Starting phenix.real_space_refine on Mon Sep 14 19:54:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5w_32322/09_2026/7w5w_32322.map" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 20317 2.51 5 N 5871 2.21 5 O 6604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 154 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33053 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2418 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10528 Classifications: {'peptide': 1336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1282} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 10344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10344 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3861 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 466} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "1" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1288 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain: "2" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1305 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "J" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 912 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15317 SG CYS D 88 119.413 89.804 73.674 1.00219.36 S ATOM 21530 SG CYS D 888 85.095 106.273 128.900 1.00 87.42 S ATOM 21581 SG CYS D 895 84.338 103.229 130.693 1.00 90.57 S Time building chain proxies: 6.60, per 1000 atoms: 0.20 Number of scatterers: 33053 At special positions: 0 Unit cell: (177.1, 199.1, 166.1, 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 2 29.99 S 133 16.00 P 125 15.00 Mg 1 11.99 O 6604 8.00 N 5871 7.00 C 20317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7210 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 43 sheets defined 39.5% alpha, 10.9% beta 27 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.559A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 212 through 227 removed outlier: 4.044A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.643A pdb=" N LEU A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 4.190A pdb=" N LYS A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.580A pdb=" N VAL A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 4.172A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.696A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.668A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.697A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.094A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.062A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.607A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.884A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.672A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.659A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.797A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.608A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.757A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.604A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.653A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.574A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.532A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 476 removed outlier: 3.636A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.707A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.119A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 506 removed outlier: 4.570A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 609 through 614 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.589A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.686A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 683 removed outlier: 3.998A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 710 removed outlier: 3.802A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.620A pdb=" N LEU C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 972 removed outlier: 3.827A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.525A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.609A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 997' Processing helix chain 'C' and resid 1008 through 1038 removed outlier: 3.555A pdb=" N GLU C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1133 removed outlier: 4.177A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C1118 " --> pdb=" O GLU C1114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C1128 " --> pdb=" O ILE C1124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 3.653A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.832A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1173 removed outlier: 3.513A pdb=" N VAL C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.773A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.742A pdb=" N GLU C1279 " --> pdb=" O VAL C1275 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 removed outlier: 3.593A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C1289 " --> pdb=" O TYR C1285 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1283 through 1290' Processing helix chain 'C' and resid 1300 through 1308 removed outlier: 3.642A pdb=" N MET C1304 " --> pdb=" O GLY C1300 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.692A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.524A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.879A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.515A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.732A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 284 removed outlier: 3.661A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.751A pdb=" N MET D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.789A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 401 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.703A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 4.254A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.665A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 removed outlier: 4.187A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.760A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.565A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 3.755A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 574 through 579' Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.942A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.809A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.710A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 627 " --> pdb=" O GLN D 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.708A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 removed outlier: 3.677A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 686 removed outlier: 3.801A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 693 Processing helix chain 'D' and resid 693 through 703 removed outlier: 3.641A pdb=" N MET D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 727 Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 776 through 802 removed outlier: 4.055A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.612A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 4.263A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 removed outlier: 3.774A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.619A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 4.078A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.528A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.635A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1259 removed outlier: 4.369A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1287 removed outlier: 3.743A pdb=" N ARG D1284 " --> pdb=" O VAL D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 4.084A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D1335 " --> pdb=" O VAL D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.525A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.844A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 removed outlier: 3.961A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.541A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 56 removed outlier: 4.308A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 4.193A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.698A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.946A pdb=" N GLY F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 4.269A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 152 removed outlier: 3.695A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 213 through 218 removed outlier: 3.642A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 213 through 218' Processing helix chain 'F' and resid 219 through 237 removed outlier: 3.650A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 removed outlier: 3.649A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 291 removed outlier: 3.555A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 281 " --> pdb=" O MET F 277 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.868A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 Processing helix chain 'F' and resid 325 through 329 removed outlier: 3.967A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS F 329 " --> pdb=" O TRP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 329' Processing helix chain 'F' and resid 334 through 352 removed outlier: 3.607A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 350 " --> pdb=" O GLN F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 383 removed outlier: 4.007A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 394 removed outlier: 3.570A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 4.029A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN F 409 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.594A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 443 removed outlier: 4.226A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.702A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.618A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 501 No H-bonds generated for 'chain 'F' and resid 499 through 501' Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 550 removed outlier: 3.842A pdb=" N SER F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA F 535 " --> pdb=" O PRO F 531 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER F 539 " --> pdb=" O ALA F 535 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.684A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 577 removed outlier: 3.567A pdb=" N VAL F 576 " --> pdb=" O THR F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 600 removed outlier: 3.797A pdb=" N ALA F 594 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU F 598 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 607 removed outlier: 3.706A pdb=" N VAL F 606 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 removed outlier: 3.806A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 613 " --> pdb=" O PHE F 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 3.656A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA J 12 " --> pdb=" O GLN J 8 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP J 13 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP J 15 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS J 17 " --> pdb=" O TRP J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 3.682A pdb=" N VAL J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 42 Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 52 through 69 removed outlier: 3.813A pdb=" N ARG J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 96 removed outlier: 4.236A pdb=" N ARG J 94 " --> pdb=" O ARG J 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN J 95 " --> pdb=" O VAL J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.534A pdb=" N ARG J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.526A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.828A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 6.089A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 202 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.269A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.610A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 4.642A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 94 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.679A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.425A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.688A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.837A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.659A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 600 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.659A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.744A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.911A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 802 removed outlier: 3.697A pdb=" N LEU C1233 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 830 through 841 removed outlier: 7.208A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.855A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 887 " --> pdb=" O GLU C 849 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.593A pdb=" N LEU C 883 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.215A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.989A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.743A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.530A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.520A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.635A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AD6, first strand: chain 'D' and resid 550 through 556 removed outlier: 3.653A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 809 through 811 removed outlier: 7.702A pdb=" N VAL D 894 " --> pdb=" O THR D 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.507A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.773A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.987A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 993 removed outlier: 4.191A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.955A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.621A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1161 through 1162 removed outlier: 3.872A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1173 through 1174 Processing sheet with id=AE7, first strand: chain 'D' and resid 1264 through 1265 850 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9583 1.33 - 1.45: 6205 1.45 - 1.58: 17538 1.58 - 1.70: 248 1.70 - 1.82: 235 Bond restraints: 33809 Sorted by residual: bond pdb=" C1' DC 1 88 " pdb=" N1 DC 1 88 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" C1' DT 2 24 " pdb=" N1 DT 2 24 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" C1' DC 1 82 " pdb=" N1 DC 1 82 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" C1' DT 2 21 " pdb=" N1 DT 2 21 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.69e+01 bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.36e-02 5.41e+03 2.49e+01 ... (remaining 33804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 44134 2.18 - 4.36: 1822 4.36 - 6.55: 182 6.55 - 8.73: 46 8.73 - 10.91: 8 Bond angle restraints: 46192 Sorted by residual: angle pdb=" N VAL F 166 " pdb=" CA VAL F 166 " pdb=" C VAL F 166 " ideal model delta sigma weight residual 110.62 119.73 -9.11 1.02e+00 9.61e-01 7.98e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.74 132.65 -10.91 1.32e+00 5.74e-01 6.83e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 111.91 106.29 5.62 8.90e-01 1.26e+00 3.99e+01 angle pdb=" N THR F 163 " pdb=" CA THR F 163 " pdb=" C THR F 163 " ideal model delta sigma weight residual 111.28 104.66 6.62 1.09e+00 8.42e-01 3.69e+01 angle pdb=" C LYS F 502 " pdb=" N GLU F 503 " pdb=" CA GLU F 503 " ideal model delta sigma weight residual 122.48 132.21 -9.73 1.62e+00 3.81e-01 3.60e+01 ... (remaining 46187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 19515 34.20 - 68.40: 921 68.40 - 102.60: 50 102.60 - 136.81: 2 136.81 - 171.01: 4 Dihedral angle restraints: 20492 sinusoidal: 9321 harmonic: 11171 Sorted by residual: dihedral pdb=" CA GLY C 45 " pdb=" C GLY C 45 " pdb=" N GLN C 46 " pdb=" CA GLN C 46 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N LYS B 200 " pdb=" CA LYS B 200 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA TYR D 457 " pdb=" C TYR D 457 " pdb=" N ASN D 458 " pdb=" CA ASN D 458 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 20489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3713 0.056 - 0.111: 1230 0.111 - 0.167: 265 0.167 - 0.223: 39 0.223 - 0.279: 12 Chirality restraints: 5259 Sorted by residual: chirality pdb=" CB ILE F 212 " pdb=" CA ILE F 212 " pdb=" CG1 ILE F 212 " pdb=" CG2 ILE F 212 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' DG 1 73 " pdb=" C4' DG 1 73 " pdb=" O3' DG 1 73 " pdb=" C2' DG 1 73 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 5256 not shown) Planarity restraints: 5591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO D1139 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO C 552 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C1204 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO C1205 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C1205 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C1205 " -0.038 5.00e-02 4.00e+02 ... (remaining 5588 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 326 2.55 - 3.14: 24218 3.14 - 3.73: 51742 3.73 - 4.31: 67602 4.31 - 4.90: 104836 Nonbonded interactions: 248724 Sorted by model distance: nonbonded pdb=" N GLU B 193 " pdb=" OE1 GLU B 193 " model vdw 1.968 3.120 nonbonded pdb=" N7 DG 1 73 " pdb=" N1 DA 1 74 " model vdw 1.978 3.200 nonbonded pdb=" N GLU C 374 " pdb=" OE1 GLU C 374 " model vdw 1.985 3.120 nonbonded pdb=" O4 DT 1 86 " pdb=" O6 DG 1 87 " model vdw 2.039 3.040 nonbonded pdb=" O6 DG 1 84 " pdb=" N6 DA 1 85 " model vdw 2.092 3.120 ... (remaining 248719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 36.490 Find NCS groups from input model: 0.350 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.007 0.199 33812 Z= 0.399 Angle : 1.010 10.911 46192 Z= 0.630 Chirality : 0.058 0.279 5259 Planarity : 0.007 0.088 5591 Dihedral : 18.253 171.007 13282 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 0.91 % Allowed : 11.30 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -4.65 (0.10), residues: 3845 helix: -4.08 (0.08), residues: 1217 sheet: -2.34 (0.24), residues: 356 loop : -2.70 (0.11), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1059 TYR 0.035 0.002 TYR C1231 PHE 0.025 0.002 PHE C1265 TRP 0.033 0.003 TRP D 580 HIS 0.008 0.002 HIS D 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.39 (33809) covalent geometry : angle 1.01032 / 0.63 (46192) hydrogen bonds : bond 0.31887 / 21.16 ( 910) hydrogen bonds : angle 10.73053 / 7.44 ( 2492) metal coordination : bond 0.17975 / 8.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 624 time to evaluate : 1.231 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: A 8 PHE cc_start: 0.7238 (m-10) cc_final: 0.6914 (m-80) REVERT: A 51 MET cc_start: 0.9058 (mmm) cc_final: 0.8848 (mmm) REVERT: A 188 GLU cc_start: 0.7918 (mp0) cc_final: 0.7710 (mp0) REVERT: B 96 ASP cc_start: 0.7806 (m-30) cc_final: 0.5689 (t0) REVERT: B 226 GLU cc_start: 0.8339 (tp30) cc_final: 0.8112 (tp30) REVERT: C 92 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7448 (p90) REVERT: C 213 LEU cc_start: 0.9060 (mt) cc_final: 0.8816 (mt) REVERT: C 224 PHE cc_start: 0.8486 (m-80) cc_final: 0.7929 (m-10) REVERT: C 410 LEU cc_start: 0.8901 (mt) cc_final: 0.8375 (pp) REVERT: C 429 MET cc_start: 0.9396 (mmm) cc_final: 0.9109 (mmm) REVERT: C 504 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7755 (mt-10) REVERT: C 542 ARG cc_start: 0.6639 (mtt-85) cc_final: 0.5631 (tmt-80) REVERT: C 696 ASP cc_start: 0.8767 (t0) cc_final: 0.8257 (t0) REVERT: C 704 MET cc_start: 0.8534 (mtm) cc_final: 0.8267 (mmp) REVERT: C 705 GLU cc_start: 0.9120 (mp0) cc_final: 0.8801 (mp0) REVERT: C 706 ARG cc_start: 0.8799 (mtt-85) cc_final: 0.8537 (mmt90) REVERT: C 738 GLU cc_start: 0.7303 (pm20) cc_final: 0.6740 (pm20) REVERT: C 798 GLN cc_start: 0.8816 (mp10) cc_final: 0.8216 (mp10) REVERT: C 805 MET cc_start: 0.8842 (pmm) cc_final: 0.8416 (pmm) REVERT: C 955 GLN cc_start: 0.8695 (tp40) cc_final: 0.7895 (tm-30) REVERT: C 965 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 976 ARG cc_start: -0.4779 (OUTLIER) cc_final: -0.5631 (ttt-90) REVERT: C 1066 MET cc_start: 0.8439 (mmm) cc_final: 0.8085 (ttm) REVERT: C 1182 ILE cc_start: 0.9295 (mt) cc_final: 0.9090 (mm) REVERT: C 1214 ASP cc_start: 0.8974 (t70) cc_final: 0.8521 (t70) REVERT: C 1272 GLU cc_start: 0.8843 (pm20) cc_final: 0.8569 (pm20) REVERT: C 1273 MET cc_start: 0.9251 (mpp) cc_final: 0.8868 (mtt) REVERT: C 1290 MET cc_start: 0.8867 (mmt) cc_final: 0.8539 (mmp) REVERT: C 1321 GLU cc_start: 0.8880 (mp0) cc_final: 0.8548 (mp0) REVERT: D 76 LYS cc_start: 0.5507 (mmtt) cc_final: 0.4991 (tptp) REVERT: D 128 LEU cc_start: 0.9361 (mt) cc_final: 0.9114 (mm) REVERT: D 130 MET cc_start: 0.8295 (ttm) cc_final: 0.7817 (mtp) REVERT: D 134 ASP cc_start: 0.8984 (m-30) cc_final: 0.8665 (p0) REVERT: D 148 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 180 MET cc_start: 0.7970 (ttp) cc_final: 0.7285 (ttp) REVERT: D 192 MET cc_start: 0.8618 (ptm) cc_final: 0.8222 (ptp) REVERT: D 222 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8609 (tttp) REVERT: D 237 MET cc_start: 0.8926 (mmt) cc_final: 0.8554 (mmt) REVERT: D 264 ASP cc_start: 0.9191 (m-30) cc_final: 0.8916 (m-30) REVERT: D 300 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 360 TYR cc_start: 0.8462 (p90) cc_final: 0.8111 (p90) REVERT: D 435 GLN cc_start: 0.9071 (mt0) cc_final: 0.8694 (mp10) REVERT: D 438 GLU cc_start: 0.8391 (tt0) cc_final: 0.7869 (tt0) REVERT: D 457 TYR cc_start: 0.8915 (m-80) cc_final: 0.8443 (m-10) REVERT: D 487 THR cc_start: 0.9432 (m) cc_final: 0.9176 (t) REVERT: D 587 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8874 (pp) REVERT: D 601 ILE cc_start: 0.9609 (mt) cc_final: 0.9326 (tt) REVERT: D 622 ASP cc_start: 0.8116 (t0) cc_final: 0.7893 (t0) REVERT: D 625 MET cc_start: 0.8871 (mpp) cc_final: 0.8616 (mpp) REVERT: D 743 MET cc_start: 0.5058 (pmm) cc_final: 0.4787 (ppp) REVERT: D 747 MET cc_start: 0.5479 (mpp) cc_final: 0.5076 (mpp) REVERT: D 1040 MET cc_start: 0.1677 (mtm) cc_final: 0.1310 (ptt) REVERT: D 1229 VAL cc_start: 0.8459 (t) cc_final: 0.8144 (t) REVERT: D 1254 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8542 (tt0) REVERT: D 1290 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7470 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9402 (pt) cc_final: 0.8805 (mt) REVERT: D 1352 ILE cc_start: 0.9637 (pt) cc_final: 0.9352 (tp) REVERT: E 10 VAL cc_start: 0.8730 (m) cc_final: 0.8490 (m) REVERT: E 25 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7477 (ptp-170) REVERT: E 30 MET cc_start: 0.8769 (mtp) cc_final: 0.8500 (ttt) REVERT: E 65 ASP cc_start: 0.8405 (m-30) cc_final: 0.7998 (p0) REVERT: F 104 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8267 (mm-30) REVERT: F 109 GLU cc_start: 0.7025 (pm20) cc_final: 0.6779 (tm-30) REVERT: F 227 GLN cc_start: 0.6854 (mm-40) cc_final: 0.5535 (tm-30) REVERT: F 281 ARG cc_start: 0.9167 (ttt180) cc_final: 0.8962 (ttp80) REVERT: F 338 HIS cc_start: 0.5877 (p90) cc_final: 0.5098 (t70) REVERT: F 365 MET cc_start: 0.8443 (tmm) cc_final: 0.8000 (ptm) REVERT: F 386 LEU cc_start: 0.9128 (tt) cc_final: 0.8815 (mt) REVERT: F 499 LYS cc_start: 0.8476 (pttp) cc_final: 0.8002 (ttmt) REVERT: F 555 GLU cc_start: 0.8701 (mp0) cc_final: 0.8415 (mp0) REVERT: J 42 PHE cc_start: 0.4074 (t80) cc_final: 0.3677 (t80) REVERT: J 50 LEU cc_start: 0.7693 (tp) cc_final: 0.7241 (pt) REVERT: J 78 MET cc_start: 0.5548 (ttp) cc_final: 0.5344 (ttp) outliers start: 30 outliers final: 11 residues processed: 651 average time/residue: 0.2477 time to fit residues: 247.4314 Evaluate side-chains 402 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 388 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS A 41 ASN B 66 HIS B 117 HIS B 132 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 462 ASN C 613 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C 832 HIS C1157 GLN C1220 GLN D 157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 488 ASN D 606 ASN D 702 GLN D 720 ASN D1114 GLN D1268 ASN D1326 GLN E 43 ASN F 128 ASN F 210 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 ASN F 568 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098538 restraints weight = 101966.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098173 restraints weight = 87119.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099129 restraints weight = 71322.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098974 restraints weight = 57970.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099073 restraints weight = 55752.512| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33812 Z= 0.163 Angle : 0.712 8.796 46192 Z= 0.388 Chirality : 0.047 0.295 5259 Planarity : 0.006 0.062 5591 Dihedral : 16.886 179.463 5643 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -3.74 (0.11), residues: 3845 helix: -2.87 (0.11), residues: 1315 sheet: -1.76 (0.24), residues: 375 loop : -2.38 (0.12), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 541 TYR 0.040 0.002 TYR J 37 PHE 0.016 0.002 PHE C 972 TRP 0.009 0.001 TRP F 433 HIS 0.015 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (33809) covalent geometry : angle 0.71240 / 0.39 (46192) hydrogen bonds : bond 0.07160 / 4.78 ( 910) hydrogen bonds : angle 6.62690 / 4.62 ( 2492) metal coordination : bond 0.00943 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 542 time to evaluate : 0.913 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: A 114 ASP cc_start: 0.8562 (p0) cc_final: 0.6939 (t0) REVERT: B 41 ASN cc_start: 0.8900 (t0) cc_final: 0.8594 (t0) REVERT: B 96 ASP cc_start: 0.7528 (m-30) cc_final: 0.6352 (t0) REVERT: C 118 LYS cc_start: 0.8093 (pttt) cc_final: 0.7110 (pttt) REVERT: C 130 MET cc_start: 0.8013 (ttm) cc_final: 0.7760 (ttp) REVERT: C 148 GLN cc_start: 0.8698 (tt0) cc_final: 0.8438 (tt0) REVERT: C 224 PHE cc_start: 0.7989 (m-80) cc_final: 0.7456 (m-10) REVERT: C 410 LEU cc_start: 0.8896 (mt) cc_final: 0.8359 (pp) REVERT: C 542 ARG cc_start: 0.6854 (mtt-85) cc_final: 0.5876 (tmt-80) REVERT: C 677 ASN cc_start: 0.8795 (m-40) cc_final: 0.8265 (t0) REVERT: C 696 ASP cc_start: 0.8407 (t0) cc_final: 0.8112 (t0) REVERT: C 732 ILE cc_start: 0.8929 (pt) cc_final: 0.8697 (mm) REVERT: C 768 MET cc_start: 0.8422 (ttp) cc_final: 0.8065 (mtp) REVERT: C 794 LEU cc_start: 0.9187 (tp) cc_final: 0.8766 (tp) REVERT: C 798 GLN cc_start: 0.8867 (mp10) cc_final: 0.8252 (mp10) REVERT: C 955 GLN cc_start: 0.8622 (tp40) cc_final: 0.8081 (tm-30) REVERT: C 965 GLN cc_start: 0.6491 (tm-30) cc_final: 0.6144 (tm-30) REVERT: C 1016 GLU cc_start: 0.1538 (tm-30) cc_final: 0.1215 (pt0) REVERT: C 1023 HIS cc_start: 0.6560 (m170) cc_final: 0.6209 (m170) REVERT: C 1214 ASP cc_start: 0.8918 (t70) cc_final: 0.8404 (t70) REVERT: C 1240 ASP cc_start: 0.8748 (m-30) cc_final: 0.8360 (t0) REVERT: C 1253 LEU cc_start: 0.9377 (tp) cc_final: 0.9075 (tp) REVERT: C 1276 TRP cc_start: 0.8515 (m-10) cc_final: 0.8037 (m-90) REVERT: C 1290 MET cc_start: 0.8777 (mmt) cc_final: 0.7982 (mmp) REVERT: D 76 LYS cc_start: 0.4801 (mmtt) cc_final: 0.4230 (tptp) REVERT: D 113 HIS cc_start: 0.9022 (t-90) cc_final: 0.8444 (t-170) REVERT: D 130 MET cc_start: 0.7882 (ttm) cc_final: 0.7453 (mtp) REVERT: D 134 ASP cc_start: 0.8638 (m-30) cc_final: 0.8325 (m-30) REVERT: D 180 MET cc_start: 0.7669 (ttp) cc_final: 0.7255 (ttp) REVERT: D 192 MET cc_start: 0.7944 (ptt) cc_final: 0.7727 (ptp) REVERT: D 237 MET cc_start: 0.8782 (mmt) cc_final: 0.8515 (mmt) REVERT: D 269 TYR cc_start: 0.9048 (m-80) cc_final: 0.8764 (m-80) REVERT: D 298 MET cc_start: 0.7424 (ptp) cc_final: 0.6671 (ptp) REVERT: D 321 LYS cc_start: 0.7706 (mttp) cc_final: 0.7505 (mttp) REVERT: D 355 ILE cc_start: 0.9340 (pt) cc_final: 0.9138 (pt) REVERT: D 360 TYR cc_start: 0.8338 (p90) cc_final: 0.7936 (p90) REVERT: D 370 LYS cc_start: 0.9457 (tppt) cc_final: 0.9240 (tppt) REVERT: D 435 GLN cc_start: 0.8814 (mt0) cc_final: 0.8427 (mp10) REVERT: D 457 TYR cc_start: 0.8648 (m-80) cc_final: 0.7170 (m-10) REVERT: D 487 THR cc_start: 0.9395 (m) cc_final: 0.9139 (t) REVERT: D 625 MET cc_start: 0.8267 (mpp) cc_final: 0.8037 (mpp) REVERT: D 747 MET cc_start: 0.5782 (mpp) cc_final: 0.5287 (mpp) REVERT: D 800 LEU cc_start: 0.9533 (mt) cc_final: 0.9312 (mm) REVERT: D 1254 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 1290 ARG cc_start: 0.7800 (mtt180) cc_final: 0.7392 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9194 (pt) cc_final: 0.8719 (mt) REVERT: D 1326 GLN cc_start: 0.8355 (mt0) cc_final: 0.7931 (mt0) REVERT: D 1330 ARG cc_start: 0.7058 (mmt180) cc_final: 0.6834 (mmt-90) REVERT: E 25 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7517 (ptp-170) REVERT: E 30 MET cc_start: 0.8682 (mtp) cc_final: 0.8342 (ttt) REVERT: E 31 GLN cc_start: 0.8502 (tp40) cc_final: 0.7840 (tp40) REVERT: F 109 GLU cc_start: 0.6928 (pm20) cc_final: 0.6682 (tp30) REVERT: F 227 GLN cc_start: 0.6704 (mm-40) cc_final: 0.5526 (tm-30) REVERT: F 338 HIS cc_start: 0.5882 (p90) cc_final: 0.5371 (t70) REVERT: F 470 MET cc_start: 0.8363 (mmt) cc_final: 0.7701 (mmt) REVERT: F 499 LYS cc_start: 0.8085 (pttp) cc_final: 0.7701 (ttmt) REVERT: J 17 HIS cc_start: 0.6666 (m170) cc_final: 0.6225 (m170) REVERT: J 50 LEU cc_start: 0.7367 (tp) cc_final: 0.7075 (pt) REVERT: J 86 GLN cc_start: 0.8895 (mp10) cc_final: 0.8619 (mm-40) outliers start: 7 outliers final: 2 residues processed: 548 average time/residue: 0.2184 time to fit residues: 194.1404 Evaluate side-chains 397 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 354 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 381 optimal weight: 50.0000 chunk 90 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 374 optimal weight: 50.0000 chunk 319 optimal weight: 0.0570 chunk 294 optimal weight: 40.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1209 GLN C1244 HIS D 45 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 72 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 HIS F 406 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096274 restraints weight = 101145.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.095329 restraints weight = 93344.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.095859 restraints weight = 80667.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096364 restraints weight = 68856.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.096440 restraints weight = 60264.999| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 33812 Z= 0.220 Angle : 0.717 9.014 46192 Z= 0.385 Chirality : 0.046 0.283 5259 Planarity : 0.005 0.056 5591 Dihedral : 16.897 178.907 5643 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.20 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.12), residues: 3845 helix: -2.17 (0.12), residues: 1328 sheet: -1.74 (0.25), residues: 366 loop : -2.13 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 364 TYR 0.020 0.002 TYR C1231 PHE 0.021 0.002 PHE F 259 TRP 0.022 0.002 TRP D 115 HIS 0.014 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (33809) covalent geometry : angle 0.71690 / 0.39 (46192) hydrogen bonds : bond 0.05929 / 4.02 ( 910) hydrogen bonds : angle 6.19643 / 4.27 ( 2492) metal coordination : bond 0.00425 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.168 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: A 48 LEU cc_start: 0.9557 (mt) cc_final: 0.9342 (mt) REVERT: A 183 ILE cc_start: 0.9091 (tt) cc_final: 0.8797 (mm) REVERT: B 17 GLU cc_start: 0.6691 (pm20) cc_final: 0.5898 (tm-30) REVERT: B 41 ASN cc_start: 0.8882 (t0) cc_final: 0.8609 (t0) REVERT: B 96 ASP cc_start: 0.7465 (m-30) cc_final: 0.6083 (t0) REVERT: B 198 LEU cc_start: 0.8852 (mt) cc_final: 0.8399 (pp) REVERT: C 224 PHE cc_start: 0.8046 (m-80) cc_final: 0.7472 (m-10) REVERT: C 542 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.5892 (tmt-80) REVERT: C 667 LEU cc_start: 0.8847 (mt) cc_final: 0.8467 (tt) REVERT: C 768 MET cc_start: 0.8168 (ttp) cc_final: 0.7935 (mtm) REVERT: C 903 ARG cc_start: 0.8670 (tmt-80) cc_final: 0.8003 (ttp80) REVERT: C 1214 ASP cc_start: 0.8944 (t70) cc_final: 0.8486 (t70) REVERT: C 1240 ASP cc_start: 0.8789 (m-30) cc_final: 0.8484 (t0) REVERT: C 1253 LEU cc_start: 0.9371 (tp) cc_final: 0.9095 (tp) REVERT: C 1276 TRP cc_start: 0.8602 (m-10) cc_final: 0.8120 (m-90) REVERT: D 29 MET cc_start: 0.7962 (tmm) cc_final: 0.7591 (tmm) REVERT: D 76 LYS cc_start: 0.4660 (mmtt) cc_final: 0.4446 (tptp) REVERT: D 130 MET cc_start: 0.7798 (ttm) cc_final: 0.7541 (mtp) REVERT: D 192 MET cc_start: 0.8025 (ptt) cc_final: 0.7798 (ptp) REVERT: D 269 TYR cc_start: 0.9113 (m-80) cc_final: 0.8811 (m-80) REVERT: D 298 MET cc_start: 0.8479 (ptp) cc_final: 0.8210 (ptp) REVERT: D 360 TYR cc_start: 0.8325 (p90) cc_final: 0.7992 (p90) REVERT: D 445 LYS cc_start: 0.9077 (mttt) cc_final: 0.8675 (mttt) REVERT: D 487 THR cc_start: 0.9408 (m) cc_final: 0.9191 (t) REVERT: D 555 TYR cc_start: 0.8056 (m-80) cc_final: 0.7446 (m-10) REVERT: D 747 MET cc_start: 0.5810 (mpp) cc_final: 0.5470 (mpp) REVERT: D 869 CYS cc_start: 0.8163 (m) cc_final: 0.7951 (m) REVERT: D 1040 MET cc_start: 0.1628 (ptt) cc_final: 0.0875 (ptp) REVERT: D 1254 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8203 (mt-10) REVERT: D 1290 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7519 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9258 (pt) cc_final: 0.8781 (mt) REVERT: E 31 GLN cc_start: 0.8677 (tp40) cc_final: 0.8396 (tp40) REVERT: E 65 ASP cc_start: 0.8013 (t0) cc_final: 0.7789 (t70) REVERT: F 227 GLN cc_start: 0.6789 (mm-40) cc_final: 0.5497 (tm-30) REVERT: F 416 VAL cc_start: 0.8980 (p) cc_final: 0.8620 (p) REVERT: F 499 LYS cc_start: 0.8043 (pttp) cc_final: 0.7716 (ttmt) REVERT: J 41 MET cc_start: 0.1561 (mmm) cc_final: 0.1359 (mmm) REVERT: J 50 LEU cc_start: 0.7247 (tp) cc_final: 0.6960 (pt) REVERT: J 86 GLN cc_start: 0.8965 (mp10) cc_final: 0.8714 (mm-40) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.2137 time to fit residues: 168.1047 Evaluate side-chains 349 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 150 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 329 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 43 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.121813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094538 restraints weight = 102108.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092754 restraints weight = 86075.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093366 restraints weight = 76162.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093745 restraints weight = 64903.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093845 restraints weight = 58853.508| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33812 Z= 0.232 Angle : 0.714 11.902 46192 Z= 0.384 Chirality : 0.047 0.265 5259 Planarity : 0.005 0.058 5591 Dihedral : 16.815 179.510 5643 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.88 % Favored : 92.09 % Rotamer: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.12), residues: 3845 helix: -1.84 (0.13), residues: 1330 sheet: -1.69 (0.24), residues: 369 loop : -2.12 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C1246 TYR 0.033 0.002 TYR F 137 PHE 0.035 0.002 PHE C 972 TRP 0.015 0.002 TRP J 36 HIS 0.016 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (33809) covalent geometry : angle 0.71384 / 0.38 (46192) hydrogen bonds : bond 0.05207 / 3.51 ( 910) hydrogen bonds : angle 6.01740 / 4.13 ( 2492) metal coordination : bond 0.00302 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 459 time to evaluate : 1.390 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: A 23 HIS cc_start: 0.8965 (t70) cc_final: 0.8310 (t-90) REVERT: A 131 CYS cc_start: 0.8511 (m) cc_final: 0.8147 (m) REVERT: A 183 ILE cc_start: 0.9196 (tt) cc_final: 0.8846 (mm) REVERT: B 41 ASN cc_start: 0.8922 (t0) cc_final: 0.8659 (t0) REVERT: B 96 ASP cc_start: 0.7632 (m-30) cc_final: 0.6185 (t0) REVERT: B 198 LEU cc_start: 0.8954 (mt) cc_final: 0.8516 (pp) REVERT: B 226 GLU cc_start: 0.7928 (tp30) cc_final: 0.7672 (tp30) REVERT: C 85 CYS cc_start: 0.8393 (m) cc_final: 0.8165 (m) REVERT: C 224 PHE cc_start: 0.8190 (m-80) cc_final: 0.7542 (m-10) REVERT: C 245 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6671 (mmp80) REVERT: C 542 ARG cc_start: 0.6734 (mtt-85) cc_final: 0.5785 (tmt-80) REVERT: C 667 LEU cc_start: 0.8811 (mt) cc_final: 0.8427 (tt) REVERT: C 768 MET cc_start: 0.8264 (ttp) cc_final: 0.7954 (mtm) REVERT: C 781 ASP cc_start: 0.8029 (m-30) cc_final: 0.7768 (m-30) REVERT: C 798 GLN cc_start: 0.9197 (mm110) cc_final: 0.8614 (mp10) REVERT: C 903 ARG cc_start: 0.8714 (tmt-80) cc_final: 0.7918 (ttp80) REVERT: C 1214 ASP cc_start: 0.8947 (t70) cc_final: 0.8459 (t70) REVERT: C 1240 ASP cc_start: 0.8860 (m-30) cc_final: 0.8440 (t0) REVERT: C 1272 GLU cc_start: 0.8971 (pm20) cc_final: 0.8702 (pm20) REVERT: C 1273 MET cc_start: 0.8860 (mmm) cc_final: 0.8613 (mmm) REVERT: C 1276 TRP cc_start: 0.8612 (m-10) cc_final: 0.8361 (m-90) REVERT: D 29 MET cc_start: 0.8293 (tmm) cc_final: 0.7598 (tmm) REVERT: D 76 LYS cc_start: 0.4860 (mmtt) cc_final: 0.4517 (tptp) REVERT: D 130 MET cc_start: 0.7955 (ttm) cc_final: 0.7626 (ttm) REVERT: D 180 MET cc_start: 0.7900 (ttm) cc_final: 0.7490 (ttp) REVERT: D 192 MET cc_start: 0.8168 (ptt) cc_final: 0.7867 (ptp) REVERT: D 237 MET cc_start: 0.8921 (tpp) cc_final: 0.8710 (mmt) REVERT: D 269 TYR cc_start: 0.9090 (m-80) cc_final: 0.8846 (m-80) REVERT: D 294 ASN cc_start: 0.8111 (t0) cc_final: 0.7897 (t0) REVERT: D 298 MET cc_start: 0.8512 (ptp) cc_final: 0.8021 (ptp) REVERT: D 360 TYR cc_start: 0.8367 (p90) cc_final: 0.8076 (p90) REVERT: D 435 GLN cc_start: 0.8740 (mt0) cc_final: 0.8396 (mp10) REVERT: D 555 TYR cc_start: 0.7844 (m-80) cc_final: 0.7370 (m-10) REVERT: D 719 PHE cc_start: 0.4350 (m-10) cc_final: 0.3933 (m-10) REVERT: D 790 THR cc_start: 0.8455 (p) cc_final: 0.8069 (t) REVERT: D 913 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8181 (tm-30) REVERT: D 1101 LEU cc_start: 0.7399 (mp) cc_final: 0.6912 (pt) REVERT: D 1254 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8179 (mt-10) REVERT: D 1290 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7495 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9133 (pt) cc_final: 0.8753 (mt) REVERT: D 1330 ARG cc_start: 0.6850 (mmt180) cc_final: 0.6570 (mmt180) REVERT: E 31 GLN cc_start: 0.8693 (tp40) cc_final: 0.8418 (tp40) REVERT: E 65 ASP cc_start: 0.8053 (t0) cc_final: 0.7816 (t70) REVERT: F 227 GLN cc_start: 0.6917 (mm-40) cc_final: 0.5534 (tm-30) REVERT: F 288 MET cc_start: 0.4668 (mtp) cc_final: 0.4348 (mtm) REVERT: F 499 LYS cc_start: 0.8076 (pttp) cc_final: 0.7757 (ttmt) REVERT: J 17 HIS cc_start: 0.6436 (m170) cc_final: 0.6177 (m170) REVERT: J 50 LEU cc_start: 0.7251 (tp) cc_final: 0.6867 (pt) REVERT: J 86 GLN cc_start: 0.8794 (mp10) cc_final: 0.8437 (mm-40) outliers start: 2 outliers final: 0 residues processed: 461 average time/residue: 0.2034 time to fit residues: 156.3665 Evaluate side-chains 349 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 393 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 318 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 277 optimal weight: 3.9990 chunk 326 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS C 120 GLN C 148 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1244 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 43 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 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 = 0.3832 r_free = 0.3832 target = 0.123313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.095373 restraints weight = 101044.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094027 restraints weight = 81255.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094868 restraints weight = 71549.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.094961 restraints weight = 65482.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.095193 restraints weight = 55640.302| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33812 Z= 0.143 Angle : 0.626 9.041 46192 Z= 0.337 Chirality : 0.044 0.241 5259 Planarity : 0.004 0.075 5591 Dihedral : 16.687 178.060 5643 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.76 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.13), residues: 3845 helix: -1.57 (0.13), residues: 1331 sheet: -1.59 (0.25), residues: 368 loop : -1.94 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1242 TYR 0.023 0.001 TYR C1229 PHE 0.030 0.001 PHE C 972 TRP 0.016 0.001 TRP J 36 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (33809) covalent geometry : angle 0.62641 / 0.34 (46192) hydrogen bonds : bond 0.04568 / 3.07 ( 910) hydrogen bonds : angle 5.59317 / 3.86 ( 2492) metal coordination : bond 0.00338 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.224 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: A 23 HIS cc_start: 0.8884 (t70) cc_final: 0.8258 (t-90) REVERT: A 131 CYS cc_start: 0.8741 (m) cc_final: 0.8358 (m) REVERT: A 183 ILE cc_start: 0.9162 (tt) cc_final: 0.8793 (mm) REVERT: B 32 GLU cc_start: 0.7655 (pt0) cc_final: 0.7430 (pt0) REVERT: B 41 ASN cc_start: 0.8909 (t0) cc_final: 0.8663 (t0) REVERT: B 96 ASP cc_start: 0.7562 (m-30) cc_final: 0.6020 (t0) REVERT: C 85 CYS cc_start: 0.8445 (m) cc_final: 0.8133 (m) REVERT: C 224 PHE cc_start: 0.8119 (m-80) cc_final: 0.7447 (m-10) REVERT: C 386 GLU cc_start: 0.7833 (mm-30) cc_final: 0.6499 (pt0) REVERT: C 429 MET cc_start: 0.9316 (mmm) cc_final: 0.9111 (mmm) REVERT: C 667 LEU cc_start: 0.8775 (mt) cc_final: 0.8398 (tt) REVERT: C 781 ASP cc_start: 0.8011 (m-30) cc_final: 0.7722 (m-30) REVERT: C 798 GLN cc_start: 0.9186 (mm110) cc_final: 0.8929 (mm110) REVERT: C 850 ILE cc_start: 0.9211 (mm) cc_final: 0.9000 (mm) REVERT: C 903 ARG cc_start: 0.8732 (tmt-80) cc_final: 0.7907 (ttp80) REVERT: C 1021 LEU cc_start: 0.4778 (mt) cc_final: 0.4533 (pp) REVERT: C 1066 MET cc_start: 0.7921 (ttm) cc_final: 0.7591 (mtp) REVERT: C 1214 ASP cc_start: 0.8940 (t70) cc_final: 0.8420 (t70) REVERT: C 1240 ASP cc_start: 0.8818 (m-30) cc_final: 0.8423 (t0) REVERT: C 1276 TRP cc_start: 0.8489 (m-10) cc_final: 0.8230 (m-90) REVERT: D 29 MET cc_start: 0.8277 (tmm) cc_final: 0.7649 (tmm) REVERT: D 76 LYS cc_start: 0.5200 (mmtt) cc_final: 0.4794 (tptp) REVERT: D 130 MET cc_start: 0.7872 (ttm) cc_final: 0.7516 (ttm) REVERT: D 180 MET cc_start: 0.7719 (ttm) cc_final: 0.7358 (ttp) REVERT: D 237 MET cc_start: 0.8849 (tpp) cc_final: 0.8605 (mmt) REVERT: D 269 TYR cc_start: 0.9118 (m-80) cc_final: 0.8901 (m-80) REVERT: D 299 LEU cc_start: 0.9235 (tp) cc_final: 0.8955 (tp) REVERT: D 360 TYR cc_start: 0.8322 (p90) cc_final: 0.7999 (p90) REVERT: D 435 GLN cc_start: 0.8615 (mt0) cc_final: 0.8314 (mp10) REVERT: D 457 TYR cc_start: 0.8677 (m-10) cc_final: 0.8044 (m-10) REVERT: D 487 THR cc_start: 0.9386 (m) cc_final: 0.9172 (t) REVERT: D 555 TYR cc_start: 0.7678 (m-80) cc_final: 0.7030 (m-10) REVERT: D 724 MET cc_start: 0.7791 (mtt) cc_final: 0.7391 (mtt) REVERT: D 747 MET cc_start: 0.5752 (mpp) cc_final: 0.5439 (mpp) REVERT: D 790 THR cc_start: 0.8377 (p) cc_final: 0.8004 (t) REVERT: D 1040 MET cc_start: 0.0869 (ptt) cc_final: -0.0126 (ptp) REVERT: D 1075 ARG cc_start: 0.4968 (mmt90) cc_final: 0.2952 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7413 (mp) cc_final: 0.6961 (pt) REVERT: D 1254 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7869 (tt0) REVERT: D 1286 LYS cc_start: 0.8995 (pttt) cc_final: 0.8699 (mttt) REVERT: D 1290 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7647 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9043 (pt) cc_final: 0.8768 (mt) REVERT: D 1330 ARG cc_start: 0.6939 (mmt180) cc_final: 0.6659 (mmt180) REVERT: E 25 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7360 (mmt90) REVERT: E 31 GLN cc_start: 0.8627 (tp40) cc_final: 0.8344 (tp40) REVERT: E 65 ASP cc_start: 0.7956 (t0) cc_final: 0.7611 (t70) REVERT: F 227 GLN cc_start: 0.6738 (mm-40) cc_final: 0.5361 (tm-30) REVERT: F 277 MET cc_start: 0.7990 (mtp) cc_final: 0.7609 (mtt) REVERT: F 416 VAL cc_start: 0.8983 (t) cc_final: 0.8575 (t) REVERT: F 499 LYS cc_start: 0.8103 (pttp) cc_final: 0.7724 (ttmt) REVERT: J 17 HIS cc_start: 0.6529 (m170) cc_final: 0.6080 (m170) REVERT: J 22 LEU cc_start: 0.7571 (tp) cc_final: 0.7301 (mt) REVERT: J 50 LEU cc_start: 0.7391 (tp) cc_final: 0.7034 (pt) REVERT: J 58 ARG cc_start: 0.7400 (mtt90) cc_final: 0.6867 (tpp80) REVERT: J 78 MET cc_start: 0.6292 (ttp) cc_final: 0.4854 (tpt) REVERT: J 86 GLN cc_start: 0.8705 (mp10) cc_final: 0.8334 (mm-40) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.2019 time to fit residues: 157.5257 Evaluate side-chains 351 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 185 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 93 GLN C 120 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN C 952 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 716 GLN E 15 ASN E 43 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094572 restraints weight = 100967.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093206 restraints weight = 80959.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093579 restraints weight = 73485.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.093894 restraints weight = 68099.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.094178 restraints weight = 57347.720| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33812 Z= 0.188 Angle : 0.656 8.393 46192 Z= 0.351 Chirality : 0.045 0.204 5259 Planarity : 0.005 0.081 5591 Dihedral : 16.649 178.394 5643 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.13), residues: 3845 helix: -1.45 (0.13), residues: 1345 sheet: -1.49 (0.26), residues: 341 loop : -1.96 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 538 TYR 0.033 0.002 TYR J 37 PHE 0.027 0.002 PHE C 972 TRP 0.012 0.001 TRP D 580 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (33809) covalent geometry : angle 0.65603 / 0.35 (46192) hydrogen bonds : bond 0.04494 / 3.03 ( 910) hydrogen bonds : angle 5.58406 / 3.85 ( 2492) metal coordination : bond 0.00502 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.119 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: A 23 HIS cc_start: 0.8875 (t70) cc_final: 0.8271 (t-90) REVERT: B 41 ASN cc_start: 0.8875 (t0) cc_final: 0.8636 (t0) REVERT: B 96 ASP cc_start: 0.7536 (m-30) cc_final: 0.5845 (t0) REVERT: C 83 GLN cc_start: 0.8275 (mm-40) cc_final: 0.8047 (mm-40) REVERT: C 85 CYS cc_start: 0.8484 (m) cc_final: 0.8262 (m) REVERT: C 118 LYS cc_start: 0.8155 (pttt) cc_final: 0.7941 (pttt) REVERT: C 224 PHE cc_start: 0.8095 (m-80) cc_final: 0.7462 (m-80) REVERT: C 386 GLU cc_start: 0.7900 (mm-30) cc_final: 0.6525 (pt0) REVERT: C 667 LEU cc_start: 0.8788 (mt) cc_final: 0.8342 (tt) REVERT: C 781 ASP cc_start: 0.8012 (m-30) cc_final: 0.7776 (m-30) REVERT: C 798 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8609 (mp10) REVERT: C 850 ILE cc_start: 0.9244 (mm) cc_final: 0.9019 (mm) REVERT: C 903 ARG cc_start: 0.8718 (tmt-80) cc_final: 0.7852 (ttp80) REVERT: C 1021 LEU cc_start: 0.4757 (mt) cc_final: 0.4507 (pp) REVERT: C 1066 MET cc_start: 0.8126 (ttm) cc_final: 0.7722 (mtp) REVERT: C 1214 ASP cc_start: 0.8959 (t70) cc_final: 0.8508 (t70) REVERT: C 1272 GLU cc_start: 0.8846 (pm20) cc_final: 0.8433 (pm20) REVERT: C 1276 TRP cc_start: 0.8509 (m-10) cc_final: 0.8137 (m-90) REVERT: D 29 MET cc_start: 0.8339 (tmm) cc_final: 0.7652 (ptt) REVERT: D 76 LYS cc_start: 0.4967 (mmtt) cc_final: 0.4683 (tptp) REVERT: D 130 MET cc_start: 0.7915 (ttm) cc_final: 0.7549 (ttm) REVERT: D 180 MET cc_start: 0.7782 (ttm) cc_final: 0.7327 (ttp) REVERT: D 269 TYR cc_start: 0.9111 (m-80) cc_final: 0.8910 (m-80) REVERT: D 299 LEU cc_start: 0.9322 (tp) cc_final: 0.9011 (tp) REVERT: D 360 TYR cc_start: 0.8315 (p90) cc_final: 0.8074 (p90) REVERT: D 435 GLN cc_start: 0.8773 (mt0) cc_final: 0.8372 (mp10) REVERT: D 445 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8522 (mttt) REVERT: D 555 TYR cc_start: 0.7782 (m-80) cc_final: 0.7099 (m-10) REVERT: D 724 MET cc_start: 0.7995 (mtt) cc_final: 0.7423 (mtt) REVERT: D 1075 ARG cc_start: 0.5128 (mmt90) cc_final: 0.3055 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7386 (mp) cc_final: 0.7017 (pt) REVERT: D 1286 LYS cc_start: 0.8992 (pttt) cc_final: 0.8725 (mttt) REVERT: D 1290 ARG cc_start: 0.7968 (mtt180) cc_final: 0.7645 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9090 (pt) cc_final: 0.8823 (mt) REVERT: D 1330 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6536 (mmt180) REVERT: E 65 ASP cc_start: 0.7944 (t0) cc_final: 0.7716 (t70) REVERT: F 276 MET cc_start: 0.8915 (tmm) cc_final: 0.8672 (tpp) REVERT: F 487 MET cc_start: 0.8163 (tpp) cc_final: 0.7613 (tpt) REVERT: F 499 LYS cc_start: 0.8106 (pttp) cc_final: 0.7777 (ttmt) REVERT: J 17 HIS cc_start: 0.7108 (m170) cc_final: 0.6665 (m170) REVERT: J 22 LEU cc_start: 0.7621 (tp) cc_final: 0.7348 (mt) REVERT: J 50 LEU cc_start: 0.7312 (tp) cc_final: 0.6986 (pt) REVERT: J 58 ARG cc_start: 0.7517 (mtt90) cc_final: 0.6992 (tpp80) REVERT: J 86 GLN cc_start: 0.8780 (mp10) cc_final: 0.8411 (mm-40) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.1925 time to fit residues: 144.2543 Evaluate side-chains 335 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 115 optimal weight: 0.0020 chunk 305 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 375 optimal weight: 50.0000 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 15 ASN F 242 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095928 restraints weight = 101199.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094925 restraints weight = 77459.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095597 restraints weight = 65962.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095949 restraints weight = 58006.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096072 restraints weight = 51507.228| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33812 Z= 0.126 Angle : 0.625 8.648 46192 Z= 0.333 Chirality : 0.044 0.190 5259 Planarity : 0.005 0.139 5591 Dihedral : 16.566 177.087 5643 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.13), residues: 3845 helix: -1.34 (0.13), residues: 1354 sheet: -1.24 (0.27), residues: 348 loop : -1.88 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 363 TYR 0.035 0.001 TYR J 37 PHE 0.050 0.001 PHE B 35 TRP 0.012 0.001 TRP D 580 HIS 0.018 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (33809) covalent geometry : angle 0.62468 / 0.33 (46192) hydrogen bonds : bond 0.04129 / 2.79 ( 910) hydrogen bonds : angle 5.32093 / 3.67 ( 2492) metal coordination : bond 0.00182 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.287 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: A 23 HIS cc_start: 0.8854 (t70) cc_final: 0.8266 (t-90) REVERT: A 214 GLU cc_start: 0.7864 (tt0) cc_final: 0.7641 (tt0) REVERT: B 96 ASP cc_start: 0.7628 (m-30) cc_final: 0.5964 (t0) REVERT: B 185 TYR cc_start: 0.9052 (p90) cc_final: 0.8669 (p90) REVERT: C 83 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8075 (mm-40) REVERT: C 85 CYS cc_start: 0.8426 (m) cc_final: 0.8170 (m) REVERT: C 118 LYS cc_start: 0.7994 (pttt) cc_final: 0.7757 (pttt) REVERT: C 224 PHE cc_start: 0.8077 (m-80) cc_final: 0.7412 (m-10) REVERT: C 386 GLU cc_start: 0.7777 (mm-30) cc_final: 0.6388 (pt0) REVERT: C 667 LEU cc_start: 0.8764 (mt) cc_final: 0.8356 (tt) REVERT: C 781 ASP cc_start: 0.7910 (m-30) cc_final: 0.7686 (m-30) REVERT: C 850 ILE cc_start: 0.9150 (mm) cc_final: 0.8937 (mm) REVERT: C 903 ARG cc_start: 0.8715 (tmt-80) cc_final: 0.7826 (ttp80) REVERT: C 1021 LEU cc_start: 0.4713 (mt) cc_final: 0.4488 (pp) REVERT: C 1066 MET cc_start: 0.7981 (ttm) cc_final: 0.7532 (mtp) REVERT: C 1214 ASP cc_start: 0.8971 (t70) cc_final: 0.8443 (t70) REVERT: C 1240 ASP cc_start: 0.8719 (m-30) cc_final: 0.8446 (t0) REVERT: C 1246 ARG cc_start: 0.8749 (tmt170) cc_final: 0.8002 (ttt-90) REVERT: C 1272 GLU cc_start: 0.8817 (pm20) cc_final: 0.8334 (pm20) REVERT: C 1273 MET cc_start: 0.8612 (mmm) cc_final: 0.8159 (mmm) REVERT: C 1276 TRP cc_start: 0.8475 (m-10) cc_final: 0.8168 (m-90) REVERT: D 29 MET cc_start: 0.8230 (tmm) cc_final: 0.7483 (ptm) REVERT: D 76 LYS cc_start: 0.5006 (mmtt) cc_final: 0.4642 (tptp) REVERT: D 130 MET cc_start: 0.7873 (ttm) cc_final: 0.7530 (ttm) REVERT: D 137 ARG cc_start: 0.7477 (mmp80) cc_final: 0.7275 (mmp80) REVERT: D 180 MET cc_start: 0.7702 (ttm) cc_final: 0.7250 (ttp) REVERT: D 237 MET cc_start: 0.9000 (tpp) cc_final: 0.8684 (tpp) REVERT: D 298 MET cc_start: 0.8602 (ptp) cc_final: 0.8385 (pmm) REVERT: D 299 LEU cc_start: 0.9278 (tp) cc_final: 0.8839 (tp) REVERT: D 360 TYR cc_start: 0.8328 (p90) cc_final: 0.8049 (p90) REVERT: D 370 LYS cc_start: 0.9486 (tppt) cc_final: 0.9217 (tppt) REVERT: D 555 TYR cc_start: 0.7775 (m-80) cc_final: 0.7075 (m-10) REVERT: D 724 MET cc_start: 0.7904 (mtt) cc_final: 0.7348 (mtt) REVERT: D 747 MET cc_start: 0.5366 (mpp) cc_final: 0.5053 (mpp) REVERT: D 790 THR cc_start: 0.8441 (p) cc_final: 0.8067 (t) REVERT: D 1040 MET cc_start: 0.0686 (ptt) cc_final: -0.0236 (ptp) REVERT: D 1075 ARG cc_start: 0.5076 (mmt90) cc_final: 0.3030 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7402 (mp) cc_final: 0.6948 (pt) REVERT: D 1143 ASP cc_start: 0.8017 (m-30) cc_final: 0.7702 (t0) REVERT: D 1254 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7767 (tt0) REVERT: D 1286 LYS cc_start: 0.8960 (pttt) cc_final: 0.8683 (mttt) REVERT: D 1290 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7559 (mtt-85) REVERT: D 1325 PHE cc_start: 0.8592 (p90) cc_final: 0.8187 (p90) REVERT: D 1330 ARG cc_start: 0.6814 (mmt180) cc_final: 0.6537 (mmt180) REVERT: E 25 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6920 (ptp-170) REVERT: E 65 ASP cc_start: 0.8024 (t0) cc_final: 0.7799 (t0) REVERT: F 487 MET cc_start: 0.8041 (tpp) cc_final: 0.7084 (tmm) REVERT: F 499 LYS cc_start: 0.8005 (pttp) cc_final: 0.7689 (ttmt) REVERT: J 17 HIS cc_start: 0.7248 (m170) cc_final: 0.6841 (m170) REVERT: J 22 LEU cc_start: 0.7643 (tp) cc_final: 0.7384 (mt) REVERT: J 50 LEU cc_start: 0.7271 (tp) cc_final: 0.6983 (pt) REVERT: J 58 ARG cc_start: 0.7387 (mtt90) cc_final: 0.6993 (tpp80) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1983 time to fit residues: 154.8897 Evaluate side-chains 356 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 322 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 116 optimal weight: 0.4980 chunk 31 optimal weight: 40.0000 chunk 250 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 288 optimal weight: 30.0000 chunk 387 optimal weight: 0.8980 chunk 373 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 overall best weight: 3.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN C 120 GLN C 387 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1336 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 72 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.122594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093933 restraints weight = 101756.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.092915 restraints weight = 78209.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093265 restraints weight = 67636.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093480 restraints weight = 61897.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094098 restraints weight = 54921.617| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33812 Z= 0.171 Angle : 0.647 8.103 46192 Z= 0.344 Chirality : 0.045 0.211 5259 Planarity : 0.005 0.063 5591 Dihedral : 16.544 177.782 5643 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.38 (0.13), residues: 3845 helix: -1.24 (0.14), residues: 1347 sheet: -1.20 (0.27), residues: 338 loop : -1.90 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 538 TYR 0.032 0.002 TYR J 37 PHE 0.021 0.002 PHE C 972 TRP 0.013 0.001 TRP D 580 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (33809) covalent geometry : angle 0.64667 / 0.34 (46192) hydrogen bonds : bond 0.04203 / 2.85 ( 910) hydrogen bonds : angle 5.33224 / 3.67 ( 2492) metal coordination : bond 0.00471 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.471 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: A 23 HIS cc_start: 0.8882 (t70) cc_final: 0.8283 (t-90) REVERT: A 205 MET cc_start: 0.8462 (ttp) cc_final: 0.8222 (ttm) REVERT: A 214 GLU cc_start: 0.7908 (tt0) cc_final: 0.7684 (tt0) REVERT: B 185 TYR cc_start: 0.9103 (p90) cc_final: 0.8749 (p90) REVERT: C 83 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8238 (mm-40) REVERT: C 118 LYS cc_start: 0.8114 (pttt) cc_final: 0.7458 (pttt) REVERT: C 224 PHE cc_start: 0.8146 (m-80) cc_final: 0.7524 (m-80) REVERT: C 386 GLU cc_start: 0.7805 (mm-30) cc_final: 0.6372 (pt0) REVERT: C 410 LEU cc_start: 0.8509 (mp) cc_final: 0.8220 (pp) REVERT: C 667 LEU cc_start: 0.8809 (mt) cc_final: 0.8283 (tt) REVERT: C 781 ASP cc_start: 0.7993 (m-30) cc_final: 0.7737 (m-30) REVERT: C 903 ARG cc_start: 0.8731 (tmt-80) cc_final: 0.7804 (ttp80) REVERT: C 1021 LEU cc_start: 0.4823 (mt) cc_final: 0.4521 (pp) REVERT: C 1066 MET cc_start: 0.8023 (ttm) cc_final: 0.7692 (mtp) REVERT: C 1117 LEU cc_start: 0.9474 (mm) cc_final: 0.9252 (mt) REVERT: C 1214 ASP cc_start: 0.8967 (t70) cc_final: 0.8435 (t70) REVERT: C 1238 LEU cc_start: 0.9237 (mp) cc_final: 0.8784 (mp) REVERT: C 1246 ARG cc_start: 0.8646 (tmt170) cc_final: 0.7995 (ttt-90) REVERT: C 1272 GLU cc_start: 0.8881 (pm20) cc_final: 0.8376 (pm20) REVERT: C 1273 MET cc_start: 0.8692 (mmm) cc_final: 0.8269 (mmm) REVERT: C 1276 TRP cc_start: 0.8546 (m-10) cc_final: 0.8206 (m-90) REVERT: D 29 MET cc_start: 0.8250 (tmm) cc_final: 0.7421 (ptt) REVERT: D 76 LYS cc_start: 0.5160 (mmtt) cc_final: 0.4801 (tptp) REVERT: D 130 MET cc_start: 0.7936 (ttm) cc_final: 0.7569 (ttm) REVERT: D 137 ARG cc_start: 0.7609 (mmp80) cc_final: 0.7331 (mmp80) REVERT: D 180 MET cc_start: 0.7721 (ttm) cc_final: 0.7273 (ttp) REVERT: D 299 LEU cc_start: 0.9390 (tp) cc_final: 0.9128 (tp) REVERT: D 360 TYR cc_start: 0.8343 (p90) cc_final: 0.8129 (p90) REVERT: D 400 MET cc_start: 0.8549 (tpp) cc_final: 0.8258 (tpp) REVERT: D 435 GLN cc_start: 0.8697 (mt0) cc_final: 0.8393 (mm-40) REVERT: D 538 ARG cc_start: 0.8855 (tpp-160) cc_final: 0.8533 (tpp-160) REVERT: D 555 TYR cc_start: 0.7859 (m-80) cc_final: 0.7092 (m-10) REVERT: D 724 MET cc_start: 0.7988 (mtt) cc_final: 0.7355 (mtt) REVERT: D 747 MET cc_start: 0.5322 (mpp) cc_final: 0.5022 (mpp) REVERT: D 1075 ARG cc_start: 0.4967 (mmt90) cc_final: 0.2970 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7524 (mp) cc_final: 0.7027 (pt) REVERT: D 1286 LYS cc_start: 0.9014 (pttt) cc_final: 0.8732 (mttt) REVERT: D 1290 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7534 (mtt-85) REVERT: D 1330 ARG cc_start: 0.6858 (mmt180) cc_final: 0.6578 (mmt180) REVERT: E 65 ASP cc_start: 0.8003 (t0) cc_final: 0.7764 (t0) REVERT: F 102 MET cc_start: 0.7844 (tmm) cc_final: 0.7355 (tmm) REVERT: F 487 MET cc_start: 0.8140 (tpp) cc_final: 0.7482 (tmm) REVERT: F 499 LYS cc_start: 0.8125 (pttp) cc_final: 0.7798 (ttmt) REVERT: F 571 TYR cc_start: 0.5738 (m-10) cc_final: 0.5470 (m-80) REVERT: J 17 HIS cc_start: 0.7304 (m170) cc_final: 0.6837 (m170) REVERT: J 18 ILE cc_start: 0.7489 (pt) cc_final: 0.7197 (pt) REVERT: J 22 LEU cc_start: 0.7629 (tp) cc_final: 0.7336 (mt) REVERT: J 50 LEU cc_start: 0.7336 (tp) cc_final: 0.7030 (pt) REVERT: J 58 ARG cc_start: 0.7433 (mtt90) cc_final: 0.6996 (tpp80) REVERT: J 86 GLN cc_start: 0.8541 (mp10) cc_final: 0.8232 (mm-40) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2008 time to fit residues: 148.5697 Evaluate side-chains 347 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 348 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 191 optimal weight: 0.0980 chunk 146 optimal weight: 0.1980 chunk 167 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 214 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** 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 = 0.3869 r_free = 0.3869 target = 0.125767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097804 restraints weight = 100106.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096346 restraints weight = 78276.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097154 restraints weight = 70422.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097411 restraints weight = 60944.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097598 restraints weight = 53878.133| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 33812 Z= 0.117 Angle : 0.624 13.615 46192 Z= 0.329 Chirality : 0.044 0.223 5259 Planarity : 0.004 0.063 5591 Dihedral : 16.417 175.622 5643 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.23 (0.13), residues: 3845 helix: -1.14 (0.14), residues: 1363 sheet: -1.00 (0.27), residues: 346 loop : -1.81 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 364 TYR 0.032 0.001 TYR J 37 PHE 0.023 0.001 PHE B 35 TRP 0.016 0.001 TRP D 580 HIS 0.008 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (33809) covalent geometry : angle 0.62387 / 0.33 (46192) hydrogen bonds : bond 0.03860 / 2.63 ( 910) hydrogen bonds : angle 5.04401 / 3.49 ( 2492) metal coordination : bond 0.00112 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8798 (t70) cc_final: 0.8265 (t-90) REVERT: A 114 ASP cc_start: 0.8475 (p0) cc_final: 0.6905 (t0) REVERT: A 131 CYS cc_start: 0.8698 (m) cc_final: 0.8190 (m) REVERT: B 185 TYR cc_start: 0.8996 (p90) cc_final: 0.8623 (p90) REVERT: C 130 MET cc_start: 0.8225 (ttm) cc_final: 0.7698 (ttm) REVERT: C 213 LEU cc_start: 0.8951 (mm) cc_final: 0.8645 (mm) REVERT: C 224 PHE cc_start: 0.8067 (m-80) cc_final: 0.7384 (m-10) REVERT: C 315 MET cc_start: 0.7093 (ttp) cc_final: 0.6861 (ttp) REVERT: C 386 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6316 (pt0) REVERT: C 410 LEU cc_start: 0.8537 (mp) cc_final: 0.8252 (pp) REVERT: C 659 GLN cc_start: 0.8717 (pt0) cc_final: 0.8455 (pt0) REVERT: C 781 ASP cc_start: 0.7862 (m-30) cc_final: 0.7567 (m-30) REVERT: C 850 ILE cc_start: 0.9173 (mm) cc_final: 0.8900 (mm) REVERT: C 903 ARG cc_start: 0.8685 (tmt-80) cc_final: 0.7758 (ttp80) REVERT: C 1021 LEU cc_start: 0.4653 (mt) cc_final: 0.4412 (pp) REVERT: C 1066 MET cc_start: 0.8083 (ttm) cc_final: 0.7783 (mtp) REVERT: C 1117 LEU cc_start: 0.9442 (mm) cc_final: 0.9228 (mt) REVERT: C 1214 ASP cc_start: 0.8864 (t70) cc_final: 0.8302 (t70) REVERT: C 1238 LEU cc_start: 0.9193 (mp) cc_final: 0.8722 (mp) REVERT: C 1240 ASP cc_start: 0.8740 (m-30) cc_final: 0.8436 (t0) REVERT: C 1246 ARG cc_start: 0.8586 (tmt170) cc_final: 0.7935 (ttt-90) REVERT: C 1272 GLU cc_start: 0.8737 (pm20) cc_final: 0.8302 (pm20) REVERT: C 1273 MET cc_start: 0.8541 (mmm) cc_final: 0.8097 (mmm) REVERT: C 1276 TRP cc_start: 0.8261 (m-10) cc_final: 0.8004 (m-90) REVERT: C 1290 MET cc_start: 0.8948 (mmp) cc_final: 0.8109 (mmp) REVERT: C 1338 GLU cc_start: 0.8086 (pp20) cc_final: 0.7275 (mt-10) REVERT: D 29 MET cc_start: 0.8247 (tmm) cc_final: 0.7484 (ptm) REVERT: D 76 LYS cc_start: 0.5064 (mmtt) cc_final: 0.4427 (tptp) REVERT: D 102 MET cc_start: 0.8483 (ptp) cc_final: 0.8247 (ptm) REVERT: D 130 MET cc_start: 0.7861 (ttm) cc_final: 0.7427 (ttt) REVERT: D 147 ILE cc_start: 0.9606 (mp) cc_final: 0.9345 (tt) REVERT: D 180 MET cc_start: 0.7489 (ttm) cc_final: 0.7112 (ttp) REVERT: D 298 MET cc_start: 0.8478 (ptp) cc_final: 0.7926 (pmm) REVERT: D 299 LEU cc_start: 0.9324 (tp) cc_final: 0.8944 (tp) REVERT: D 341 ASN cc_start: 0.8921 (m-40) cc_final: 0.8505 (m-40) REVERT: D 370 LYS cc_start: 0.9423 (tppt) cc_final: 0.9205 (tppt) REVERT: D 400 MET cc_start: 0.8554 (tpp) cc_final: 0.8278 (tpp) REVERT: D 435 GLN cc_start: 0.8652 (mt0) cc_final: 0.8256 (mm-40) REVERT: D 465 GLN cc_start: 0.8635 (mp10) cc_final: 0.8292 (mp10) REVERT: D 555 TYR cc_start: 0.7769 (m-80) cc_final: 0.6959 (m-10) REVERT: D 644 MET cc_start: 0.6847 (mtm) cc_final: 0.6451 (mtp) REVERT: D 724 MET cc_start: 0.7890 (mtt) cc_final: 0.7319 (mtt) REVERT: D 747 MET cc_start: 0.5587 (mpp) cc_final: 0.5252 (mpp) REVERT: D 790 THR cc_start: 0.8463 (p) cc_final: 0.8126 (t) REVERT: D 1075 ARG cc_start: 0.4928 (mmt90) cc_final: 0.2992 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7508 (mp) cc_final: 0.7081 (pt) REVERT: D 1254 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7940 (tt0) REVERT: D 1256 ILE cc_start: 0.9525 (pt) cc_final: 0.9028 (tt) REVERT: D 1286 LYS cc_start: 0.9009 (pttt) cc_final: 0.8712 (mttt) REVERT: D 1290 ARG cc_start: 0.7877 (mtt180) cc_final: 0.7522 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9217 (mt) cc_final: 0.8886 (mm) REVERT: D 1330 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6686 (mmt180) REVERT: E 25 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7019 (ptp-170) REVERT: E 65 ASP cc_start: 0.7938 (t0) cc_final: 0.7677 (t0) REVERT: F 102 MET cc_start: 0.7767 (tmm) cc_final: 0.7305 (tmm) REVERT: F 277 MET cc_start: 0.7397 (mtt) cc_final: 0.7093 (mtt) REVERT: F 365 MET cc_start: 0.7108 (ptt) cc_final: 0.6693 (tmm) REVERT: F 461 ASN cc_start: 0.8632 (m-40) cc_final: 0.7936 (t0) REVERT: F 499 LYS cc_start: 0.8147 (pttp) cc_final: 0.7734 (ttmt) REVERT: J 17 HIS cc_start: 0.7192 (m170) cc_final: 0.6738 (m170) REVERT: J 18 ILE cc_start: 0.7371 (pt) cc_final: 0.6333 (mt) REVERT: J 22 LEU cc_start: 0.7583 (tp) cc_final: 0.7273 (mt) REVERT: J 50 LEU cc_start: 0.7353 (tp) cc_final: 0.7051 (pt) REVERT: J 58 ARG cc_start: 0.7222 (mtt90) cc_final: 0.6814 (tpp80) REVERT: J 86 GLN cc_start: 0.8399 (mp10) cc_final: 0.8033 (mm-40) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1964 time to fit residues: 150.8944 Evaluate side-chains 356 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 385 optimal weight: 50.0000 chunk 302 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 360 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 318 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 362 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 391 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.123364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095138 restraints weight = 101004.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093785 restraints weight = 78229.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.094399 restraints weight = 70218.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094830 restraints weight = 60290.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095006 restraints weight = 52713.928| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33812 Z= 0.168 Angle : 0.644 8.671 46192 Z= 0.341 Chirality : 0.044 0.210 5259 Planarity : 0.005 0.055 5591 Dihedral : 16.428 177.140 5643 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.32 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.14 (0.13), residues: 3845 helix: -1.00 (0.14), residues: 1348 sheet: -1.01 (0.28), residues: 338 loop : -1.78 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1148 TYR 0.047 0.002 TYR C1229 PHE 0.025 0.002 PHE D1325 TRP 0.012 0.001 TRP D 580 HIS 0.007 0.001 HIS D 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (33809) covalent geometry : angle 0.64384 / 0.34 (46192) hydrogen bonds : bond 0.04038 / 2.77 ( 910) hydrogen bonds : angle 5.14015 / 3.54 ( 2492) metal coordination : bond 0.00443 / 0.17 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.104 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: A 8 PHE cc_start: 0.6577 (m-80) cc_final: 0.6229 (m-80) REVERT: A 23 HIS cc_start: 0.8864 (t70) cc_final: 0.8292 (t-90) REVERT: A 114 ASP cc_start: 0.8657 (p0) cc_final: 0.7027 (t0) REVERT: B 185 TYR cc_start: 0.9080 (p90) cc_final: 0.8692 (p90) REVERT: C 118 LYS cc_start: 0.8209 (pttt) cc_final: 0.7926 (pttt) REVERT: C 224 PHE cc_start: 0.8140 (m-80) cc_final: 0.7444 (m-80) REVERT: C 386 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6369 (pt0) REVERT: C 410 LEU cc_start: 0.8464 (mp) cc_final: 0.8195 (pp) REVERT: C 768 MET cc_start: 0.8682 (mtm) cc_final: 0.8250 (mtt) REVERT: C 781 ASP cc_start: 0.7930 (m-30) cc_final: 0.7643 (m-30) REVERT: C 903 ARG cc_start: 0.8710 (tmt-80) cc_final: 0.7812 (ttp80) REVERT: C 1021 LEU cc_start: 0.4659 (mt) cc_final: 0.4390 (pp) REVERT: C 1066 MET cc_start: 0.8203 (ttm) cc_final: 0.7791 (mtp) REVERT: C 1117 LEU cc_start: 0.9459 (mm) cc_final: 0.9224 (mt) REVERT: C 1238 LEU cc_start: 0.9202 (mp) cc_final: 0.8834 (mp) REVERT: C 1240 ASP cc_start: 0.8814 (m-30) cc_final: 0.8455 (t0) REVERT: C 1272 GLU cc_start: 0.8783 (pm20) cc_final: 0.8310 (pm20) REVERT: C 1273 MET cc_start: 0.8685 (mmm) cc_final: 0.8177 (mmm) REVERT: C 1276 TRP cc_start: 0.8521 (m-10) cc_final: 0.8159 (m-90) REVERT: C 1290 MET cc_start: 0.8910 (mmp) cc_final: 0.8579 (mmp) REVERT: D 29 MET cc_start: 0.8313 (tmm) cc_final: 0.7446 (ptm) REVERT: D 76 LYS cc_start: 0.4899 (mmtt) cc_final: 0.4693 (tptp) REVERT: D 130 MET cc_start: 0.7988 (ttm) cc_final: 0.7540 (ttt) REVERT: D 147 ILE cc_start: 0.9624 (mp) cc_final: 0.9281 (mm) REVERT: D 180 MET cc_start: 0.7675 (ttm) cc_final: 0.7156 (ttp) REVERT: D 299 LEU cc_start: 0.9321 (tp) cc_final: 0.8991 (tp) REVERT: D 400 MET cc_start: 0.8660 (tpp) cc_final: 0.7341 (tpp) REVERT: D 435 GLN cc_start: 0.8652 (mt0) cc_final: 0.8269 (mm-40) REVERT: D 644 MET cc_start: 0.6875 (mtm) cc_final: 0.6492 (mtp) REVERT: D 724 MET cc_start: 0.8020 (mtt) cc_final: 0.7358 (mtt) REVERT: D 747 MET cc_start: 0.5619 (mpp) cc_final: 0.5230 (mpp) REVERT: D 1040 MET cc_start: 0.1066 (ptt) cc_final: 0.0688 (ptp) REVERT: D 1075 ARG cc_start: 0.4996 (mmt90) cc_final: 0.3012 (mmp-170) REVERT: D 1256 ILE cc_start: 0.9504 (pt) cc_final: 0.9059 (tt) REVERT: D 1286 LYS cc_start: 0.8995 (pttt) cc_final: 0.8720 (mttt) REVERT: D 1290 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7537 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9217 (mt) cc_final: 0.8919 (mm) REVERT: D 1330 ARG cc_start: 0.6747 (mmt180) cc_final: 0.6501 (mmt180) REVERT: E 25 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7021 (ptp-170) REVERT: E 38 LEU cc_start: 0.8921 (mt) cc_final: 0.8346 (mt) REVERT: E 53 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8105 (mt-10) REVERT: E 65 ASP cc_start: 0.7964 (t0) cc_final: 0.7721 (t0) REVERT: E 72 GLN cc_start: 0.8397 (tp40) cc_final: 0.8158 (tp-100) REVERT: F 365 MET cc_start: 0.7226 (ptt) cc_final: 0.6843 (tmm) REVERT: F 416 VAL cc_start: 0.8622 (t) cc_final: 0.8198 (t) REVERT: F 461 ASN cc_start: 0.8761 (m-40) cc_final: 0.7974 (t0) REVERT: F 499 LYS cc_start: 0.8251 (pttp) cc_final: 0.7887 (ttmt) REVERT: F 571 TYR cc_start: 0.5881 (m-10) cc_final: 0.5609 (m-80) REVERT: J 17 HIS cc_start: 0.7321 (m170) cc_final: 0.6887 (m170) REVERT: J 18 ILE cc_start: 0.7362 (pt) cc_final: 0.6252 (mt) REVERT: J 22 LEU cc_start: 0.7674 (tp) cc_final: 0.7413 (mt) REVERT: J 50 LEU cc_start: 0.7414 (tp) cc_final: 0.7113 (pt) REVERT: J 58 ARG cc_start: 0.7338 (mtt90) cc_final: 0.7064 (tpp80) REVERT: J 86 GLN cc_start: 0.8404 (mp10) cc_final: 0.8060 (mm-40) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.1885 time to fit residues: 137.5039 Evaluate side-chains 354 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 354 optimal weight: 7.9990 chunk 381 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 291 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 255 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 336 optimal weight: 0.5980 chunk 102 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN ** J 85 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.122195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094373 restraints weight = 100695.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093122 restraints weight = 80888.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093643 restraints weight = 69886.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093867 restraints weight = 65930.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094018 restraints weight = 58282.771| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33812 Z= 0.182 Angle : 0.662 8.526 46192 Z= 0.352 Chirality : 0.045 0.203 5259 Planarity : 0.005 0.061 5591 Dihedral : 16.457 177.183 5643 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.17 (0.13), residues: 3845 helix: -1.02 (0.14), residues: 1349 sheet: -1.03 (0.28), residues: 338 loop : -1.80 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 12 TYR 0.048 0.002 TYR C1229 PHE 0.025 0.002 PHE B 35 TRP 0.011 0.001 TRP D 115 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (33809) covalent geometry : angle 0.66247 / 0.35 (46192) hydrogen bonds : bond 0.04194 / 2.88 ( 910) hydrogen bonds : angle 5.21008 / 3.59 ( 2492) metal coordination : bond 0.00499 / 0.19 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5219.48 seconds wall clock time: 91 minutes 12.39 seconds (5472.39 seconds total)