Starting phenix.real_space_refine on Fri Mar 6 17:30:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w5w_32322/03_2026/7w5w_32322.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w5w_32322/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w5w_32322/03_2026/7w5w_32322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w5w_32322/03_2026/7w5w_32322.map" model { file = "/net/cci-nas-00/data/ceres_data/7w5w_32322/03_2026/7w5w_32322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w5w_32322/03_2026/7w5w_32322.cif" } 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-dev-5986/lib/python3.9/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: 6.87, per 1000 atoms: 0.21 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: 2.74 Conformation dependent library (CDL) restraints added in 972.2 milliseconds 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: 4.23 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: 6.46 Time building geometry restraints manager: 3.70 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=" 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 bond pdb=" C VAL C 550 " pdb=" N HIS C 551 " ideal model delta sigma weight residual 1.331 1.232 0.099 2.83e-02 1.25e+03 1.23e+01 bond pdb=" C LEU D 449 " pdb=" N HIS D 450 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.07e-02 2.33e+03 1.20e+01 bond pdb=" C ARG J 71 " pdb=" N PRO J 72 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.68e+00 bond pdb=" C GLN C1256 " pdb=" N GLN C1257 " ideal model delta sigma weight residual 1.327 1.284 0.042 1.39e-02 5.18e+03 9.26e+00 ... (remaining 33804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 44224 2.18 - 4.36: 1735 4.36 - 6.55: 179 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: 3801 0.056 - 0.111: 1175 0.111 - 0.167: 235 0.167 - 0.223: 37 0.223 - 0.279: 11 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=" 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 chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+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: 0.010 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.730 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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= 0.322 Angle : 0.996 10.911 46192 Z= 0.580 Chirality : 0.056 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 covalent geometry : bond 0.00666 (33809) covalent geometry : angle 0.99581 (46192) hydrogen bonds : bond 0.31887 ( 910) hydrogen bonds : angle 10.73053 ( 2492) metal coordination : bond 0.17975 ( 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 : 1.137 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: 0.8815 (mt) REVERT: C 224 PHE cc_start: 0.8486 (m-80) cc_final: 0.7928 (m-10) REVERT: C 410 LEU cc_start: 0.8901 (mt) cc_final: 0.8376 (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: 0.7896 (tm-30) REVERT: C 965 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7414 (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: 0.4992 (tptp) REVERT: D 128 LEU cc_start: 0.9361 (mt) cc_final: 0.9113 (mm) REVERT: D 130 MET cc_start: 0.8295 (ttm) cc_final: 0.7818 (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: 0.7776 (tm-30) REVERT: D 180 MET cc_start: 0.7970 (ttp) cc_final: 0.7287 (ttp) REVERT: D 192 MET cc_start: 0.8618 (ptm) cc_final: 0.8220 (ptp) REVERT: D 222 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8607 (tttp) REVERT: D 237 MET cc_start: 0.8926 (mmt) cc_final: 0.8553 (mmt) REVERT: D 264 ASP cc_start: 0.9191 (m-30) cc_final: 0.8915 (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: 0.9177 (t) REVERT: D 587 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8873 (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: 0.4786 (ppp) REVERT: D 747 MET cc_start: 0.5479 (mpp) cc_final: 0.5078 (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: 0.8143 (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: 0.7471 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9402 (pt) cc_final: 0.8802 (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: 0.8266 (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: 0.8961 (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: 0.7999 (ptm) REVERT: F 386 LEU cc_start: 0.9128 (tt) cc_final: 0.8818 (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: 0.3676 (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: 0.5343 (ttp) outliers start: 30 outliers final: 11 residues processed: 651 average time/residue: 0.2376 time to fit residues: 237.1075 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 : 1.163 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 41 ASN A 75 GLN B 66 HIS B 117 HIS B 132 HIS C 120 GLN ** 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 45 ASN 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 D 951 GLN 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 ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.126650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.098693 restraints weight = 101904.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098199 restraints weight = 88223.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098954 restraints weight = 74146.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098936 restraints weight = 63188.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098938 restraints weight = 60261.184| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2498 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= 0.136 Angle : 0.637 7.585 46192 Z= 0.343 Chirality : 0.043 0.175 5259 Planarity : 0.005 0.060 5591 Dihedral : 16.848 175.477 5643 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 0.15 % Allowed : 4.85 % Favored : 95.00 % 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: -3.62 (0.11), residues: 3845 helix: -2.77 (0.11), residues: 1320 sheet: -1.84 (0.24), residues: 376 loop : -2.28 (0.12), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1106 TYR 0.025 0.001 TYR C1149 PHE 0.016 0.001 PHE C 972 TRP 0.012 0.001 TRP C1276 HIS 0.012 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00290 (33809) covalent geometry : angle 0.63723 (46192) hydrogen bonds : bond 0.05656 ( 910) hydrogen bonds : angle 6.14534 ( 2492) metal coordination : bond 0.00088 ( 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 569 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 564 time to evaluate : 1.174 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: 0.8549 (p0) cc_final: 0.6981 (t0) REVERT: B 41 ASN cc_start: 0.8916 (t0) cc_final: 0.8690 (t0) REVERT: B 96 ASP cc_start: 0.7579 (m-30) cc_final: 0.6260 (t0) REVERT: C 118 LYS cc_start: 0.8219 (pttt) cc_final: 0.7049 (pttt) REVERT: C 130 MET cc_start: 0.8179 (ttm) cc_final: 0.7891 (ttp) REVERT: C 148 GLN cc_start: 0.8676 (tt0) cc_final: 0.8432 (tt0) REVERT: C 224 PHE cc_start: 0.8058 (m-80) cc_final: 0.7535 (m-10) REVERT: C 410 LEU cc_start: 0.8969 (mt) cc_final: 0.8458 (pp) REVERT: C 542 ARG cc_start: 0.6807 (mtt-85) cc_final: 0.5745 (tmt-80) REVERT: C 696 ASP cc_start: 0.8462 (t0) cc_final: 0.8086 (t0) REVERT: C 732 ILE cc_start: 0.8821 (pt) cc_final: 0.8621 (mm) REVERT: C 768 MET cc_start: 0.8098 (ttp) cc_final: 0.7772 (mtp) REVERT: C 794 LEU cc_start: 0.9239 (tp) cc_final: 0.8828 (tp) REVERT: C 798 GLN cc_start: 0.8853 (mp10) cc_final: 0.8189 (mp10) REVERT: C 816 ILE cc_start: 0.9241 (pt) cc_final: 0.8942 (pt) REVERT: C 850 ILE cc_start: 0.9070 (mm) cc_final: 0.8808 (mm) REVERT: C 955 GLN cc_start: 0.8672 (tp40) cc_final: 0.8210 (tm-30) REVERT: C 965 GLN cc_start: 0.6422 (tm-30) cc_final: 0.6187 (tm-30) REVERT: C 1016 GLU cc_start: 0.1788 (tm-30) cc_final: 0.1555 (pt0) REVERT: C 1023 HIS cc_start: 0.6785 (m170) cc_final: 0.6478 (m170) REVERT: C 1214 ASP cc_start: 0.8943 (t70) cc_final: 0.8326 (t70) REVERT: C 1240 ASP cc_start: 0.8766 (m-30) cc_final: 0.8448 (t0) REVERT: C 1253 LEU cc_start: 0.9353 (tp) cc_final: 0.9007 (tp) REVERT: C 1276 TRP cc_start: 0.8480 (m-10) cc_final: 0.8146 (m-90) REVERT: C 1279 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8330 (mm-30) REVERT: D 29 MET cc_start: 0.7419 (ttp) cc_final: 0.7138 (tmm) REVERT: D 76 LYS cc_start: 0.4940 (mmtt) cc_final: 0.4587 (tptp) REVERT: D 113 HIS cc_start: 0.9063 (t-90) cc_final: 0.8559 (t-170) REVERT: D 130 MET cc_start: 0.7892 (ttm) cc_final: 0.7512 (mtp) REVERT: D 134 ASP cc_start: 0.8671 (m-30) cc_final: 0.8390 (m-30) REVERT: D 237 MET cc_start: 0.8784 (mmt) cc_final: 0.8555 (mmt) REVERT: D 269 TYR cc_start: 0.9039 (m-80) cc_final: 0.8662 (m-80) REVERT: D 298 MET cc_start: 0.7335 (ptp) cc_final: 0.6618 (ptp) REVERT: D 360 TYR cc_start: 0.8383 (p90) cc_final: 0.7953 (p90) REVERT: D 435 GLN cc_start: 0.8920 (mt0) cc_final: 0.8441 (mp10) REVERT: D 438 GLU cc_start: 0.8145 (tt0) cc_final: 0.7460 (tt0) REVERT: D 457 TYR cc_start: 0.8540 (m-80) cc_final: 0.7966 (m-10) REVERT: D 487 THR cc_start: 0.9399 (m) cc_final: 0.9130 (t) REVERT: D 625 MET cc_start: 0.8446 (mpp) cc_final: 0.8082 (mpp) REVERT: D 869 CYS cc_start: 0.8459 (m) cc_final: 0.8254 (m) REVERT: D 995 TYR cc_start: 0.7589 (m-80) cc_final: 0.7341 (m-80) REVERT: D 1254 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8272 (mt-10) REVERT: D 1286 LYS cc_start: 0.8914 (pttt) cc_final: 0.8629 (mmmt) REVERT: D 1290 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7543 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9185 (pt) cc_final: 0.8712 (mt) REVERT: E 25 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7052 (ptp-170) REVERT: E 30 MET cc_start: 0.8633 (mtp) cc_final: 0.8321 (ttt) REVERT: E 31 GLN cc_start: 0.8514 (tp40) cc_final: 0.7810 (tp40) REVERT: F 109 GLU cc_start: 0.7106 (pm20) cc_final: 0.6794 (tm-30) REVERT: F 227 GLN cc_start: 0.6662 (mm-40) cc_final: 0.5475 (tm-30) REVERT: F 470 MET cc_start: 0.8433 (mmt) cc_final: 0.7932 (mmt) REVERT: F 499 LYS cc_start: 0.8115 (pttp) cc_final: 0.7741 (ttmt) REVERT: F 555 GLU cc_start: 0.8443 (mp0) cc_final: 0.8239 (mp0) REVERT: J 17 HIS cc_start: 0.6675 (m170) cc_final: 0.6096 (m170) REVERT: J 50 LEU cc_start: 0.7401 (tp) cc_final: 0.7095 (pt) REVERT: J 86 GLN cc_start: 0.8761 (mp10) cc_final: 0.8517 (mm-40) outliers start: 5 outliers final: 0 residues processed: 568 average time/residue: 0.2070 time to fit residues: 189.7806 Evaluate side-chains 382 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 319 optimal weight: 0.0000 chunk 294 optimal weight: 0.0050 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN C1244 HIS C1288 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 716 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN F 406 GLN F 589 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.127676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.099631 restraints weight = 100672.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098942 restraints weight = 81309.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099571 restraints weight = 68469.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099836 restraints weight = 62325.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100078 restraints weight = 54908.671| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33812 Z= 0.117 Angle : 0.580 10.129 46192 Z= 0.309 Chirality : 0.042 0.203 5259 Planarity : 0.004 0.055 5591 Dihedral : 16.577 179.996 5643 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % 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: -2.93 (0.12), residues: 3845 helix: -2.03 (0.12), residues: 1325 sheet: -1.41 (0.26), residues: 358 loop : -1.99 (0.12), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 352 TYR 0.015 0.001 TYR C1149 PHE 0.014 0.001 PHE F 266 TRP 0.028 0.001 TRP D 115 HIS 0.012 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00248 (33809) covalent geometry : angle 0.57972 (46192) hydrogen bonds : bond 0.04265 ( 910) hydrogen bonds : angle 5.31796 ( 2492) metal coordination : bond 0.00058 ( 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 535 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 532 time to evaluate : 1.240 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 23 HIS cc_start: 0.8778 (t70) cc_final: 0.8237 (t-90) REVERT: A 114 ASP cc_start: 0.8430 (p0) cc_final: 0.6763 (t0) REVERT: A 131 CYS cc_start: 0.8470 (m) cc_final: 0.8211 (m) REVERT: A 183 ILE cc_start: 0.9192 (tt) cc_final: 0.8824 (mm) REVERT: B 41 ASN cc_start: 0.8893 (t0) cc_final: 0.8675 (t0) REVERT: B 46 ILE cc_start: 0.9117 (pt) cc_final: 0.8743 (tt) REVERT: B 96 ASP cc_start: 0.7493 (m-30) cc_final: 0.6320 (t0) REVERT: B 185 TYR cc_start: 0.8884 (p90) cc_final: 0.8514 (p90) REVERT: C 130 MET cc_start: 0.8002 (ttm) cc_final: 0.7711 (ttp) REVERT: C 386 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6428 (pt0) REVERT: C 410 LEU cc_start: 0.8917 (mt) cc_final: 0.8420 (pp) REVERT: C 542 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.5726 (tmt-80) REVERT: C 798 GLN cc_start: 0.8884 (mp10) cc_final: 0.8335 (mp10) REVERT: C 850 ILE cc_start: 0.9111 (mm) cc_final: 0.8835 (mm) REVERT: C 903 ARG cc_start: 0.8689 (tmt-80) cc_final: 0.7952 (ttp80) REVERT: C 965 GLN cc_start: 0.6443 (tm-30) cc_final: 0.6237 (tm-30) REVERT: C 1023 HIS cc_start: 0.6828 (m170) cc_final: 0.6545 (m170) REVERT: C 1240 ASP cc_start: 0.8744 (m-30) cc_final: 0.8362 (t0) REVERT: C 1276 TRP cc_start: 0.8502 (m-10) cc_final: 0.8077 (m-90) REVERT: D 113 HIS cc_start: 0.8930 (t-90) cc_final: 0.8295 (t-170) REVERT: D 114 ILE cc_start: 0.9425 (tp) cc_final: 0.9191 (tp) REVERT: D 269 TYR cc_start: 0.8973 (m-80) cc_final: 0.8720 (m-80) REVERT: D 355 ILE cc_start: 0.9344 (pt) cc_final: 0.8906 (mt) REVERT: D 360 TYR cc_start: 0.8305 (p90) cc_final: 0.7946 (p90) REVERT: D 400 MET cc_start: 0.8784 (ttm) cc_final: 0.8440 (tpp) REVERT: D 429 LEU cc_start: 0.8690 (mm) cc_final: 0.8444 (mt) REVERT: D 435 GLN cc_start: 0.8780 (mt0) cc_final: 0.8192 (mp10) REVERT: D 475 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8284 (mm-30) REVERT: D 487 THR cc_start: 0.9296 (m) cc_final: 0.8974 (t) REVERT: D 796 LEU cc_start: 0.9099 (tp) cc_final: 0.8790 (tt) REVERT: D 869 CYS cc_start: 0.8439 (m) cc_final: 0.8194 (m) REVERT: D 1040 MET cc_start: 0.0986 (ptt) cc_final: 0.0377 (ptp) REVERT: D 1189 MET cc_start: 0.5476 (ttm) cc_final: 0.5213 (ttt) REVERT: D 1286 LYS cc_start: 0.8917 (pttt) cc_final: 0.8642 (mttt) REVERT: D 1290 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7456 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9062 (pt) cc_final: 0.8824 (mt) REVERT: D 1326 GLN cc_start: 0.8237 (mt0) cc_final: 0.7750 (mt0) REVERT: D 1330 ARG cc_start: 0.6631 (mmt180) cc_final: 0.6299 (mmt180) REVERT: E 25 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.6808 (ptp-170) REVERT: E 30 MET cc_start: 0.8528 (mtp) cc_final: 0.8265 (ttt) REVERT: E 31 GLN cc_start: 0.8455 (tp40) cc_final: 0.7732 (tp40) REVERT: E 72 GLN cc_start: 0.8348 (pt0) cc_final: 0.8082 (tp-100) REVERT: F 109 GLU cc_start: 0.7311 (pm20) cc_final: 0.6961 (tp30) REVERT: F 227 GLN cc_start: 0.6525 (mm-40) cc_final: 0.5334 (tm-30) REVERT: F 277 MET cc_start: 0.5929 (mtt) cc_final: 0.5703 (mtt) REVERT: F 288 MET cc_start: 0.5078 (mtp) cc_final: 0.4820 (mtm) REVERT: F 338 HIS cc_start: 0.5847 (p90) cc_final: 0.5361 (t70) REVERT: F 445 ASP cc_start: 0.8777 (p0) cc_final: 0.8448 (p0) REVERT: F 499 LYS cc_start: 0.8020 (pttp) cc_final: 0.7619 (ttmt) REVERT: J 50 LEU cc_start: 0.7180 (tp) cc_final: 0.6976 (pt) REVERT: J 86 GLN cc_start: 0.8830 (mp10) cc_final: 0.8603 (mm-40) outliers start: 3 outliers final: 1 residues processed: 534 average time/residue: 0.2004 time to fit residues: 176.0344 Evaluate side-chains 383 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 382 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 0.0070 chunk 193 optimal weight: 0.9980 chunk 43 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 329 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 345 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN C1209 GLN C1244 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN E 75 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.125879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098035 restraints weight = 101363.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096973 restraints weight = 83902.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097540 restraints weight = 71599.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097892 restraints weight = 61573.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097991 restraints weight = 56589.760| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33812 Z= 0.137 Angle : 0.584 7.795 46192 Z= 0.311 Chirality : 0.042 0.213 5259 Planarity : 0.004 0.069 5591 Dihedral : 16.525 179.554 5643 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % 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: -2.55 (0.13), residues: 3845 helix: -1.51 (0.13), residues: 1321 sheet: -1.30 (0.25), residues: 368 loop : -1.89 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 293 TYR 0.032 0.002 TYR J 37 PHE 0.014 0.001 PHE D1325 TRP 0.015 0.001 TRP D 115 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00306 (33809) covalent geometry : angle 0.58405 (46192) hydrogen bonds : bond 0.03916 ( 910) hydrogen bonds : angle 5.11570 ( 2492) metal coordination : bond 0.00276 ( 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 491 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 1.209 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 23 HIS cc_start: 0.8758 (t70) cc_final: 0.8198 (t-90) REVERT: A 114 ASP cc_start: 0.8535 (p0) cc_final: 0.6819 (t0) REVERT: A 131 CYS cc_start: 0.8679 (m) cc_final: 0.8311 (m) REVERT: B 41 ASN cc_start: 0.8904 (t0) cc_final: 0.8648 (t0) REVERT: B 46 ILE cc_start: 0.9152 (pt) cc_final: 0.8834 (tt) REVERT: B 96 ASP cc_start: 0.7421 (m-30) cc_final: 0.5966 (t0) REVERT: B 185 TYR cc_start: 0.8977 (p90) cc_final: 0.8581 (p90) REVERT: C 386 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6524 (pt0) REVERT: C 410 LEU cc_start: 0.8854 (mt) cc_final: 0.8396 (pp) REVERT: C 542 ARG cc_start: 0.6711 (mtt-85) cc_final: 0.5785 (tmt-80) REVERT: C 798 GLN cc_start: 0.8914 (mp10) cc_final: 0.8101 (mp10) REVERT: C 850 ILE cc_start: 0.9167 (mm) cc_final: 0.8893 (mm) REVERT: C 903 ARG cc_start: 0.8646 (tmt-80) cc_final: 0.7813 (ttp80) REVERT: C 965 GLN cc_start: 0.6484 (tm-30) cc_final: 0.6275 (tm-30) REVERT: C 1023 HIS cc_start: 0.6849 (m170) cc_final: 0.6600 (m170) REVERT: C 1214 ASP cc_start: 0.8764 (t70) cc_final: 0.8349 (t70) REVERT: C 1240 ASP cc_start: 0.8766 (m-30) cc_final: 0.8380 (t0) REVERT: D 113 HIS cc_start: 0.8981 (t-90) cc_final: 0.8209 (t-170) REVERT: D 114 ILE cc_start: 0.9425 (tp) cc_final: 0.9211 (tp) REVERT: D 269 TYR cc_start: 0.9045 (m-80) cc_final: 0.8199 (m-80) REVERT: D 298 MET cc_start: 0.8328 (ptp) cc_final: 0.8046 (ptp) REVERT: D 330 MET cc_start: 0.8193 (mmm) cc_final: 0.7909 (mmm) REVERT: D 341 ASN cc_start: 0.8655 (m-40) cc_final: 0.8212 (m-40) REVERT: D 355 ILE cc_start: 0.9367 (pt) cc_final: 0.9151 (pt) REVERT: D 360 TYR cc_start: 0.8239 (p90) cc_final: 0.7951 (p90) REVERT: D 400 MET cc_start: 0.8760 (ttm) cc_final: 0.8437 (tpp) REVERT: D 435 GLN cc_start: 0.8749 (mt0) cc_final: 0.8194 (mp10) REVERT: D 465 GLN cc_start: 0.8702 (mp10) cc_final: 0.8419 (mp10) REVERT: D 475 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8382 (mm-30) REVERT: D 487 THR cc_start: 0.9287 (m) cc_final: 0.8984 (t) REVERT: D 605 LEU cc_start: 0.9396 (mp) cc_final: 0.9166 (mp) REVERT: D 719 PHE cc_start: 0.4173 (m-10) cc_final: 0.3720 (m-10) REVERT: D 747 MET cc_start: 0.5602 (mpp) cc_final: 0.5063 (mpp) REVERT: D 796 LEU cc_start: 0.9142 (tp) cc_final: 0.8877 (tt) REVERT: D 869 CYS cc_start: 0.8479 (m) cc_final: 0.8188 (m) REVERT: D 1075 ARG cc_start: 0.4850 (mmt90) cc_final: 0.2974 (mmp-170) REVERT: D 1286 LYS cc_start: 0.8947 (pttt) cc_final: 0.8715 (mttt) REVERT: D 1290 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7387 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9041 (pt) cc_final: 0.8822 (mt) REVERT: D 1330 ARG cc_start: 0.6693 (mmt180) cc_final: 0.6386 (mmt180) REVERT: E 30 MET cc_start: 0.8459 (mtp) cc_final: 0.8242 (ttt) REVERT: E 31 GLN cc_start: 0.8569 (tp40) cc_final: 0.7893 (tp40) REVERT: E 72 GLN cc_start: 0.8390 (pt0) cc_final: 0.8145 (tp-100) REVERT: F 227 GLN cc_start: 0.6544 (mm-40) cc_final: 0.5339 (tm-30) REVERT: F 338 HIS cc_start: 0.5796 (p90) cc_final: 0.5358 (m-70) REVERT: F 499 LYS cc_start: 0.8035 (pttp) cc_final: 0.7680 (ttmt) REVERT: J 18 ILE cc_start: 0.7333 (pt) cc_final: 0.7016 (pt) REVERT: J 22 LEU cc_start: 0.7767 (mt) cc_final: 0.7504 (mt) REVERT: J 86 GLN cc_start: 0.8645 (mp10) cc_final: 0.8342 (mm-40) outliers start: 2 outliers final: 1 residues processed: 491 average time/residue: 0.1939 time to fit residues: 159.0152 Evaluate side-chains 371 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 370 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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: 1.9990 chunk 222 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 220 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1157 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D 716 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.124930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097052 restraints weight = 100404.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.095681 restraints weight = 79276.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096598 restraints weight = 66910.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096683 restraints weight = 60851.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096831 restraints weight = 54971.479| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33812 Z= 0.147 Angle : 0.593 7.520 46192 Z= 0.314 Chirality : 0.043 0.220 5259 Planarity : 0.004 0.062 5591 Dihedral : 16.449 179.411 5643 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -2.29 (0.13), residues: 3845 helix: -1.20 (0.14), residues: 1333 sheet: -1.13 (0.25), residues: 366 loop : -1.82 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C1246 TYR 0.033 0.001 TYR J 37 PHE 0.028 0.001 PHE C 972 TRP 0.026 0.001 TRP C1276 HIS 0.006 0.001 HIS J 17 Details of bonding type rmsd covalent geometry : bond 0.00330 (33809) covalent geometry : angle 0.59323 (46192) hydrogen bonds : bond 0.03784 ( 910) hydrogen bonds : angle 5.01583 ( 2492) metal coordination : bond 0.00308 ( 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 478 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 1.200 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 23 HIS cc_start: 0.8792 (t70) cc_final: 0.8274 (t-90) REVERT: A 31 LEU cc_start: 0.9193 (mt) cc_final: 0.8945 (tp) REVERT: A 168 ILE cc_start: 0.8887 (mp) cc_final: 0.8680 (tt) REVERT: B 41 ASN cc_start: 0.8933 (t0) cc_final: 0.8722 (t0) REVERT: B 46 ILE cc_start: 0.9272 (pt) cc_final: 0.8971 (tt) REVERT: B 96 ASP cc_start: 0.7570 (m-30) cc_final: 0.6013 (t0) REVERT: B 185 TYR cc_start: 0.9049 (p90) cc_final: 0.8694 (p90) REVERT: C 386 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6587 (pt0) REVERT: C 410 LEU cc_start: 0.8871 (mt) cc_final: 0.8413 (pp) REVERT: C 798 GLN cc_start: 0.8705 (mp10) cc_final: 0.8113 (mp10) REVERT: C 850 ILE cc_start: 0.9194 (mm) cc_final: 0.8883 (mm) REVERT: C 881 ASP cc_start: 0.6280 (m-30) cc_final: 0.6056 (m-30) REVERT: C 903 ARG cc_start: 0.8706 (tmt-80) cc_final: 0.7803 (ttp80) REVERT: C 1214 ASP cc_start: 0.8911 (t70) cc_final: 0.8394 (t70) REVERT: C 1240 ASP cc_start: 0.8751 (m-30) cc_final: 0.8447 (t0) REVERT: C 1273 MET cc_start: 0.8716 (mmm) cc_final: 0.8513 (mmt) REVERT: C 1276 TRP cc_start: 0.8585 (m-90) cc_final: 0.8288 (m-90) REVERT: D 269 TYR cc_start: 0.9029 (m-80) cc_final: 0.8229 (m-80) REVERT: D 341 ASN cc_start: 0.8714 (m-40) cc_final: 0.8305 (m-40) REVERT: D 360 TYR cc_start: 0.8320 (p90) cc_final: 0.8080 (p90) REVERT: D 400 MET cc_start: 0.8724 (ttm) cc_final: 0.8445 (tpp) REVERT: D 475 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8436 (mm-30) REVERT: D 487 THR cc_start: 0.9371 (m) cc_final: 0.9137 (t) REVERT: D 525 MET cc_start: 0.8532 (mtt) cc_final: 0.8329 (mtt) REVERT: D 644 MET cc_start: 0.6505 (mtm) cc_final: 0.6161 (mtp) REVERT: D 747 MET cc_start: 0.5330 (mpp) cc_final: 0.4762 (mpp) REVERT: D 796 LEU cc_start: 0.9204 (tp) cc_final: 0.8927 (tt) REVERT: D 1040 MET cc_start: 0.0976 (ptt) cc_final: 0.0534 (ptp) REVERT: D 1075 ARG cc_start: 0.4770 (mmt90) cc_final: 0.2893 (mmp-170) REVERT: D 1286 LYS cc_start: 0.8989 (pttt) cc_final: 0.8756 (mttt) REVERT: D 1290 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7411 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9159 (pt) cc_final: 0.8880 (mt) REVERT: D 1330 ARG cc_start: 0.6717 (mmt180) cc_final: 0.6391 (mmt180) REVERT: E 30 MET cc_start: 0.8512 (mtp) cc_final: 0.8298 (ttt) REVERT: E 31 GLN cc_start: 0.8597 (tp40) cc_final: 0.7815 (tp40) REVERT: E 46 THR cc_start: 0.8776 (p) cc_final: 0.8543 (p) REVERT: E 72 GLN cc_start: 0.8452 (pt0) cc_final: 0.8090 (tp-100) REVERT: F 100 MET cc_start: 0.8147 (mtm) cc_final: 0.7867 (mtm) REVERT: F 102 MET cc_start: 0.7903 (ttp) cc_final: 0.7579 (tmm) REVERT: F 227 GLN cc_start: 0.6678 (mm-40) cc_final: 0.5262 (tm-30) REVERT: F 338 HIS cc_start: 0.5825 (p90) cc_final: 0.5349 (t70) REVERT: F 499 LYS cc_start: 0.8133 (pttp) cc_final: 0.7772 (ttmt) REVERT: J 86 GLN cc_start: 0.8408 (mp10) cc_final: 0.8026 (mm-40) outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.1958 time to fit residues: 155.5361 Evaluate side-chains 372 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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: 2.9990 chunk 15 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 301 optimal weight: 0.0010 chunk 115 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 209 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 93 optimal weight: 0.0980 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C 808 ASN C1157 GLN C1244 HIS ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 716 GLN F 242 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097667 restraints weight = 100324.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.096714 restraints weight = 79353.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097373 restraints weight = 70948.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097793 restraints weight = 60398.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097933 restraints weight = 53851.553| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33812 Z= 0.116 Angle : 0.566 8.562 46192 Z= 0.297 Chirality : 0.042 0.213 5259 Planarity : 0.004 0.058 5591 Dihedral : 16.386 178.110 5643 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.59 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -2.02 (0.13), residues: 3845 helix: -0.95 (0.14), residues: 1319 sheet: -0.95 (0.26), residues: 341 loop : -1.67 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1246 TYR 0.031 0.001 TYR J 37 PHE 0.026 0.001 PHE C 972 TRP 0.025 0.001 TRP C1276 HIS 0.005 0.001 HIS F 338 Details of bonding type rmsd covalent geometry : bond 0.00259 (33809) covalent geometry : angle 0.56599 (46192) hydrogen bonds : bond 0.03634 ( 910) hydrogen bonds : angle 4.80347 ( 2492) metal coordination : bond 0.00264 ( 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 479 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.251 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: 0.8792 (t70) cc_final: 0.8270 (t-90) REVERT: A 31 LEU cc_start: 0.9145 (mt) cc_final: 0.8810 (tp) REVERT: A 114 ASP cc_start: 0.8576 (p0) cc_final: 0.6934 (t0) REVERT: A 168 ILE cc_start: 0.8847 (mp) cc_final: 0.8578 (tt) REVERT: B 41 ASN cc_start: 0.8922 (t0) cc_final: 0.8712 (t0) REVERT: B 46 ILE cc_start: 0.9274 (pt) cc_final: 0.8992 (tt) REVERT: B 96 ASP cc_start: 0.7416 (m-30) cc_final: 0.5947 (t0) REVERT: B 107 ILE cc_start: 0.7098 (mt) cc_final: 0.6896 (mt) REVERT: B 185 TYR cc_start: 0.9009 (p90) cc_final: 0.8648 (p90) REVERT: C 130 MET cc_start: 0.8197 (ttm) cc_final: 0.7776 (ttm) REVERT: C 386 GLU cc_start: 0.7778 (mm-30) cc_final: 0.6538 (pt0) REVERT: C 410 LEU cc_start: 0.8877 (mt) cc_final: 0.8422 (pp) REVERT: C 429 MET cc_start: 0.9277 (mmm) cc_final: 0.9070 (mmm) REVERT: C 798 GLN cc_start: 0.8555 (mp10) cc_final: 0.8059 (mp10) REVERT: C 818 VAL cc_start: 0.9594 (m) cc_final: 0.9334 (p) REVERT: C 850 ILE cc_start: 0.9073 (mm) cc_final: 0.8777 (mm) REVERT: C 881 ASP cc_start: 0.6259 (m-30) cc_final: 0.6038 (m-30) REVERT: C 903 ARG cc_start: 0.8717 (tmt-80) cc_final: 0.7795 (ttp80) REVERT: C 1117 LEU cc_start: 0.9360 (mt) cc_final: 0.9112 (mt) REVERT: C 1214 ASP cc_start: 0.8884 (t70) cc_final: 0.8370 (t70) REVERT: C 1240 ASP cc_start: 0.8773 (m-30) cc_final: 0.8366 (t0) REVERT: C 1272 GLU cc_start: 0.8723 (pm20) cc_final: 0.8382 (pm20) REVERT: C 1276 TRP cc_start: 0.8411 (m-90) cc_final: 0.8074 (m-90) REVERT: C 1296 ASP cc_start: 0.8282 (m-30) cc_final: 0.7922 (m-30) REVERT: C 1338 GLU cc_start: 0.7351 (pt0) cc_final: 0.7092 (mt-10) REVERT: D 237 MET cc_start: 0.8660 (tpp) cc_final: 0.8360 (tpp) REVERT: D 269 TYR cc_start: 0.9045 (m-80) cc_final: 0.8220 (m-80) REVERT: D 298 MET cc_start: 0.8489 (ptp) cc_final: 0.8276 (ptp) REVERT: D 299 LEU cc_start: 0.9101 (tp) cc_final: 0.8890 (tp) REVERT: D 341 ASN cc_start: 0.8512 (m-40) cc_final: 0.8274 (m-40) REVERT: D 355 ILE cc_start: 0.9310 (pt) cc_final: 0.8715 (mt) REVERT: D 360 TYR cc_start: 0.8339 (p90) cc_final: 0.8024 (p90) REVERT: D 435 GLN cc_start: 0.8670 (mt0) cc_final: 0.8229 (mp10) REVERT: D 457 TYR cc_start: 0.8471 (m-10) cc_final: 0.7984 (m-80) REVERT: D 487 THR cc_start: 0.9385 (m) cc_final: 0.9089 (t) REVERT: D 513 MET cc_start: 0.9191 (mmm) cc_final: 0.8942 (mmm) REVERT: D 644 MET cc_start: 0.6594 (mtm) cc_final: 0.6211 (mtp) REVERT: D 747 MET cc_start: 0.5392 (mpp) cc_final: 0.4759 (mpp) REVERT: D 790 THR cc_start: 0.8625 (p) cc_final: 0.8290 (t) REVERT: D 796 LEU cc_start: 0.9155 (tp) cc_final: 0.8829 (tt) REVERT: D 1075 ARG cc_start: 0.4825 (mmt90) cc_final: 0.2963 (mmp-170) REVERT: D 1256 ILE cc_start: 0.9398 (pt) cc_final: 0.9004 (tt) REVERT: D 1290 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7377 (mtt-85) REVERT: D 1330 ARG cc_start: 0.6659 (mmt180) cc_final: 0.6353 (mmt180) REVERT: E 31 GLN cc_start: 0.8600 (tp40) cc_final: 0.7820 (tp40) REVERT: E 46 THR cc_start: 0.8692 (p) cc_final: 0.8419 (p) REVERT: E 72 GLN cc_start: 0.8437 (pt0) cc_final: 0.8047 (tp-100) REVERT: F 102 MET cc_start: 0.7859 (ttp) cc_final: 0.7475 (tmm) REVERT: F 227 GLN cc_start: 0.6709 (mm-40) cc_final: 0.5294 (tm-30) REVERT: F 338 HIS cc_start: 0.5803 (p90) cc_final: 0.5376 (t70) REVERT: F 474 MET cc_start: 0.8291 (ttt) cc_final: 0.6512 (tmm) REVERT: F 487 MET cc_start: 0.8109 (tpp) cc_final: 0.7418 (tmm) REVERT: F 499 LYS cc_start: 0.8117 (pttp) cc_final: 0.7681 (ttmt) REVERT: F 571 TYR cc_start: 0.6317 (m-80) cc_final: 0.6092 (m-80) outliers start: 0 outliers final: 0 residues processed: 479 average time/residue: 0.1908 time to fit residues: 152.4701 Evaluate side-chains 362 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 4.9990 chunk 305 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 199 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 281 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 375 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 93 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1111 GLN C1157 GLN C1288 GLN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN F 131 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN ** 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** J 105 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094487 restraints weight = 101360.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093707 restraints weight = 79041.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094275 restraints weight = 66193.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.094664 restraints weight = 60419.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.094881 restraints weight = 52518.524| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33812 Z= 0.177 Angle : 0.634 9.072 46192 Z= 0.333 Chirality : 0.044 0.211 5259 Planarity : 0.004 0.053 5591 Dihedral : 16.459 179.563 5643 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.15 % Favored : 92.82 % Rotamer: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.30 % 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: -2.02 (0.13), residues: 3845 helix: -0.92 (0.14), residues: 1341 sheet: -1.03 (0.26), residues: 350 loop : -1.68 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 540 TYR 0.031 0.002 TYR J 37 PHE 0.025 0.002 PHE C 972 TRP 0.019 0.001 TRP D 580 HIS 0.006 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00395 (33809) covalent geometry : angle 0.63403 (46192) hydrogen bonds : bond 0.04185 ( 910) hydrogen bonds : angle 5.01751 ( 2492) metal coordination : bond 0.00516 ( 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 454 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 453 time to evaluate : 1.214 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: 0.8797 (t70) cc_final: 0.8262 (t-90) REVERT: A 31 LEU cc_start: 0.9247 (mt) cc_final: 0.9000 (tp) REVERT: A 168 ILE cc_start: 0.8931 (mp) cc_final: 0.8706 (tt) REVERT: B 41 ASN cc_start: 0.8960 (t0) cc_final: 0.8749 (t0) REVERT: B 46 ILE cc_start: 0.9287 (pt) cc_final: 0.9006 (tt) REVERT: B 185 TYR cc_start: 0.9097 (p90) cc_final: 0.8766 (p90) REVERT: C 130 MET cc_start: 0.8246 (ttm) cc_final: 0.7817 (ttm) REVERT: C 245 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6346 (mmp80) REVERT: C 386 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6434 (pt0) REVERT: C 410 LEU cc_start: 0.8914 (mt) cc_final: 0.8402 (pp) REVERT: C 768 MET cc_start: 0.8713 (mtp) cc_final: 0.8461 (mtt) REVERT: C 781 ASP cc_start: 0.8095 (m-30) cc_final: 0.7826 (m-30) REVERT: C 903 ARG cc_start: 0.8624 (tmt-80) cc_final: 0.7708 (ttp80) REVERT: C 1117 LEU cc_start: 0.9445 (mt) cc_final: 0.9210 (mt) REVERT: C 1214 ASP cc_start: 0.8873 (t70) cc_final: 0.8400 (t70) REVERT: C 1240 ASP cc_start: 0.8836 (m-30) cc_final: 0.8405 (t0) REVERT: C 1256 GLN cc_start: 0.8875 (mp10) cc_final: 0.8569 (mp10) REVERT: C 1272 GLU cc_start: 0.8682 (pm20) cc_final: 0.8223 (pm20) REVERT: C 1273 MET cc_start: 0.8528 (mmm) cc_final: 0.8321 (mmt) REVERT: C 1276 TRP cc_start: 0.8576 (m-10) cc_final: 0.8143 (m-90) REVERT: C 1338 GLU cc_start: 0.7225 (pt0) cc_final: 0.6907 (mt-10) REVERT: D 180 MET cc_start: 0.8044 (mtp) cc_final: 0.7511 (mtt) REVERT: D 269 TYR cc_start: 0.9014 (m-80) cc_final: 0.8229 (m-80) REVERT: D 298 MET cc_start: 0.8573 (ptp) cc_final: 0.8335 (ptp) REVERT: D 299 LEU cc_start: 0.9363 (tp) cc_final: 0.9092 (tp) REVERT: D 400 MET cc_start: 0.8744 (tpp) cc_final: 0.7532 (tpp) REVERT: D 435 GLN cc_start: 0.8708 (mt0) cc_final: 0.8245 (mp10) REVERT: D 487 THR cc_start: 0.9419 (m) cc_final: 0.9176 (t) REVERT: D 644 MET cc_start: 0.6658 (mtm) cc_final: 0.6269 (mtp) REVERT: D 1040 MET cc_start: 0.1045 (ptt) cc_final: 0.0594 (ptp) REVERT: D 1075 ARG cc_start: 0.4842 (mmt90) cc_final: 0.3011 (mmp-170) REVERT: D 1290 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7528 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9323 (mt) cc_final: 0.9046 (mm) REVERT: D 1330 ARG cc_start: 0.6702 (mmt180) cc_final: 0.6459 (mmt180) REVERT: E 31 GLN cc_start: 0.8618 (tp40) cc_final: 0.7868 (tp40) REVERT: E 46 THR cc_start: 0.8796 (p) cc_final: 0.8467 (p) REVERT: E 72 GLN cc_start: 0.8406 (pt0) cc_final: 0.7975 (tp-100) REVERT: F 102 MET cc_start: 0.7841 (ttp) cc_final: 0.7481 (tmm) REVERT: F 227 GLN cc_start: 0.6787 (mm-40) cc_final: 0.5340 (tm-30) REVERT: F 276 MET cc_start: 0.8823 (tmm) cc_final: 0.8603 (tpp) REVERT: F 338 HIS cc_start: 0.5754 (p90) cc_final: 0.5343 (t70) REVERT: F 416 VAL cc_start: 0.9033 (t) cc_final: 0.8766 (t) REVERT: F 499 LYS cc_start: 0.8150 (pttp) cc_final: 0.7740 (ttmt) REVERT: F 525 ASP cc_start: 0.7797 (t0) cc_final: 0.7327 (p0) REVERT: F 571 TYR cc_start: 0.6371 (m-80) cc_final: 0.5966 (m-80) REVERT: J 86 GLN cc_start: 0.8247 (mp10) cc_final: 0.7896 (mm-40) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 0.1828 time to fit residues: 139.2497 Evaluate side-chains 352 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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: 30.0000 chunk 304 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 250 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 288 optimal weight: 40.0000 chunk 387 optimal weight: 20.0000 chunk 373 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 41 ASN A 128 HIS B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 702 GLN D 716 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.120710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091836 restraints weight = 102982.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.090693 restraints weight = 80318.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091461 restraints weight = 70069.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.091739 restraints weight = 61114.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.091895 restraints weight = 54873.054| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33812 Z= 0.227 Angle : 0.698 10.965 46192 Z= 0.365 Chirality : 0.045 0.180 5259 Planarity : 0.005 0.066 5591 Dihedral : 16.590 179.987 5643 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -2.18 (0.13), residues: 3845 helix: -1.02 (0.14), residues: 1336 sheet: -1.20 (0.27), residues: 335 loop : -1.78 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1246 TYR 0.034 0.002 TYR J 37 PHE 0.028 0.002 PHE A 8 TRP 0.028 0.002 TRP D 33 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00507 (33809) covalent geometry : angle 0.69792 (46192) hydrogen bonds : bond 0.04686 ( 910) hydrogen bonds : angle 5.33623 ( 2492) metal coordination : bond 0.00614 ( 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 432 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.129 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: 0.8923 (t70) cc_final: 0.8647 (t-90) REVERT: A 168 ILE cc_start: 0.8938 (mp) cc_final: 0.8699 (tt) REVERT: B 185 TYR cc_start: 0.9142 (p90) cc_final: 0.8762 (p90) REVERT: C 85 CYS cc_start: 0.8478 (m) cc_final: 0.8154 (m) REVERT: C 130 MET cc_start: 0.8396 (ttm) cc_final: 0.7944 (ttm) REVERT: C 245 ARG cc_start: 0.6961 (mtt180) cc_final: 0.6261 (mmp80) REVERT: C 429 MET cc_start: 0.9336 (mmm) cc_final: 0.9123 (mmm) REVERT: C 659 GLN cc_start: 0.8845 (pt0) cc_final: 0.8279 (tt0) REVERT: C 667 LEU cc_start: 0.8885 (mt) cc_final: 0.8573 (tt) REVERT: C 685 MET cc_start: 0.9312 (mmt) cc_final: 0.8708 (mmm) REVERT: C 781 ASP cc_start: 0.8221 (m-30) cc_final: 0.7847 (m-30) REVERT: C 820 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7699 (mm-30) REVERT: C 903 ARG cc_start: 0.8607 (tmt-80) cc_final: 0.7739 (ttp80) REVERT: C 1214 ASP cc_start: 0.8859 (t70) cc_final: 0.8415 (t70) REVERT: C 1240 ASP cc_start: 0.8835 (m-30) cc_final: 0.8399 (t0) REVERT: C 1272 GLU cc_start: 0.8685 (pm20) cc_final: 0.7978 (pm20) REVERT: C 1273 MET cc_start: 0.8619 (mmm) cc_final: 0.8204 (mmt) REVERT: C 1276 TRP cc_start: 0.8616 (m-10) cc_final: 0.8021 (m-90) REVERT: D 130 MET cc_start: 0.8020 (ptm) cc_final: 0.7369 (ptm) REVERT: D 298 MET cc_start: 0.8859 (ptp) cc_final: 0.8574 (ptp) REVERT: D 355 ILE cc_start: 0.9410 (pt) cc_final: 0.8732 (mt) REVERT: D 400 MET cc_start: 0.8764 (tpp) cc_final: 0.7625 (tpp) REVERT: D 435 GLN cc_start: 0.8691 (mt0) cc_final: 0.8208 (mp10) REVERT: D 487 THR cc_start: 0.9456 (m) cc_final: 0.9245 (t) REVERT: D 624 ILE cc_start: 0.9722 (mt) cc_final: 0.9507 (mt) REVERT: D 644 MET cc_start: 0.6754 (mtm) cc_final: 0.6340 (mtp) REVERT: D 1040 MET cc_start: 0.0749 (ptt) cc_final: 0.0467 (ptp) REVERT: D 1075 ARG cc_start: 0.4818 (mmt90) cc_final: 0.2964 (mmp-170) REVERT: D 1101 LEU cc_start: 0.7673 (mp) cc_final: 0.7004 (pt) REVERT: D 1290 ARG cc_start: 0.7798 (mtt180) cc_final: 0.7366 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9381 (mt) cc_final: 0.9103 (mm) REVERT: D 1326 GLN cc_start: 0.8788 (tt0) cc_final: 0.8425 (mt0) REVERT: D 1330 ARG cc_start: 0.6946 (mmt180) cc_final: 0.6645 (mmt180) REVERT: E 31 GLN cc_start: 0.8649 (tp40) cc_final: 0.8228 (tp-100) REVERT: E 46 THR cc_start: 0.8974 (p) cc_final: 0.8628 (p) REVERT: E 72 GLN cc_start: 0.8542 (pt0) cc_final: 0.8049 (tp-100) REVERT: F 102 MET cc_start: 0.7716 (ttp) cc_final: 0.7360 (tmm) REVERT: F 416 VAL cc_start: 0.9205 (t) cc_final: 0.8889 (t) REVERT: F 456 MET cc_start: 0.8990 (mmm) cc_final: 0.8595 (mmt) REVERT: F 499 LYS cc_start: 0.8243 (pttp) cc_final: 0.7848 (ttmt) REVERT: F 525 ASP cc_start: 0.7882 (t0) cc_final: 0.7566 (p0) REVERT: F 555 GLU cc_start: 0.8771 (mp0) cc_final: 0.8463 (mp0) REVERT: F 571 TYR cc_start: 0.6475 (m-80) cc_final: 0.5858 (m-80) REVERT: J 86 GLN cc_start: 0.8124 (mp10) cc_final: 0.7713 (mm-40) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1899 time to fit residues: 136.8919 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 : 0.964 ------------------------------------------------------------------------------- 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: 7.9990 chunk 47 optimal weight: 30.0000 chunk 348 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 191 optimal weight: 50.0000 chunk 146 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 60 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN D1326 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 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 = 0.3780 r_free = 0.3780 target = 0.120037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092178 restraints weight = 100776.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090914 restraints weight = 79935.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091599 restraints weight = 67167.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091766 restraints weight = 60685.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091941 restraints weight = 55823.754| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33812 Z= 0.221 Angle : 0.703 10.267 46192 Z= 0.367 Chirality : 0.045 0.205 5259 Planarity : 0.005 0.085 5591 Dihedral : 16.653 179.164 5643 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.62 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: -2.20 (0.13), residues: 3845 helix: -1.00 (0.14), residues: 1347 sheet: -1.21 (0.28), residues: 331 loop : -1.83 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1246 TYR 0.033 0.002 TYR J 37 PHE 0.025 0.002 PHE C 972 TRP 0.030 0.002 TRP D 33 HIS 0.006 0.001 HIS D 419 Details of bonding type rmsd covalent geometry : bond 0.00493 (33809) covalent geometry : angle 0.70329 (46192) hydrogen bonds : bond 0.04673 ( 910) hydrogen bonds : angle 5.32536 ( 2492) metal coordination : bond 0.00635 ( 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 422 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.157 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: 0.8877 (t70) cc_final: 0.8642 (t-90) REVERT: B 185 TYR cc_start: 0.9104 (p90) cc_final: 0.8749 (p90) REVERT: C 130 MET cc_start: 0.8351 (ttm) cc_final: 0.7885 (ttm) REVERT: C 245 ARG cc_start: 0.6998 (mtt180) cc_final: 0.6295 (mmp80) REVERT: C 429 MET cc_start: 0.9285 (mmm) cc_final: 0.9038 (mmm) REVERT: C 659 GLN cc_start: 0.8802 (pt0) cc_final: 0.8359 (tt0) REVERT: C 667 LEU cc_start: 0.8862 (mt) cc_final: 0.8468 (tt) REVERT: C 768 MET cc_start: 0.8509 (mtp) cc_final: 0.8253 (mtm) REVERT: C 781 ASP cc_start: 0.8189 (m-30) cc_final: 0.7838 (m-30) REVERT: C 819 SER cc_start: 0.9227 (p) cc_final: 0.9013 (m) REVERT: C 903 ARG cc_start: 0.8587 (tmt-80) cc_final: 0.7712 (ttp80) REVERT: C 1214 ASP cc_start: 0.8895 (t70) cc_final: 0.8377 (t70) REVERT: C 1240 ASP cc_start: 0.8816 (m-30) cc_final: 0.8438 (t0) REVERT: C 1246 ARG cc_start: 0.8749 (tmt170) cc_final: 0.8121 (ttt-90) REVERT: C 1272 GLU cc_start: 0.8660 (pm20) cc_final: 0.8232 (pm20) REVERT: C 1273 MET cc_start: 0.8519 (mmm) cc_final: 0.8196 (mmt) REVERT: C 1276 TRP cc_start: 0.8617 (m-10) cc_final: 0.8143 (m-90) REVERT: D 180 MET cc_start: 0.7968 (mtp) cc_final: 0.7698 (mtm) REVERT: D 298 MET cc_start: 0.8696 (ptp) cc_final: 0.8409 (ptp) REVERT: D 370 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9102 (mmmm) REVERT: D 400 MET cc_start: 0.8777 (tpp) cc_final: 0.8097 (tpp) REVERT: D 435 GLN cc_start: 0.8760 (mt0) cc_final: 0.8218 (mp10) REVERT: D 487 THR cc_start: 0.9470 (m) cc_final: 0.9232 (t) REVERT: D 624 ILE cc_start: 0.9720 (mt) cc_final: 0.9514 (mt) REVERT: D 644 MET cc_start: 0.6922 (mtm) cc_final: 0.6518 (mtp) REVERT: D 796 LEU cc_start: 0.9185 (tp) cc_final: 0.8978 (tt) REVERT: D 1040 MET cc_start: 0.1502 (ptt) cc_final: 0.1148 (ptp) REVERT: D 1075 ARG cc_start: 0.5134 (mmt90) cc_final: 0.3119 (mmp-170) REVERT: D 1210 ILE cc_start: 0.8339 (mm) cc_final: 0.8105 (mt) REVERT: D 1290 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7387 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9403 (mt) cc_final: 0.9163 (mm) REVERT: D 1330 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6675 (mmt180) REVERT: E 72 GLN cc_start: 0.8582 (pt0) cc_final: 0.8097 (tp-100) REVERT: F 102 MET cc_start: 0.7634 (ttp) cc_final: 0.7374 (tmm) REVERT: F 363 ARG cc_start: 0.8720 (tmm160) cc_final: 0.8469 (ttp80) REVERT: F 456 MET cc_start: 0.8971 (mmm) cc_final: 0.8614 (mmt) REVERT: F 499 LYS cc_start: 0.8176 (pttp) cc_final: 0.7827 (ttmt) REVERT: J 86 GLN cc_start: 0.8202 (mp10) cc_final: 0.7790 (mm-40) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1990 time to fit residues: 139.1217 Evaluate side-chains 327 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 20.0000 chunk 302 optimal weight: 10.0000 chunk 212 optimal weight: 0.0870 chunk 360 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 362 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 391 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 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 = 0.3814 r_free = 0.3814 target = 0.122229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093470 restraints weight = 102492.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092661 restraints weight = 78990.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093440 restraints weight = 66599.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093778 restraints weight = 57383.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093957 restraints weight = 51535.892| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33812 Z= 0.153 Angle : 0.633 9.413 46192 Z= 0.329 Chirality : 0.043 0.198 5259 Planarity : 0.004 0.077 5591 Dihedral : 16.566 178.824 5643 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.95 (0.13), residues: 3845 helix: -0.78 (0.14), residues: 1356 sheet: -0.99 (0.28), residues: 339 loop : -1.70 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 91 TYR 0.032 0.002 TYR J 37 PHE 0.021 0.001 PHE C 972 TRP 0.026 0.001 TRP D 33 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00345 (33809) covalent geometry : angle 0.63290 (46192) hydrogen bonds : bond 0.04189 ( 910) hydrogen bonds : angle 5.00972 ( 2492) metal coordination : bond 0.00355 ( 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 431 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 1.130 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: 0.8916 (t70) cc_final: 0.8343 (t-90) REVERT: A 61 ILE cc_start: 0.9313 (tt) cc_final: 0.9069 (pt) REVERT: A 66 HIS cc_start: 0.8200 (p90) cc_final: 0.7978 (p90) REVERT: B 46 ILE cc_start: 0.9385 (pt) cc_final: 0.9073 (tt) REVERT: B 185 TYR cc_start: 0.8989 (p90) cc_final: 0.8634 (p90) REVERT: C 130 MET cc_start: 0.8509 (ttm) cc_final: 0.8001 (ttm) REVERT: C 245 ARG cc_start: 0.6931 (mtt180) cc_final: 0.6279 (mmp80) REVERT: C 386 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6371 (pt0) REVERT: C 429 MET cc_start: 0.9297 (mmm) cc_final: 0.9063 (mmm) REVERT: C 659 GLN cc_start: 0.8703 (pt0) cc_final: 0.8208 (tt0) REVERT: C 667 LEU cc_start: 0.8850 (mt) cc_final: 0.8604 (tt) REVERT: C 732 ILE cc_start: 0.8638 (pt) cc_final: 0.8429 (mm) REVERT: C 781 ASP cc_start: 0.8095 (m-30) cc_final: 0.7764 (m-30) REVERT: C 819 SER cc_start: 0.9264 (p) cc_final: 0.8909 (m) REVERT: C 903 ARG cc_start: 0.8585 (tmt-80) cc_final: 0.7710 (ttp80) REVERT: C 965 GLN cc_start: 0.8303 (tt0) cc_final: 0.7910 (tm-30) REVERT: C 1085 MET cc_start: 0.8623 (mtt) cc_final: 0.8371 (mtt) REVERT: C 1214 ASP cc_start: 0.8814 (t70) cc_final: 0.8255 (t70) REVERT: C 1240 ASP cc_start: 0.8818 (m-30) cc_final: 0.8374 (t0) REVERT: C 1256 GLN cc_start: 0.9077 (mp10) cc_final: 0.8670 (mp10) REVERT: C 1272 GLU cc_start: 0.8616 (pm20) cc_final: 0.8207 (pm20) REVERT: C 1276 TRP cc_start: 0.8514 (m-10) cc_final: 0.8087 (m-90) REVERT: D 192 MET cc_start: 0.8183 (ptp) cc_final: 0.7929 (ptp) REVERT: D 298 MET cc_start: 0.8698 (ptp) cc_final: 0.8458 (ptp) REVERT: D 355 ILE cc_start: 0.9399 (pt) cc_final: 0.8484 (mt) REVERT: D 370 LYS cc_start: 0.9368 (mmmm) cc_final: 0.8961 (mmmm) REVERT: D 400 MET cc_start: 0.8775 (tpp) cc_final: 0.7671 (tpp) REVERT: D 435 GLN cc_start: 0.8684 (mt0) cc_final: 0.8130 (mp10) REVERT: D 487 THR cc_start: 0.9490 (m) cc_final: 0.9260 (t) REVERT: D 644 MET cc_start: 0.6721 (mtm) cc_final: 0.6315 (mtp) REVERT: D 1040 MET cc_start: 0.1425 (ptt) cc_final: 0.1075 (ptp) REVERT: D 1075 ARG cc_start: 0.5003 (mmt90) cc_final: 0.3082 (mmp-170) REVERT: D 1210 ILE cc_start: 0.8457 (mm) cc_final: 0.8211 (mt) REVERT: D 1290 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7344 (mtt-85) REVERT: D 1330 ARG cc_start: 0.6896 (mmt180) cc_final: 0.6622 (mmt180) REVERT: E 21 LEU cc_start: 0.8820 (mt) cc_final: 0.8384 (tt) REVERT: E 72 GLN cc_start: 0.8540 (pt0) cc_final: 0.8027 (tp-100) REVERT: E 73 GLN cc_start: 0.9016 (mt0) cc_final: 0.8799 (mt0) REVERT: F 100 MET cc_start: 0.8519 (mtm) cc_final: 0.8211 (mtm) REVERT: F 102 MET cc_start: 0.7476 (ttp) cc_final: 0.7248 (tmm) REVERT: F 227 GLN cc_start: 0.6930 (mm-40) cc_final: 0.5447 (tm-30) REVERT: F 365 MET cc_start: 0.7475 (ptt) cc_final: 0.7274 (ptt) REVERT: F 379 MET cc_start: 0.8713 (tpt) cc_final: 0.8469 (tpt) REVERT: F 456 MET cc_start: 0.8972 (mmm) cc_final: 0.8593 (mmt) REVERT: J 97 ASP cc_start: 0.4178 (m-30) cc_final: 0.3969 (t0) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.1843 time to fit residues: 133.2381 Evaluate side-chains 329 residues out of total 3327 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 0.9980 chunk 381 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 291 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 20.0000 chunk 275 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 GLN C1157 GLN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN ** F 406 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 = 0.3798 r_free = 0.3798 target = 0.121161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092056 restraints weight = 102227.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091970 restraints weight = 74706.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092618 restraints weight = 63568.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092935 restraints weight = 55012.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093058 restraints weight = 47897.838| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33812 Z= 0.177 Angle : 0.655 9.040 46192 Z= 0.341 Chirality : 0.044 0.256 5259 Planarity : 0.005 0.070 5591 Dihedral : 16.578 176.089 5643 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: -1.93 (0.13), residues: 3845 helix: -0.77 (0.14), residues: 1357 sheet: -1.01 (0.28), residues: 339 loop : -1.68 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 363 TYR 0.032 0.002 TYR J 37 PHE 0.028 0.002 PHE A 8 TRP 0.025 0.001 TRP D 33 HIS 0.020 0.001 HIS J 17 Details of bonding type rmsd covalent geometry : bond 0.00398 (33809) covalent geometry : angle 0.65467 (46192) hydrogen bonds : bond 0.04319 ( 910) hydrogen bonds : angle 5.11466 ( 2492) metal coordination : bond 0.00466 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5020.45 seconds wall clock time: 87 minutes 32.94 seconds (5252.94 seconds total)