 ( 4687) metal coordination : bond 0.01334 / 0.73 ( 26) metal coordination : angle 6.55320 / 4.07 ( 21) Misc. bond : bond 0.00453 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9406 (mmmm) cc_final: 0.9124 (mmmm) REVERT: Z 726 ASP cc_start: 0.8417 (t0) cc_final: 0.8104 (t0) REVERT: Z 746 ASP cc_start: 0.9436 (m-30) cc_final: 0.9152 (p0) REVERT: M 346 MET cc_start: 0.0814 (tpt) cc_final: -0.0045 (mmt) REVERT: A 78 MET cc_start: 0.8487 (ttm) cc_final: 0.7938 (ttt) REVERT: A 104 MET cc_start: 0.9562 (mtp) cc_final: 0.8902 (tmm) REVERT: A 248 MET cc_start: 0.9256 (mtp) cc_final: 0.8378 (ttm) REVERT: A 346 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8655 (ttmt) REVERT: A 467 MET cc_start: 0.9075 (mpp) cc_final: 0.8681 (mpp) REVERT: A 501 MET cc_start: 0.9234 (mmm) cc_final: 0.8600 (mmm) REVERT: A 524 MET cc_start: 0.8742 (mtp) cc_final: 0.8416 (ttm) REVERT: A 561 MET cc_start: 0.9215 (mmm) cc_final: 0.8952 (mmm) REVERT: A 769 MET cc_start: 0.9251 (mtt) cc_final: 0.9043 (mtt) REVERT: A 986 MET cc_start: 0.9462 (OUTLIER) cc_final: 0.8875 (mpp) REVERT: A 1102 MET cc_start: 0.9281 (ppp) cc_final: 0.9068 (ppp) REVERT: A 1228 MET cc_start: 0.8782 (mmm) cc_final: 0.8138 (mtt) REVERT: A 1344 MET cc_start: 0.8571 (ppp) cc_final: 0.8232 (ppp) REVERT: A 1412 MET cc_start: 0.8807 (tpp) cc_final: 0.8586 (tpp) REVERT: A 1440 MET cc_start: 0.9361 (mmm) cc_final: 0.8558 (mmm) REVERT: B 108 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8376 (ppp) REVERT: B 109 MET cc_start: 0.9118 (mmm) cc_final: 0.8605 (mmm) REVERT: B 155 MET cc_start: 0.8987 (ptt) cc_final: 0.8475 (ptt) REVERT: B 298 MET cc_start: 0.9590 (mtt) cc_final: 0.9375 (ptp) REVERT: B 347 MET cc_start: 0.9001 (ppp) cc_final: 0.8582 (ppp) REVERT: B 529 MET cc_start: 0.9078 (mmm) cc_final: 0.8853 (mmm) REVERT: B 675 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9371 (tp) REVERT: B 677 MET cc_start: 0.8992 (mmm) cc_final: 0.8362 (tpp) REVERT: B 702 MET cc_start: 0.9264 (mmm) cc_final: 0.8958 (mmm) REVERT: B 840 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.4449 (tmm) REVERT: B 908 MET cc_start: 0.8783 (tmm) cc_final: 0.8324 (tmm) REVERT: B 1075 MET cc_start: 0.9194 (mmm) cc_final: 0.8685 (mmm) REVERT: B 1163 MET cc_start: 0.9658 (mtm) cc_final: 0.9297 (mtm) REVERT: C 15 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9263 (p) REVERT: E 121 MET cc_start: 0.9002 (pmm) cc_final: 0.8771 (pmm) REVERT: J 48 MET cc_start: 0.9637 (mmm) cc_final: 0.9376 (mmm) REVERT: L 44 MET cc_start: 0.8273 (mmt) cc_final: 0.7968 (mmm) REVERT: G 164 MET cc_start: 0.7913 (mtt) cc_final: 0.7499 (mmm) REVERT: O 300 MET cc_start: 0.2469 (ttp) cc_final: 0.1463 (tpp) REVERT: O 594 MET cc_start: 0.3897 (pmm) cc_final: 0.3515 (pmm) REVERT: O 654 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8187 (mmtm) REVERT: O 832 MET cc_start: 0.7645 (tmm) cc_final: 0.7413 (ppp) outliers start: 56 outliers final: 36 residues processed: 241 average time/residue: 0.2410 time to fit residues: 99.7306 Evaluate side-chains 236 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 751 THR Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 481 LEU Chi-restraints excluded: chain M residue 482 LEU Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1214 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1127 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 49 optimal weight: 10.0000 chunk 367 optimal weight: 1.9990 chunk 375 optimal weight: 0.9990 chunk 455 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 196 optimal weight: 30.0000 chunk 271 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 407 optimal weight: 30.0000 chunk 332 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.055202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034461 restraints weight = 305907.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034727 restraints weight = 173003.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.035257 restraints weight = 114414.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.035471 restraints weight = 85566.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035739 restraints weight = 70230.722| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42215 Z= 0.118 Angle : 0.651 17.881 57364 Z= 0.317 Chirality : 0.045 0.334 6384 Planarity : 0.004 0.043 7139 Dihedral : 13.486 173.595 6321 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 1.17 % Allowed : 11.50 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 4884 helix: 1.43 (0.13), residues: 1662 sheet: -0.72 (0.18), residues: 845 loop : -0.44 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 58 TYR 0.016 0.001 TYR A 444 PHE 0.021 0.001 PHE E 73 TRP 0.012 0.001 TRP A 679 HIS 0.008 0.001 HIS C 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (42187) covalent geometry : angle 0.64390 / 0.32 (57343) hydrogen bonds : bond 0.03209 / 2.15 ( 1669) hydrogen bonds : angle 4.60951 / 3.18 ( 4687) metal coordination : bond 0.00450 / 0.29 ( 26) metal coordination : angle 5.00033 / 3.01 ( 21) Misc. bond : bond 0.00455 / 0.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9352 (mmmm) cc_final: 0.9074 (mmmm) REVERT: Z 726 ASP cc_start: 0.8389 (t0) cc_final: 0.8081 (t0) REVERT: Z 746 ASP cc_start: 0.9428 (m-30) cc_final: 0.9204 (p0) REVERT: Z 747 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8574 (ttm110) REVERT: A 78 MET cc_start: 0.8479 (ttm) cc_final: 0.8239 (ttm) REVERT: A 104 MET cc_start: 0.9545 (mtp) cc_final: 0.8903 (tmm) REVERT: A 248 MET cc_start: 0.9191 (mtp) cc_final: 0.8257 (ttm) REVERT: A 329 MET cc_start: 0.8766 (tpp) cc_final: 0.8387 (tpp) REVERT: A 388 MET cc_start: 0.9268 (mmt) cc_final: 0.8761 (mmt) REVERT: A 501 MET cc_start: 0.9273 (mmm) cc_final: 0.8559 (mmm) REVERT: A 769 MET cc_start: 0.9241 (mtt) cc_final: 0.8979 (mtt) REVERT: A 959 MET cc_start: 0.9500 (mmt) cc_final: 0.9191 (mmp) REVERT: A 1102 MET cc_start: 0.9180 (ppp) cc_final: 0.8960 (ppp) REVERT: A 1228 MET cc_start: 0.8666 (mmm) cc_final: 0.7940 (mtt) REVERT: A 1344 MET cc_start: 0.8503 (ppp) cc_final: 0.8057 (ppp) REVERT: A 1412 MET cc_start: 0.8611 (tpp) cc_final: 0.7531 (tpp) REVERT: A 1440 MET cc_start: 0.9299 (mmm) cc_final: 0.8478 (mmm) REVERT: A 1459 MET cc_start: 0.9308 (mtm) cc_final: 0.9083 (mtm) REVERT: B 108 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8329 (ppp) REVERT: B 109 MET cc_start: 0.9010 (mmm) cc_final: 0.8226 (mmm) REVERT: B 155 MET cc_start: 0.8779 (ptt) cc_final: 0.8299 (ptt) REVERT: B 200 MET cc_start: 0.8630 (mmm) cc_final: 0.8176 (mmt) REVERT: B 240 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9128 (mm) REVERT: B 298 MET cc_start: 0.9566 (mtt) cc_final: 0.8934 (mpp) REVERT: B 347 MET cc_start: 0.8924 (ppp) cc_final: 0.8460 (ppp) REVERT: B 361 LYS cc_start: 0.9766 (OUTLIER) cc_final: 0.9340 (mmtp) REVERT: B 508 MET cc_start: 0.9363 (mmm) cc_final: 0.8633 (mmm) REVERT: B 529 MET cc_start: 0.9046 (mmm) cc_final: 0.8796 (mmm) REVERT: B 603 MET cc_start: 0.8763 (mpp) cc_final: 0.8472 (pmm) REVERT: B 675 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9333 (tp) REVERT: B 677 MET cc_start: 0.8878 (mmm) cc_final: 0.8265 (tpp) REVERT: B 702 MET cc_start: 0.9140 (mmm) cc_final: 0.8883 (mmm) REVERT: B 840 MET cc_start: 0.5949 (OUTLIER) cc_final: 0.4770 (tmm) REVERT: B 908 MET cc_start: 0.8790 (tmm) cc_final: 0.8399 (tmm) REVERT: B 1075 MET cc_start: 0.9174 (mmm) cc_final: 0.8635 (mmm) REVERT: B 1163 MET cc_start: 0.9650 (mtm) cc_final: 0.9310 (mtm) REVERT: C 15 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9297 (p) REVERT: E 121 MET cc_start: 0.8951 (pmm) cc_final: 0.8634 (pmm) REVERT: H 123 MET cc_start: 0.9536 (tmm) cc_final: 0.9145 (tmm) REVERT: O 594 MET cc_start: 0.4151 (pmm) cc_final: 0.3810 (pmm) REVERT: O 654 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8111 (mmtm) outliers start: 51 outliers final: 28 residues processed: 246 average time/residue: 0.2499 time to fit residues: 104.3003 Evaluate side-chains 235 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 747 ARG Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 21 GLU Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 379 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 453 optimal weight: 9.9990 chunk 482 optimal weight: 9.9990 chunk 475 optimal weight: 6.9990 chunk 387 optimal weight: 40.0000 chunk 373 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 370 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.054559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033911 restraints weight = 308243.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034346 restraints weight = 172888.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034556 restraints weight = 113970.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034850 restraints weight = 95168.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.034964 restraints weight = 77156.959| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42215 Z= 0.174 Angle : 0.664 15.478 57364 Z= 0.324 Chirality : 0.044 0.320 6384 Planarity : 0.004 0.047 7139 Dihedral : 13.442 173.539 6321 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 0.87 % Allowed : 12.00 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.22 (0.13), residues: 4884 helix: 1.47 (0.13), residues: 1666 sheet: -0.74 (0.18), residues: 830 loop : -0.41 (0.14), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG G 63 TYR 0.014 0.001 TYR A 413 PHE 0.019 0.001 PHE E 73 TRP 0.012 0.001 TRP B 27 HIS 0.007 0.001 HIS C 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (42187) covalent geometry : angle 0.65637 / 0.32 (57343) hydrogen bonds : bond 0.03389 / 2.28 ( 1669) hydrogen bonds : angle 4.62948 / 3.20 ( 4687) metal coordination : bond 0.00711 / 0.41 ( 26) metal coordination : angle 5.25577 / 3.25 ( 21) Misc. bond : bond 0.00465 / 0.24 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9768 Ramachandran restraints generated. 4884 Oldfield, 0 Emsley, 4884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 725 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9086 (mmmm) REVERT: Z 726 ASP cc_start: 0.8407 (t0) cc_final: 0.8099 (t0) REVERT: Z 746 ASP cc_start: 0.9461 (m-30) cc_final: 0.9241 (p0) REVERT: Z 747 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8542 (ttm110) REVERT: A 78 MET cc_start: 0.8502 (ttm) cc_final: 0.8007 (ttt) REVERT: A 104 MET cc_start: 0.9550 (mtp) cc_final: 0.8920 (tmm) REVERT: A 248 MET cc_start: 0.9212 (mtp) cc_final: 0.8300 (ttm) REVERT: A 329 MET cc_start: 0.8878 (tpp) cc_final: 0.8554 (tpp) REVERT: A 388 MET cc_start: 0.9253 (mmt) cc_final: 0.8719 (mmt) REVERT: A 501 MET cc_start: 0.9257 (mmm) cc_final: 0.8580 (mmm) REVERT: A 769 MET cc_start: 0.9232 (mtt) cc_final: 0.8979 (mtt) REVERT: A 959 MET cc_start: 0.9503 (mmt) cc_final: 0.9201 (mmp) REVERT: A 1102 MET cc_start: 0.9242 (ppp) cc_final: 0.9010 (ppp) REVERT: A 1228 MET cc_start: 0.8774 (mmm) cc_final: 0.8049 (mtt) REVERT: A 1344 MET cc_start: 0.8504 (ppp) cc_final: 0.8075 (ppp) REVERT: A 1440 MET cc_start: 0.9331 (mmm) cc_final: 0.8467 (mmm) REVERT: B 108 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8353 (ppp) REVERT: B 109 MET cc_start: 0.9054 (mmm) cc_final: 0.8276 (mmm) REVERT: B 155 MET cc_start: 0.8920 (ptt) cc_final: 0.8469 (ptt) REVERT: B 298 MET cc_start: 0.9559 (mtt) cc_final: 0.8950 (mpp) REVERT: B 347 MET cc_start: 0.8858 (ppp) cc_final: 0.8280 (ppp) REVERT: B 361 LYS cc_start: 0.9737 (OUTLIER) cc_final: 0.9291 (mmtp) REVERT: B 508 MET cc_start: 0.9352 (mmm) cc_final: 0.8688 (mmm) REVERT: B 529 MET cc_start: 0.9064 (mmm) cc_final: 0.8802 (mmm) REVERT: B 603 MET cc_start: 0.8633 (mpp) cc_final: 0.8422 (pmm) REVERT: B 675 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9345 (tp) REVERT: B 677 MET cc_start: 0.8936 (mmm) cc_final: 0.8332 (tpp) REVERT: B 702 MET cc_start: 0.9180 (mmm) cc_final: 0.8887 (mmm) REVERT: B 840 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.4821 (tmm) REVERT: B 908 MET cc_start: 0.8816 (tmm) cc_final: 0.8397 (tmm) REVERT: B 954 MET cc_start: 0.8965 (mtp) cc_final: 0.8736 (mtt) REVERT: B 1075 MET cc_start: 0.9199 (mmm) cc_final: 0.8664 (mmm) REVERT: B 1163 MET cc_start: 0.9651 (mtm) cc_final: 0.9296 (mtm) REVERT: C 15 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9269 (p) REVERT: E 72 MET cc_start: 0.8609 (tpp) cc_final: 0.8279 (tpp) REVERT: E 121 MET cc_start: 0.9000 (pmm) cc_final: 0.8658 (pmm) REVERT: G 164 MET cc_start: 0.7967 (mtt) cc_final: 0.7568 (mmm) REVERT: O 240 MET cc_start: 0.7665 (ptt) cc_final: 0.6475 (tpt) REVERT: O 594 MET cc_start: 0.3751 (pmm) cc_final: 0.3358 (pmm) REVERT: O 654 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8136 (mmtm) outliers start: 38 outliers final: 27 residues processed: 228 average time/residue: 0.2474 time to fit residues: 96.2068 Evaluate side-chains 230 residues out of total 4391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 747 ARG Chi-restraints excluded: chain M residue 296 ASP Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 551 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1374 VAL Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain B residue 22 TRP Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 654 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 83 optimal weight: 5.9990 chunk 319 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 415 optimal weight: 40.0000 chunk 434 optimal weight: 20.0000 chunk 237 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 392 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.054540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033919 restraints weight = 312122.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.034482 restraints weight = 174944.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.034553 restraints weight = 114408.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034831 restraints weight = 92993.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.034857 restraints weight = 72254.074| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 42215 Z= 0.200 Angle : 0.737 59.197 57364 Z= 0.382 Chirality : 0.047 1.224 6384 Planarity : 0.004 0.044 7139 Dihedral : 13.447 173.523 6321 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.67 % Favored : 95.31 % Rotamer: Outliers : 0.85 % Allowed : 12.09 % Favored : 87.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 4884 helix: 1.48 (0.13), residues: 1665 sheet: -0.74 (0.18), residues: 830 loop : -0.41 (0.14), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 63 TYR 0.039 0.001 TYR B 388 PHE 0.019 0.001 PHE E 73 TRP 0.012 0.001 TRP B 27 HIS 0.007 0.001 HIS O 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (42187) covalent geometry : angle 0.72992 / 0.38 (57343) hydrogen bonds : bond 0.03405 / 2.28 ( 1669) hydrogen bonds : angle 4.64001 / 3.20 ( 4687) metal coordination : bond 0.00703 / 0.40 ( 26) metal coordination : angle 5.23793 / 3.24 ( 21) Misc. bond : bond 0.00467 / 0.25 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8175.18 seconds wall clock time: 142 minutes 10.63 seconds (8530.63 seconds total)