Starting phenix.real_space_refine on Mon Jul 6 09:31:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vwz_32166/07_2026/7vwz_32166.cif" } resolution = 4.0 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 128 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 21251 2.51 5 N 6113 2.21 5 O 6873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34509 Number of models: 1 Model: "" Number of chains: 11 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: 10550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1339, 10550 Classifications: {'peptide': 1339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1283} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 10361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1332, 10361 Classifications: {'peptide': 1332} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1278} Chain breaks: 5 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: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3879 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 464} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "1" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1330 Classifications: {'DNA': 65} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 64} Chain: "2" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1324 Classifications: {'DNA': 64} Link IDs: {'rna3p': 63} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1327 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 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 15207 SG CYS D 72 118.988 101.205 71.345 1.00221.96 S ATOM 15339 SG CYS D 88 119.309 102.245 75.556 1.00186.65 S ATOM 21019 SG CYS D 814 84.597 121.439 133.749 1.00116.10 S ATOM 21584 SG CYS D 888 83.578 120.327 130.022 1.00100.79 S ATOM 21656 SG CYS D 898 80.072 120.306 132.262 1.00102.28 S Time building chain proxies: 7.30, per 1000 atoms: 0.21 Number of scatterers: 34509 At special positions: 0 Unit cell: (177.1, 209, 169.4, 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 141 16.00 P 128 15.00 Mg 1 11.99 O 6873 8.00 N 6113 7.00 C 21251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7516 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 48 sheets defined 38.4% alpha, 11.1% beta 26 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.518A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.726A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.523A pdb=" N ALA A 216 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.528A pdb=" N LEU A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 590' Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.513A pdb=" N ILE A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 50 removed outlier: 3.727A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.102A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.736A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.509A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.388A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 55 removed outlier: 3.942A pdb=" N PHE C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.863A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.720A pdb=" N LEU C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.522A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.814A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 348 through 354 removed outlier: 4.161A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.810A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.627A pdb=" N ALA C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.080A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 3.844A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 removed outlier: 3.561A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.801A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.615A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 506 removed outlier: 4.056A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 4.404A pdb=" N HIS C 526 " --> pdb=" O SER C 522 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 527 " --> pdb=" O GLU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.970A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.733A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.691A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 681 removed outlier: 3.593A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 687 removed outlier: 3.881A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.906A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.696A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.883A pdb=" N ILE C 905 " --> pdb=" O LEU C 901 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 968 removed outlier: 3.962A pdb=" N LYS C 954 " --> pdb=" O GLU C 950 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 977 removed outlier: 3.988A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 976 " --> pdb=" O PHE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.581A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.839A 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 1004 through 1008 Processing helix chain 'C' and resid 1010 through 1038 removed outlier: 3.832A pdb=" N ALA C1015 " --> pdb=" O LEU C1011 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C1030 " --> pdb=" O GLU C1026 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 4.069A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1119 removed outlier: 3.749A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C1115 " --> pdb=" O GLN C1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C1118 " --> pdb=" O GLU C1114 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1128 Processing helix chain 'C' and resid 1129 through 1132 removed outlier: 3.822A pdb=" N LEU C1132 " --> pdb=" O ASN C1129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1129 through 1132' Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 4.047A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.713A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1174 removed outlier: 3.612A pdb=" N GLU C1174 " --> pdb=" O MET C1170 " (cutoff:3.500A) Processing helix chain 'C' and resid 1175 through 1179 removed outlier: 3.807A pdb=" N LYS C1178 " --> pdb=" O ASN C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.528A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU C1197 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.505A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1280 removed outlier: 3.518A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 removed outlier: 4.039A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1309 removed outlier: 3.731A pdb=" N TYR C1305 " --> pdb=" O ARG C1301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1331 removed outlier: 3.921A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C1329 " --> pdb=" O VAL C1325 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.841A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.519A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.641A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.694A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 206 removed outlier: 4.178A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.618A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.751A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 308 removed outlier: 3.752A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 305 " --> pdb=" O GLU D 301 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 removed outlier: 3.590A pdb=" N TYR D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.720A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 removed outlier: 4.297A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.613A pdb=" N GLY D 433 " --> pdb=" O HIS D 430 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 430 through 434' Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.973A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.584A pdb=" N GLN D 477 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.800A pdb=" N LEU D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR D 511 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 513 " --> pdb=" O GLY D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 538 removed outlier: 3.529A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 4.017A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.606A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 631 removed outlier: 3.811A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR D 627 " --> pdb=" O GLN D 623 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 629 " --> pdb=" O MET D 625 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 Processing helix chain 'D' and resid 650 through 659 removed outlier: 3.835A pdb=" N ILE D 654 " --> pdb=" O LYS D 650 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 674 through 697 removed outlier: 3.513A pdb=" N ARG D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN D 690 " --> pdb=" O TRP D 686 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS D 695 " --> pdb=" O ASP D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 702 Processing helix chain 'D' and resid 722 through 727 removed outlier: 3.549A pdb=" N ASP D 727 " --> pdb=" O TYR D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 740 removed outlier: 3.591A pdb=" N GLN D 739 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 785 removed outlier: 3.889A pdb=" N THR D 776 " --> pdb=" O TYR D 772 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS D 781 " --> pdb=" O HIS D 777 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 801 removed outlier: 3.589A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.631A pdb=" N LEU D 872 " --> pdb=" O TRP D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 915 through 924 removed outlier: 3.531A pdb=" N ALA D 919 " --> pdb=" O ILE D 915 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1145 removed outlier: 3.534A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1224 removed outlier: 3.516A pdb=" N ARG D1224 " --> pdb=" O ILE D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.538A pdb=" N TYR D1232 " --> pdb=" O ALA D1228 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D1233 " --> pdb=" O VAL D1229 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.345A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1284 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1338 removed outlier: 3.561A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA D1335 " --> pdb=" O VAL D1331 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA D1336 " --> pdb=" O LEU D1332 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.509A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D1351 " --> pdb=" O LEU D1347 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1346 through 1353' Processing helix chain 'D' and resid 1359 through 1375 removed outlier: 4.241A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 14 removed outlier: 3.796A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.520A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.564A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 77 removed outlier: 4.044A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.787A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 134 removed outlier: 3.815A pdb=" N LYS F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS F 132 " --> pdb=" O ASN F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 144 through 153 removed outlier: 3.742A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 220 removed outlier: 3.898A pdb=" N LYS F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 237 removed outlier: 3.908A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 removed outlier: 4.277A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 291 removed outlier: 3.595A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 281 " --> pdb=" O MET F 277 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.516A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.536A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS F 329 " --> pdb=" O TRP F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 352 removed outlier: 4.397A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU F 350 " --> pdb=" O GLN F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 381 removed outlier: 3.988A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG F 363 " --> pdb=" O LYS F 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS F 371 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.764A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 411 removed outlier: 3.656A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 416 removed outlier: 4.097A pdb=" N ALA F 415 " --> pdb=" O GLY F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.575A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.809A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN F 437 " --> pdb=" O TRP F 433 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 458 Processing helix chain 'F' and resid 459 through 475 removed outlier: 3.524A pdb=" N SER F 467 " --> pdb=" O LEU F 463 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 488 removed outlier: 3.782A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 550 removed outlier: 4.126A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 544 " --> pdb=" O LEU F 540 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 564 removed outlier: 3.555A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG F 562 " --> pdb=" O VAL F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.980A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 600 removed outlier: 4.461A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN F 589 " --> pdb=" O GLU F 585 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS F 597 " --> pdb=" O LYS F 593 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 598 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 606 No H-bonds generated for 'chain 'F' and resid 604 through 606' Processing helix chain 'F' and resid 607 through 612 removed outlier: 3.603A pdb=" N ASP F 612 " --> pdb=" O ARG F 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 11 removed outlier: 3.704A pdb=" N ASP G 9 " --> pdb=" O ILE G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 24 through 29 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 36 through 47 removed outlier: 4.107A pdb=" N ARG G 40 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL G 45 " --> pdb=" O MET G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 51 No H-bonds generated for 'chain 'G' and resid 50 through 51' Processing helix chain 'G' and resid 53 through 53 No H-bonds generated for 'chain 'G' and resid 53 through 53' Processing helix chain 'G' and resid 54 through 68 removed outlier: 4.664A pdb=" N ALA G 65 " --> pdb=" O LYS G 61 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 4.202A pdb=" N ILE G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 77 " --> pdb=" O ILE G 73 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU G 78 " --> pdb=" O LEU G 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 96 Processing helix chain 'I' and resid 148 through 150 No H-bonds generated for 'chain 'I' and resid 148 through 150' Processing helix chain 'I' and resid 151 through 168 Processing helix chain 'I' and resid 234 through 242 removed outlier: 3.778A pdb=" N GLU I 238 " --> pdb=" O THR I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 251 removed outlier: 3.940A pdb=" N MET I 250 " --> pdb=" O CYS I 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.452A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 18 removed outlier: 5.452A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.623A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 60 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (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 'B' and resid 23 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 4.254A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU B 122 " --> pdb=" O ARG B 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.558A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.161A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.910A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.643A pdb=" N THR C 141 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.709A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AB8, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.650A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 256 Processing sheet with id=AC1, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.627A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.753A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 598 through 606 removed outlier: 5.635A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 606 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC5, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.239A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 722 through 727 removed outlier: 6.611A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 3.529A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 818 through 819 removed outlier: 6.656A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.729A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD2, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD3, first strand: chain 'C' and resid 1268 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.974A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 7.893A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.556A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.607A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 365 through 369 removed outlier: 3.537A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 547 through 552 Processing sheet with id=AE1, first strand: chain 'D' and resid 555 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.537A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 849 through 850 removed outlier: 4.695A pdb=" N ASP D 855 " --> pdb=" O LYS D 850 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 958 through 959 removed outlier: 3.799A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 983 " --> pdb=" O LYS D 959 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1035 removed outlier: 3.519A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1177 through 1178 removed outlier: 3.978A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1263 through 1264 Processing sheet with id=AE9, first strand: chain 'I' and resid 127 through 133 removed outlier: 4.469A pdb=" N GLU I 127 " --> pdb=" O THR I 228 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 144 through 145 removed outlier: 3.616A pdb=" N TYR I 145 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL I 196 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE I 139 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY I 140 " --> pdb=" O HIS I 215 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 144 through 145 removed outlier: 3.616A pdb=" N TYR I 145 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL I 196 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 178 " --> pdb=" O TYR I 264 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 254 through 255 removed outlier: 4.020A pdb=" N THR I 254 " --> pdb=" O ARG I 288 " (cutoff:3.500A) 889 hydrogen bonds defined for protein. 2451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 9.56 Time building geometry restraints manager: 4.05 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: 8796 1.33 - 1.45: 7113 1.45 - 1.58: 18898 1.58 - 1.70: 254 1.70 - 1.82: 247 Bond restraints: 35308 Sorted by residual: bond pdb=" C1' DT 2 10 " pdb=" N1 DT 2 10 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" C1' DT 1 53 " pdb=" N1 DT 1 53 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C PHE D 437 " pdb=" N GLU D 438 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.07e-02 2.33e+03 1.57e+01 bond pdb=" C5' DG 1 73 " pdb=" C4' DG 1 73 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.52e+01 bond pdb=" C3' DA 1 49 " pdb=" O3' DA 1 49 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.48e+01 ... (remaining 35303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 46684 2.52 - 5.04: 1370 5.04 - 7.56: 140 7.56 - 10.08: 32 10.08 - 12.60: 3 Bond angle restraints: 48229 Sorted by residual: angle pdb=" N LEU G 18 " pdb=" CA LEU G 18 " pdb=" C LEU G 18 " ideal model delta sigma weight residual 113.17 103.05 10.12 1.26e+00 6.30e-01 6.45e+01 angle pdb=" N ILE F 505 " pdb=" CA ILE F 505 " pdb=" C ILE F 505 " ideal model delta sigma weight residual 110.62 117.72 -7.10 1.02e+00 9.61e-01 4.84e+01 angle pdb=" N ILE D 490 " pdb=" CA ILE D 490 " pdb=" C ILE D 490 " ideal model delta sigma weight residual 112.96 106.01 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" N ILE C 347 " pdb=" CA ILE C 347 " pdb=" C ILE C 347 " ideal model delta sigma weight residual 113.71 107.13 6.58 9.50e-01 1.11e+00 4.79e+01 angle pdb=" N ILE F 500 " pdb=" CA ILE F 500 " pdb=" C ILE F 500 " ideal model delta sigma weight residual 113.53 107.01 6.52 9.80e-01 1.04e+00 4.43e+01 ... (remaining 48224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.46: 19787 29.46 - 58.93: 1486 58.93 - 88.39: 98 88.39 - 117.86: 5 117.86 - 147.32: 2 Dihedral angle restraints: 21378 sinusoidal: 9729 harmonic: 11649 Sorted by residual: dihedral pdb=" CA VAL C1103 " pdb=" C VAL C1103 " pdb=" N PRO C1104 " pdb=" CA PRO C1104 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA VAL C 155 " pdb=" C VAL C 155 " pdb=" N PHE C 156 " pdb=" CA PHE C 156 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA CYS I 247 " pdb=" C CYS I 247 " pdb=" N MET I 248 " pdb=" CA MET I 248 " ideal model delta harmonic sigma weight residual -180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 21375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4442 0.074 - 0.147: 928 0.147 - 0.221: 88 0.221 - 0.294: 19 0.294 - 0.368: 1 Chirality restraints: 5478 Sorted by residual: chirality pdb=" CB ILE C 333 " pdb=" CA ILE C 333 " pdb=" CG1 ILE C 333 " pdb=" CG2 ILE C 333 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB ILE C 750 " pdb=" CA ILE C 750 " pdb=" CG1 ILE C 750 " pdb=" CG2 ILE C 750 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE A 61 " pdb=" CA ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CG2 ILE A 61 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 5475 not shown) Planarity restraints: 5839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET I 248 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO I 249 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO I 249 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO I 249 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 294 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN F 294 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN F 294 " -0.021 2.00e-02 2.50e+03 pdb=" N CYS F 295 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 567 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " 0.043 5.00e-02 4.00e+02 ... (remaining 5836 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1276 2.70 - 3.25: 31388 3.25 - 3.80: 55751 3.80 - 4.35: 69617 4.35 - 4.90: 107573 Nonbonded interactions: 265605 Sorted by model distance: nonbonded pdb=" O6 DG 2 16 " pdb=" N6 DA 2 17 " model vdw 2.148 3.120 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.163 2.310 nonbonded pdb=" O ARG G 57 " pdb=" CB LYS G 61 " model vdw 2.238 2.752 nonbonded pdb=" O GLN C1288 " pdb=" OG1 THR C1292 " model vdw 2.252 3.040 nonbonded pdb=" O ILE D 918 " pdb=" OG SER D 922 " model vdw 2.254 3.040 ... (remaining 265600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 41.690 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 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 0.529 35313 Z= 0.379 Angle : 1.030 12.605 48229 Z= 0.631 Chirality : 0.059 0.368 5478 Planarity : 0.007 0.101 5839 Dihedral : 18.640 147.321 13862 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.84 % Favored : 90.96 % Rotamer: Outliers : 1.10 % Allowed : 12.80 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -5.04 (0.10), residues: 4003 helix: -4.32 (0.07), residues: 1312 sheet: -2.95 (0.21), residues: 409 loop : -2.86 (0.11), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 594 TYR 0.024 0.003 TYR A 152 PHE 0.026 0.003 PHE C 253 TRP 0.015 0.002 TRP G 13 HIS 0.017 0.002 HIS G 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.36 (35308) covalent geometry : angle 1.03028 / 0.63 (48229) hydrogen bonds : bond 0.31908 / 21.55 ( 937) hydrogen bonds : angle 11.32209 / 7.76 ( 2563) metal coordination : bond 0.32597 / 16.44 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 485 time to evaluate : 1.172 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 51 MET cc_start: 0.6535 (mmm) cc_final: 0.6177 (tpp) REVERT: C 244 GLU cc_start: 0.6320 (mt-10) cc_final: 0.6015 (pm20) REVERT: C 378 ARG cc_start: 0.5055 (mtp180) cc_final: 0.4519 (mmm160) REVERT: C 394 ARG cc_start: 0.4968 (mtt180) cc_final: 0.4677 (ttm110) REVERT: C 477 GLU cc_start: 0.5574 (mm-30) cc_final: 0.4596 (tm-30) REVERT: C 835 GLU cc_start: 0.6088 (tt0) cc_final: 0.5835 (tt0) REVERT: C 844 LYS cc_start: 0.5708 (ptmt) cc_final: 0.5359 (tptt) REVERT: C 898 GLU cc_start: 0.6539 (mp0) cc_final: 0.5916 (mm-30) REVERT: C 1085 MET cc_start: 0.7806 (mmm) cc_final: 0.7491 (mmm) REVERT: C 1131 MET cc_start: 0.7382 (mtp) cc_final: 0.6772 (mtp) REVERT: C 1180 MET cc_start: 0.7039 (ttt) cc_final: 0.6838 (ttt) REVERT: C 1232 MET cc_start: 0.7063 (mmm) cc_final: 0.6588 (mmm) REVERT: C 1304 MET cc_start: 0.6488 (mmm) cc_final: 0.6201 (mmt) REVERT: C 1315 MET cc_start: 0.6262 (ttm) cc_final: 0.5106 (mtm) REVERT: C 1324 ASN cc_start: 0.7068 (p0) cc_final: 0.6392 (p0) REVERT: C 1326 LEU cc_start: 0.7771 (tp) cc_final: 0.7522 (tt) REVERT: D 172 PHE cc_start: 0.6141 (m-80) cc_final: 0.5761 (m-10) REVERT: D 248 ASP cc_start: 0.6701 (t0) cc_final: 0.6331 (t0) REVERT: D 301 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6790 (tp30) REVERT: D 335 GLN cc_start: 0.4292 (mp-120) cc_final: 0.3936 (mm110) REVERT: D 372 MET cc_start: 0.7364 (ttt) cc_final: 0.6963 (ttp) REVERT: D 472 LEU cc_start: 0.7461 (mt) cc_final: 0.7208 (pp) REVERT: D 479 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6193 (mt-10) REVERT: D 506 VAL cc_start: 0.7433 (m) cc_final: 0.7093 (t) REVERT: D 724 MET cc_start: 0.5007 (ptp) cc_final: 0.4792 (ppp) REVERT: D 738 ARG cc_start: 0.3895 (ttm170) cc_final: 0.3537 (ttm110) REVERT: D 849 LEU cc_start: 0.5434 (OUTLIER) cc_final: 0.4982 (pp) REVERT: D 850 LYS cc_start: 0.3544 (mttp) cc_final: 0.3018 (ttmm) REVERT: D 1214 PRO cc_start: 0.4345 (Cg_endo) cc_final: 0.3797 (Cg_exo) REVERT: D 1236 GLU cc_start: 0.6511 (tp30) cc_final: 0.5456 (mm-30) REVERT: D 1254 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6712 (mt-10) REVERT: D 1257 VAL cc_start: 0.7974 (t) cc_final: 0.7362 (p) REVERT: D 1274 PHE cc_start: 0.4748 (t80) cc_final: 0.4331 (t80) REVERT: D 1371 ARG cc_start: 0.5435 (ptt-90) cc_final: 0.4211 (tmm160) REVERT: E 19 LEU cc_start: 0.7521 (tp) cc_final: 0.7128 (mm) REVERT: E 42 GLU cc_start: 0.5877 (mt-10) cc_final: 0.5660 (pm20) REVERT: E 65 ASP cc_start: 0.6079 (m-30) cc_final: 0.5665 (p0) REVERT: E 74 GLU cc_start: 0.4562 (tp30) cc_final: 0.4298 (tp30) REVERT: F 101 TYR cc_start: 0.6826 (t80) cc_final: 0.6564 (t80) REVERT: F 277 MET cc_start: 0.3540 (mtt) cc_final: 0.3293 (mtp) REVERT: F 456 MET cc_start: 0.6868 (mpp) cc_final: 0.6495 (mmp) REVERT: F 470 MET cc_start: 0.3637 (mmt) cc_final: 0.2866 (mmm) REVERT: F 544 THR cc_start: 0.7273 (p) cc_final: 0.6632 (p) REVERT: F 561 MET cc_start: 0.5957 (ptp) cc_final: 0.5679 (ptt) outliers start: 38 outliers final: 19 residues processed: 522 average time/residue: 0.2398 time to fit residues: 194.7542 Evaluate side-chains 319 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 66 HIS B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN C 406 ASN C 568 ASN C 659 GLN C 737 ASN C 762 ASN C 832 HIS ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1237 HIS C1268 GLN C1299 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 274 ASN D 276 ASN D 277 ASN D 680 ASN D 702 GLN D1023 HIS D1049 GLN D1086 ASN D1235 ASN F 128 ASN F 309 ASN F 342 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 409 ASN F 579 GLN F 600 HIS I 157 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.084171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061545 restraints weight = 219430.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.062744 restraints weight = 126444.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.063634 restraints weight = 89520.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.064028 restraints weight = 73238.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.064028 restraints weight = 64584.438| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35313 Z= 0.196 Angle : 0.799 9.968 48229 Z= 0.430 Chirality : 0.050 0.292 5478 Planarity : 0.007 0.079 5839 Dihedral : 17.866 176.614 5885 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.99 % Favored : 91.98 % Rotamer: Outliers : 3.55 % Allowed : 16.81 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -4.40 (0.11), residues: 4003 helix: -3.37 (0.10), residues: 1419 sheet: -2.61 (0.22), residues: 390 loop : -2.68 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 678 TYR 0.031 0.002 TYR F 137 PHE 0.021 0.002 PHE G 88 TRP 0.012 0.002 TRP F 326 HIS 0.011 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (35308) covalent geometry : angle 0.79926 / 0.43 (48229) hydrogen bonds : bond 0.07181 / 4.88 ( 937) hydrogen bonds : angle 7.30079 / 4.98 ( 2563) metal coordination : bond 0.01594 / 0.86 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 315 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6595 (mmm) cc_final: 0.6170 (tpp) REVERT: A 157 THR cc_start: 0.5457 (OUTLIER) cc_final: 0.4937 (t) REVERT: A 165 GLU cc_start: 0.4317 (mp0) cc_final: 0.3989 (tp30) REVERT: B 127 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6023 (pm20) REVERT: C 67 GLU cc_start: 0.3977 (pt0) cc_final: 0.3731 (pt0) REVERT: C 105 TYR cc_start: 0.4366 (m-80) cc_final: 0.4128 (m-10) REVERT: C 244 GLU cc_start: 0.6269 (mt-10) cc_final: 0.6034 (pm20) REVERT: C 378 ARG cc_start: 0.5194 (mtp180) cc_final: 0.4625 (mmm160) REVERT: C 394 ARG cc_start: 0.5130 (mtt180) cc_final: 0.4833 (ttm110) REVERT: C 443 ASP cc_start: 0.4680 (p0) cc_final: 0.4300 (p0) REVERT: C 477 GLU cc_start: 0.5865 (mm-30) cc_final: 0.4975 (tm-30) REVERT: C 492 MET cc_start: 0.4750 (mtp) cc_final: 0.4501 (ttm) REVERT: C 844 LYS cc_start: 0.5562 (ptmt) cc_final: 0.5176 (tptt) REVERT: C 898 GLU cc_start: 0.6378 (mp0) cc_final: 0.5923 (mm-30) REVERT: C 1034 ARG cc_start: 0.6514 (tpt170) cc_final: 0.6241 (tpt170) REVERT: C 1131 MET cc_start: 0.7170 (mtp) cc_final: 0.6705 (mtp) REVERT: C 1209 GLN cc_start: 0.6509 (tt0) cc_final: 0.6167 (mt0) REVERT: C 1289 GLU cc_start: 0.7024 (tt0) cc_final: 0.6427 (tt0) REVERT: C 1315 MET cc_start: 0.6036 (ttm) cc_final: 0.4642 (mtm) REVERT: C 1324 ASN cc_start: 0.6830 (p0) cc_final: 0.6150 (p0) REVERT: D 235 GLU cc_start: 0.6362 (mp0) cc_final: 0.6089 (mm-30) REVERT: D 248 ASP cc_start: 0.6409 (t0) cc_final: 0.6011 (t0) REVERT: D 372 MET cc_start: 0.7276 (ttt) cc_final: 0.6903 (ttp) REVERT: D 466 MET cc_start: 0.7254 (mtp) cc_final: 0.6658 (mtp) REVERT: D 479 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6171 (mt-10) REVERT: D 738 ARG cc_start: 0.3606 (ttm170) cc_final: 0.3266 (ttm110) REVERT: D 849 LEU cc_start: 0.5087 (OUTLIER) cc_final: 0.4854 (pp) REVERT: D 850 LYS cc_start: 0.3454 (mttp) cc_final: 0.2955 (ttmm) REVERT: D 1236 GLU cc_start: 0.6610 (tp30) cc_final: 0.5550 (mm-30) REVERT: D 1370 MET cc_start: 0.5257 (tpp) cc_final: 0.4878 (tpt) REVERT: D 1371 ARG cc_start: 0.4806 (ptt-90) cc_final: 0.3922 (tmm160) REVERT: D 1372 ARG cc_start: 0.3623 (ttp-110) cc_final: 0.3326 (ptt-90) REVERT: E 41 GLU cc_start: 0.3299 (tt0) cc_final: 0.2718 (tt0) REVERT: E 49 ILE cc_start: 0.6261 (pt) cc_final: 0.5961 (tp) REVERT: F 365 MET cc_start: 0.6529 (tmm) cc_final: 0.6058 (tmm) REVERT: F 456 MET cc_start: 0.7058 (mpp) cc_final: 0.6758 (mmp) REVERT: F 561 MET cc_start: 0.6182 (ptp) cc_final: 0.5906 (ptt) outliers start: 123 outliers final: 76 residues processed: 429 average time/residue: 0.2013 time to fit residues: 142.7090 Evaluate side-chains 341 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 262 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain I residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 82 optimal weight: 0.0060 chunk 303 optimal weight: 0.8980 chunk 403 optimal weight: 30.0000 chunk 398 optimal weight: 5.9990 chunk 368 optimal weight: 20.0000 chunk 280 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 343 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 351 optimal weight: 10.0000 chunk 26 optimal weight: 30.0000 overall best weight: 5.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN F 579 GLN F 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.083804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.060944 restraints weight = 219078.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.062217 restraints weight = 126272.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063212 restraints weight = 90044.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063596 restraints weight = 73076.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.063976 restraints weight = 66143.466| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 35313 Z= 0.182 Angle : 0.750 13.344 48229 Z= 0.402 Chirality : 0.048 0.349 5478 Planarity : 0.006 0.071 5839 Dihedral : 17.768 173.933 5875 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.52 % Favored : 91.46 % Rotamer: Outliers : 5.11 % Allowed : 18.34 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.08 (0.11), residues: 4003 helix: -2.93 (0.11), residues: 1429 sheet: -2.59 (0.22), residues: 404 loop : -2.58 (0.12), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.024 0.002 TYR C1149 PHE 0.017 0.002 PHE F 401 TRP 0.019 0.002 TRP A 650 HIS 0.010 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (35308) covalent geometry : angle 0.74997 / 0.40 (48229) hydrogen bonds : bond 0.06223 / 4.30 ( 937) hydrogen bonds : angle 6.85139 / 4.67 ( 2563) metal coordination : bond 0.00645 / 0.30 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 280 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6618 (mmm) cc_final: 0.6167 (tpp) REVERT: A 157 THR cc_start: 0.5441 (OUTLIER) cc_final: 0.4903 (t) REVERT: B 205 MET cc_start: 0.6710 (pmm) cc_final: 0.6485 (pmm) REVERT: C 67 GLU cc_start: 0.3939 (pt0) cc_final: 0.3588 (pt0) REVERT: C 105 TYR cc_start: 0.4195 (m-80) cc_final: 0.3967 (m-10) REVERT: C 244 GLU cc_start: 0.6307 (mt-10) cc_final: 0.6018 (pm20) REVERT: C 378 ARG cc_start: 0.5122 (mtp180) cc_final: 0.4576 (mmm160) REVERT: C 394 ARG cc_start: 0.5143 (mtt180) cc_final: 0.4836 (ttm110) REVERT: C 477 GLU cc_start: 0.5823 (mm-30) cc_final: 0.4963 (tm-30) REVERT: C 538 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5207 (mm) REVERT: C 606 LEU cc_start: 0.7183 (tp) cc_final: 0.6966 (tp) REVERT: C 844 LYS cc_start: 0.5619 (ptmt) cc_final: 0.5217 (tptt) REVERT: C 1034 ARG cc_start: 0.6476 (tpt170) cc_final: 0.6177 (tpt170) REVERT: C 1137 GLU cc_start: 0.5830 (mm-30) cc_final: 0.5561 (tp30) REVERT: C 1209 GLN cc_start: 0.6492 (tt0) cc_final: 0.6093 (mt0) REVERT: D 235 GLU cc_start: 0.6286 (mp0) cc_final: 0.6037 (mm-30) REVERT: D 248 ASP cc_start: 0.6626 (t0) cc_final: 0.6262 (t0) REVERT: D 372 MET cc_start: 0.7244 (ttt) cc_final: 0.6924 (ttp) REVERT: D 466 MET cc_start: 0.7267 (mtp) cc_final: 0.6647 (mtp) REVERT: D 479 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6271 (mt-10) REVERT: D 738 ARG cc_start: 0.3612 (ttm170) cc_final: 0.3218 (ttm110) REVERT: D 1236 GLU cc_start: 0.6570 (tp30) cc_final: 0.5509 (mm-30) REVERT: D 1371 ARG cc_start: 0.4921 (ptt-90) cc_final: 0.3863 (tmm160) REVERT: D 1372 ARG cc_start: 0.3606 (ttp-110) cc_final: 0.3331 (ptt-90) REVERT: E 41 GLU cc_start: 0.3074 (tt0) cc_final: 0.2546 (tt0) REVERT: F 365 MET cc_start: 0.6421 (tmm) cc_final: 0.6090 (tmm) REVERT: F 456 MET cc_start: 0.7085 (mpp) cc_final: 0.6814 (mmp) REVERT: F 528 LEU cc_start: 0.3548 (mt) cc_final: 0.3226 (tp) REVERT: F 552 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5161 (p) REVERT: F 561 MET cc_start: 0.6253 (ptp) cc_final: 0.5936 (ptt) REVERT: G 76 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5938 (mp) outliers start: 177 outliers final: 122 residues processed: 443 average time/residue: 0.1940 time to fit residues: 145.3840 Evaluate side-chains 386 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 260 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 228 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 114 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 344 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 398 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 330 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN F 600 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.083472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062061 restraints weight = 217433.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.063264 restraints weight = 132751.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.063249 restraints weight = 99339.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063682 restraints weight = 74147.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063733 restraints weight = 68294.502| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 35313 Z= 0.226 Angle : 0.825 12.474 48229 Z= 0.438 Chirality : 0.051 0.317 5478 Planarity : 0.007 0.074 5839 Dihedral : 17.926 170.185 5873 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.49 % Favored : 89.48 % Rotamer: Outliers : 6.70 % Allowed : 19.73 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -4.02 (0.11), residues: 4003 helix: -2.81 (0.11), residues: 1407 sheet: -2.62 (0.23), residues: 393 loop : -2.61 (0.12), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 166 TYR 0.029 0.003 TYR C1149 PHE 0.028 0.003 PHE B 8 TRP 0.019 0.002 TRP A 650 HIS 0.012 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.23 (35308) covalent geometry : angle 0.82451 / 0.44 (48229) hydrogen bonds : bond 0.06045 / 4.19 ( 937) hydrogen bonds : angle 6.88344 / 4.70 ( 2563) metal coordination : bond 0.00527 / 0.25 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 275 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6411 (mmm) cc_final: 0.6068 (tpp) REVERT: A 60 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4889 (pt0) REVERT: A 93 GLN cc_start: 0.5831 (mp-120) cc_final: 0.5403 (mm-40) REVERT: A 157 THR cc_start: 0.5321 (OUTLIER) cc_final: 0.4748 (t) REVERT: B 88 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7694 (mm) REVERT: C 67 GLU cc_start: 0.3861 (pt0) cc_final: 0.3508 (pt0) REVERT: C 105 TYR cc_start: 0.4324 (m-80) cc_final: 0.4099 (m-10) REVERT: C 244 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6096 (pm20) REVERT: C 378 ARG cc_start: 0.5107 (mtp180) cc_final: 0.4592 (mmm160) REVERT: C 394 ARG cc_start: 0.5290 (mtt180) cc_final: 0.4971 (ttm110) REVERT: C 477 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5249 (tm-30) REVERT: C 478 ARG cc_start: 0.6154 (mtt180) cc_final: 0.5646 (mmt-90) REVERT: C 768 MET cc_start: 0.6103 (ptt) cc_final: 0.5869 (ptp) REVERT: C 805 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7870 (pmm) REVERT: C 844 LYS cc_start: 0.5723 (ptmt) cc_final: 0.5408 (tptt) REVERT: C 1034 ARG cc_start: 0.6401 (tpt170) cc_final: 0.6113 (tpt170) REVERT: C 1116 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6808 (m-70) REVERT: C 1137 GLU cc_start: 0.5575 (mm-30) cc_final: 0.5274 (tp30) REVERT: C 1265 PHE cc_start: 0.5662 (t80) cc_final: 0.4684 (m-80) REVERT: D 248 ASP cc_start: 0.6350 (t0) cc_final: 0.6022 (t0) REVERT: D 466 MET cc_start: 0.7208 (mtp) cc_final: 0.6594 (mtp) REVERT: D 479 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5883 (mt-10) REVERT: D 582 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7056 (mt) REVERT: D 738 ARG cc_start: 0.3789 (ttm170) cc_final: 0.3422 (ttm110) REVERT: D 878 ASP cc_start: 0.3745 (t0) cc_final: 0.2958 (m-30) REVERT: D 1236 GLU cc_start: 0.6469 (tp30) cc_final: 0.5455 (mm-30) REVERT: D 1371 ARG cc_start: 0.4913 (ptt-90) cc_final: 0.3971 (tmm160) REVERT: E 41 GLU cc_start: 0.2863 (tt0) cc_final: 0.2498 (tt0) REVERT: F 456 MET cc_start: 0.6918 (mpp) cc_final: 0.6691 (mmp) REVERT: F 561 MET cc_start: 0.5980 (ptp) cc_final: 0.5739 (ptt) outliers start: 232 outliers final: 176 residues processed: 489 average time/residue: 0.1897 time to fit residues: 156.5278 Evaluate side-chains 430 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 248 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 990 ASP Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 362 ASN Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 345 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 304 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN C 677 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 309 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.083506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062611 restraints weight = 221287.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063568 restraints weight = 140879.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.063899 restraints weight = 92757.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.064116 restraints weight = 79028.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.064111 restraints weight = 75808.476| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35313 Z= 0.150 Angle : 0.694 14.068 48229 Z= 0.372 Chirality : 0.046 0.336 5478 Planarity : 0.006 0.071 5839 Dihedral : 17.744 171.759 5873 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.29 % Favored : 91.68 % Rotamer: Outliers : 5.46 % Allowed : 22.24 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.74 (0.12), residues: 4003 helix: -2.57 (0.11), residues: 1418 sheet: -2.39 (0.24), residues: 396 loop : -2.45 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 596 TYR 0.028 0.002 TYR C1149 PHE 0.018 0.002 PHE B 8 TRP 0.019 0.001 TRP A 650 HIS 0.013 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (35308) covalent geometry : angle 0.69441 / 0.37 (48229) hydrogen bonds : bond 0.05132 / 3.55 ( 937) hydrogen bonds : angle 6.44248 / 4.41 ( 2563) metal coordination : bond 0.00310 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 272 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6529 (mmm) cc_final: 0.6118 (tpp) REVERT: A 93 GLN cc_start: 0.5655 (mp-120) cc_final: 0.4973 (mm-40) REVERT: A 157 THR cc_start: 0.5156 (OUTLIER) cc_final: 0.4657 (t) REVERT: C 67 GLU cc_start: 0.3978 (pt0) cc_final: 0.3645 (pt0) REVERT: C 105 TYR cc_start: 0.4568 (m-80) cc_final: 0.4317 (m-10) REVERT: C 244 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6092 (pm20) REVERT: C 378 ARG cc_start: 0.5337 (mtp180) cc_final: 0.4829 (mmm160) REVERT: C 477 GLU cc_start: 0.5944 (mm-30) cc_final: 0.5164 (tm-30) REVERT: C 805 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7806 (pmm) REVERT: C 844 LYS cc_start: 0.5702 (ptmt) cc_final: 0.5343 (tptt) REVERT: C 1023 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5931 (t70) REVERT: C 1034 ARG cc_start: 0.6538 (tpt170) cc_final: 0.6119 (tpt170) REVERT: C 1085 MET cc_start: 0.8117 (mmm) cc_final: 0.7664 (mmm) REVERT: C 1116 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6744 (m-70) REVERT: C 1137 GLU cc_start: 0.5563 (mm-30) cc_final: 0.5297 (tp30) REVERT: C 1265 PHE cc_start: 0.5617 (t80) cc_final: 0.4573 (m-80) REVERT: D 248 ASP cc_start: 0.6506 (t0) cc_final: 0.6139 (t0) REVERT: D 466 MET cc_start: 0.7297 (mtp) cc_final: 0.6593 (mtp) REVERT: D 582 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6965 (mt) REVERT: D 725 MET cc_start: 0.6449 (ptp) cc_final: 0.6194 (ptm) REVERT: D 738 ARG cc_start: 0.3851 (ttm170) cc_final: 0.3477 (ttm110) REVERT: D 1236 GLU cc_start: 0.6591 (tp30) cc_final: 0.5560 (mm-30) REVERT: D 1274 PHE cc_start: 0.4874 (t80) cc_final: 0.4432 (t80) REVERT: D 1371 ARG cc_start: 0.4908 (ptt-90) cc_final: 0.4028 (tmm160) REVERT: E 41 GLU cc_start: 0.3309 (tt0) cc_final: 0.2931 (tt0) REVERT: F 277 MET cc_start: 0.3434 (mtt) cc_final: 0.3030 (mtp) REVERT: F 456 MET cc_start: 0.7151 (mpp) cc_final: 0.6886 (mmp) REVERT: F 528 LEU cc_start: 0.3751 (mt) cc_final: 0.3372 (tp) outliers start: 189 outliers final: 141 residues processed: 439 average time/residue: 0.1966 time to fit residues: 145.7706 Evaluate side-chains 395 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 249 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1272 GLU Chi-restraints excluded: chain C residue 1290 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1304 MET Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 917 VAL Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 576 VAL Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 142 optimal weight: 0.0050 chunk 403 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 337 optimal weight: 0.1980 chunk 43 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 342 optimal weight: 0.0030 chunk 289 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 490 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.083786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063119 restraints weight = 223101.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064101 restraints weight = 144470.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064260 restraints weight = 96767.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064333 restraints weight = 84063.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064386 restraints weight = 78167.334| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35313 Z= 0.128 Angle : 0.643 11.316 48229 Z= 0.345 Chirality : 0.045 0.326 5478 Planarity : 0.005 0.067 5839 Dihedral : 17.566 172.858 5873 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.94 % Favored : 92.03 % Rotamer: Outliers : 5.66 % Allowed : 22.10 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.36 (0.12), residues: 4003 helix: -2.23 (0.12), residues: 1410 sheet: -2.05 (0.24), residues: 396 loop : -2.27 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 678 TYR 0.028 0.002 TYR C1149 PHE 0.020 0.001 PHE B 8 TRP 0.021 0.001 TRP A 650 HIS 0.013 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (35308) covalent geometry : angle 0.64341 / 0.34 (48229) hydrogen bonds : bond 0.04576 / 3.16 ( 937) hydrogen bonds : angle 6.11595 / 4.19 ( 2563) metal coordination : bond 0.00210 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 279 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6581 (mmm) cc_final: 0.5990 (tpp) REVERT: A 93 GLN cc_start: 0.5709 (mp-120) cc_final: 0.4979 (mm-40) REVERT: A 157 THR cc_start: 0.5251 (OUTLIER) cc_final: 0.4746 (t) REVERT: C 67 GLU cc_start: 0.3838 (pt0) cc_final: 0.3313 (pt0) REVERT: C 105 TYR cc_start: 0.4625 (m-80) cc_final: 0.4384 (m-10) REVERT: C 244 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6153 (pm20) REVERT: C 378 ARG cc_start: 0.5340 (mtp180) cc_final: 0.4919 (mmm160) REVERT: C 477 GLU cc_start: 0.5834 (mm-30) cc_final: 0.5003 (tm-30) REVERT: C 805 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7805 (pmm) REVERT: C 844 LYS cc_start: 0.5670 (ptmt) cc_final: 0.5330 (tptt) REVERT: C 1023 HIS cc_start: 0.6164 (OUTLIER) cc_final: 0.5749 (t70) REVERT: C 1085 MET cc_start: 0.7960 (mmm) cc_final: 0.7493 (mmm) REVERT: C 1119 MET cc_start: 0.6904 (tpp) cc_final: 0.6569 (tpt) REVERT: C 1197 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6893 (mt-10) REVERT: C 1265 PHE cc_start: 0.5508 (t80) cc_final: 0.4617 (m-80) REVERT: C 1338 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: D 248 ASP cc_start: 0.6508 (t0) cc_final: 0.6191 (t0) REVERT: D 466 MET cc_start: 0.7204 (mtp) cc_final: 0.6562 (mtp) REVERT: D 485 MET cc_start: 0.6545 (mmm) cc_final: 0.6255 (mmm) REVERT: D 738 ARG cc_start: 0.3882 (ttm170) cc_final: 0.3470 (ttm110) REVERT: D 878 ASP cc_start: 0.4052 (OUTLIER) cc_final: 0.3383 (m-30) REVERT: D 990 ARG cc_start: 0.2260 (OUTLIER) cc_final: 0.1701 (ptp-170) REVERT: D 1143 ASP cc_start: 0.6545 (m-30) cc_final: 0.6212 (m-30) REVERT: D 1274 PHE cc_start: 0.4850 (t80) cc_final: 0.4394 (t80) REVERT: D 1371 ARG cc_start: 0.4945 (ptt-90) cc_final: 0.4019 (tmm160) REVERT: E 41 GLU cc_start: 0.3260 (tt0) cc_final: 0.2896 (tt0) REVERT: F 277 MET cc_start: 0.3445 (mtt) cc_final: 0.3031 (mtp) REVERT: F 528 LEU cc_start: 0.3956 (mt) cc_final: 0.3536 (tp) outliers start: 196 outliers final: 142 residues processed: 458 average time/residue: 0.1962 time to fit residues: 151.9594 Evaluate side-chains 401 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 253 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 675 ASP Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 55 optimal weight: 0.0770 chunk 377 optimal weight: 50.0000 chunk 135 optimal weight: 9.9990 chunk 279 optimal weight: 0.0770 chunk 41 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 403 optimal weight: 8.9990 chunk 314 optimal weight: 0.9980 chunk 205 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.083889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063067 restraints weight = 222594.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.064039 restraints weight = 139750.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064156 restraints weight = 97808.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064325 restraints weight = 79999.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064359 restraints weight = 79832.588| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 35313 Z= 0.115 Angle : 0.616 10.617 48229 Z= 0.329 Chirality : 0.044 0.312 5478 Planarity : 0.005 0.067 5839 Dihedral : 17.422 174.237 5871 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 4.53 % Allowed : 23.19 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.12), residues: 4003 helix: -1.94 (0.12), residues: 1420 sheet: -1.84 (0.24), residues: 411 loop : -2.16 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.025 0.001 TYR C1149 PHE 0.018 0.001 PHE B 8 TRP 0.022 0.001 TRP A 650 HIS 0.011 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (35308) covalent geometry : angle 0.61577 / 0.33 (48229) hydrogen bonds : bond 0.04218 / 2.92 ( 937) hydrogen bonds : angle 5.81952 / 4.00 ( 2563) metal coordination : bond 0.00162 / 0.07 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 276 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6602 (mmm) cc_final: 0.6053 (tpp) REVERT: A 79 LEU cc_start: 0.7436 (pt) cc_final: 0.6692 (tp) REVERT: A 93 GLN cc_start: 0.5748 (mp-120) cc_final: 0.5029 (mm-40) REVERT: A 157 THR cc_start: 0.5213 (m) cc_final: 0.4730 (t) REVERT: C 67 GLU cc_start: 0.3809 (pt0) cc_final: 0.3284 (pt0) REVERT: C 105 TYR cc_start: 0.4671 (m-80) cc_final: 0.4399 (m-10) REVERT: C 244 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6173 (pm20) REVERT: C 378 ARG cc_start: 0.5439 (mtp180) cc_final: 0.4982 (mmm160) REVERT: C 477 GLU cc_start: 0.5677 (mm-30) cc_final: 0.4931 (tm-30) REVERT: C 504 GLU cc_start: 0.6120 (tp30) cc_final: 0.5889 (mm-30) REVERT: C 515 MET cc_start: 0.5873 (ttt) cc_final: 0.5226 (mtp) REVERT: C 844 LYS cc_start: 0.5600 (ptmt) cc_final: 0.5251 (tptt) REVERT: C 1023 HIS cc_start: 0.6060 (OUTLIER) cc_final: 0.5739 (t70) REVERT: C 1066 MET cc_start: 0.6767 (mmm) cc_final: 0.6391 (tpt) REVERT: C 1085 MET cc_start: 0.7977 (mmm) cc_final: 0.7693 (mmm) REVERT: C 1116 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6860 (m-70) REVERT: C 1119 MET cc_start: 0.6936 (tpp) cc_final: 0.6624 (tpt) REVERT: C 1197 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7198 (mt-10) REVERT: C 1230 MET cc_start: 0.7014 (ttm) cc_final: 0.6569 (ttp) REVERT: C 1265 PHE cc_start: 0.5490 (t80) cc_final: 0.4591 (m-80) REVERT: C 1337 ILE cc_start: 0.8234 (tt) cc_final: 0.7935 (tp) REVERT: C 1338 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6431 (pm20) REVERT: D 44 ILE cc_start: 0.7280 (mm) cc_final: 0.7010 (tp) REVERT: D 248 ASP cc_start: 0.6679 (t0) cc_final: 0.6312 (t0) REVERT: D 466 MET cc_start: 0.7211 (mtp) cc_final: 0.6422 (mtp) REVERT: D 485 MET cc_start: 0.6644 (mmm) cc_final: 0.6342 (mmm) REVERT: D 738 ARG cc_start: 0.3643 (ttm170) cc_final: 0.3279 (ttm110) REVERT: D 878 ASP cc_start: 0.4075 (OUTLIER) cc_final: 0.3356 (m-30) REVERT: D 983 LYS cc_start: 0.5040 (mtmm) cc_final: 0.4325 (tttt) REVERT: D 990 ARG cc_start: 0.2368 (OUTLIER) cc_final: 0.1904 (ptp-170) REVERT: D 1143 ASP cc_start: 0.6803 (m-30) cc_final: 0.6483 (m-30) REVERT: D 1274 PHE cc_start: 0.4919 (t80) cc_final: 0.4492 (t80) REVERT: D 1371 ARG cc_start: 0.5000 (ptt-90) cc_final: 0.4113 (tmm160) REVERT: E 41 GLU cc_start: 0.3360 (tt0) cc_final: 0.3016 (tt0) REVERT: F 277 MET cc_start: 0.3598 (mtt) cc_final: 0.3170 (mtp) outliers start: 157 outliers final: 114 residues processed: 420 average time/residue: 0.1970 time to fit residues: 139.5834 Evaluate side-chains 360 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 241 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1272 GLU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 990 ARG Chi-restraints excluded: chain D residue 1016 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 280 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 332 optimal weight: 8.9990 chunk 365 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 381 optimal weight: 50.0000 chunk 242 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D1366 HIS E 62 GLN ** F 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 ASN F 317 ASN F 600 HIS G 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.083150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061991 restraints weight = 219468.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.063672 restraints weight = 136020.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063286 restraints weight = 84497.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.063514 restraints weight = 77169.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063568 restraints weight = 73719.160| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 35313 Z= 0.175 Angle : 0.715 11.406 48229 Z= 0.377 Chirality : 0.047 0.307 5478 Planarity : 0.006 0.063 5839 Dihedral : 17.560 174.092 5867 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.39 % Favored : 90.58 % Rotamer: Outliers : 5.66 % Allowed : 22.79 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.12), residues: 4003 helix: -2.08 (0.12), residues: 1431 sheet: -1.92 (0.25), residues: 400 loop : -2.29 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 166 TYR 0.028 0.002 TYR C1149 PHE 0.020 0.002 PHE D 773 TRP 0.021 0.002 TRP A 650 HIS 0.009 0.002 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (35308) covalent geometry : angle 0.71544 / 0.38 (48229) hydrogen bonds : bond 0.04748 / 3.31 ( 937) hydrogen bonds : angle 6.07155 / 4.15 ( 2563) metal coordination : bond 0.00361 / 0.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 237 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6752 (mmm) cc_final: 0.6091 (tpp) REVERT: A 60 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.4928 (pt0) REVERT: A 93 GLN cc_start: 0.5758 (mp-120) cc_final: 0.5519 (mm-40) REVERT: A 157 THR cc_start: 0.5290 (m) cc_final: 0.4791 (t) REVERT: C 67 GLU cc_start: 0.3913 (pt0) cc_final: 0.3284 (pt0) REVERT: C 92 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.4707 (p90) REVERT: C 215 TYR cc_start: 0.4352 (m-80) cc_final: 0.3207 (m-80) REVERT: C 244 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6216 (pm20) REVERT: C 378 ARG cc_start: 0.5380 (mtp180) cc_final: 0.4899 (mmm160) REVERT: C 477 GLU cc_start: 0.5695 (mm-30) cc_final: 0.4965 (tm-30) REVERT: C 805 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (pmm) REVERT: C 833 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6963 (tt) REVERT: C 844 LYS cc_start: 0.5818 (ptmt) cc_final: 0.5439 (tptt) REVERT: C 899 GLU cc_start: 0.7300 (tt0) cc_final: 0.7004 (tp30) REVERT: C 1023 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5923 (t70) REVERT: C 1085 MET cc_start: 0.8021 (mmm) cc_final: 0.7579 (mmm) REVERT: C 1116 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6812 (m-70) REVERT: C 1119 MET cc_start: 0.7092 (tpp) cc_final: 0.6760 (tpt) REVERT: C 1265 PHE cc_start: 0.5506 (t80) cc_final: 0.4588 (m-80) REVERT: D 130 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6201 (mmm) REVERT: D 248 ASP cc_start: 0.6835 (t0) cc_final: 0.6458 (t0) REVERT: D 466 MET cc_start: 0.7308 (mtp) cc_final: 0.6892 (mtp) REVERT: D 472 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7348 (pp) REVERT: D 485 MET cc_start: 0.6691 (mmm) cc_final: 0.6331 (mmm) REVERT: D 738 ARG cc_start: 0.3811 (ttm170) cc_final: 0.3448 (ttm110) REVERT: D 1143 ASP cc_start: 0.6823 (m-30) cc_final: 0.6489 (m-30) REVERT: D 1371 ARG cc_start: 0.4902 (ptt-90) cc_final: 0.3985 (tmm160) REVERT: E 41 GLU cc_start: 0.3035 (tt0) cc_final: 0.2715 (tt0) REVERT: F 102 MET cc_start: 0.5420 (OUTLIER) cc_final: 0.5098 (mtp) REVERT: F 277 MET cc_start: 0.3328 (mtt) cc_final: 0.2956 (mtp) REVERT: F 309 ASN cc_start: 0.2902 (OUTLIER) cc_final: 0.2640 (t0) outliers start: 196 outliers final: 165 residues processed: 417 average time/residue: 0.1683 time to fit residues: 122.8246 Evaluate side-chains 409 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 234 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 788 SER Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1184 THR Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1272 GLU Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1321 GLU Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1254 GLU Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1301 THR Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 309 ASN Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 133 LEU Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 85 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 133 optimal weight: 0.3980 chunk 344 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 191 optimal weight: 0.9990 chunk 318 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 411 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN F 317 ASN ** G 79 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 = 0.4015 r_free = 0.4015 target = 0.083776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.063250 restraints weight = 222885.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.063905 restraints weight = 147895.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063949 restraints weight = 99577.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064166 restraints weight = 90263.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.064232 restraints weight = 78226.217| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 35313 Z= 0.116 Angle : 0.628 10.032 48229 Z= 0.333 Chirality : 0.044 0.305 5478 Planarity : 0.005 0.066 5839 Dihedral : 17.428 175.778 5867 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 3.81 % Allowed : 24.52 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.98 (0.12), residues: 4003 helix: -1.86 (0.12), residues: 1422 sheet: -1.73 (0.25), residues: 413 loop : -2.11 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.028 0.001 TYR C1149 PHE 0.024 0.001 PHE C1323 TRP 0.025 0.001 TRP A 650 HIS 0.012 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (35308) covalent geometry : angle 0.62785 / 0.33 (48229) hydrogen bonds : bond 0.04175 / 2.90 ( 937) hydrogen bonds : angle 5.75635 / 3.95 ( 2563) metal coordination : bond 0.00143 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 252 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6649 (mmm) cc_final: 0.6016 (tpp) REVERT: A 93 GLN cc_start: 0.5957 (mp-120) cc_final: 0.5686 (mm-40) REVERT: A 157 THR cc_start: 0.5168 (m) cc_final: 0.4696 (t) REVERT: C 215 TYR cc_start: 0.4293 (m-80) cc_final: 0.3290 (m-80) REVERT: C 244 GLU cc_start: 0.6455 (mt-10) cc_final: 0.6186 (pm20) REVERT: C 378 ARG cc_start: 0.5413 (mtp180) cc_final: 0.4916 (mmm160) REVERT: C 477 GLU cc_start: 0.5697 (mm-30) cc_final: 0.4957 (tm-30) REVERT: C 517 GLN cc_start: 0.6433 (tp40) cc_final: 0.5778 (tt0) REVERT: C 805 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7841 (pmm) REVERT: C 844 LYS cc_start: 0.5732 (ptmt) cc_final: 0.5343 (tptt) REVERT: C 899 GLU cc_start: 0.7296 (tt0) cc_final: 0.7012 (tp30) REVERT: C 1023 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5779 (t70) REVERT: C 1085 MET cc_start: 0.8002 (mmm) cc_final: 0.7590 (mmm) REVERT: C 1116 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6858 (m-70) REVERT: C 1119 MET cc_start: 0.6991 (tpp) cc_final: 0.6699 (tpt) REVERT: C 1197 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6874 (mt-10) REVERT: C 1265 PHE cc_start: 0.5337 (t80) cc_final: 0.4439 (m-80) REVERT: C 1337 ILE cc_start: 0.8251 (tt) cc_final: 0.7960 (tp) REVERT: C 1338 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: D 44 ILE cc_start: 0.7268 (mm) cc_final: 0.7050 (tp) REVERT: D 130 MET cc_start: 0.7087 (tpp) cc_final: 0.6072 (mmm) REVERT: D 248 ASP cc_start: 0.6686 (t0) cc_final: 0.6324 (t0) REVERT: D 466 MET cc_start: 0.7265 (mtp) cc_final: 0.6627 (mtp) REVERT: D 472 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7274 (pp) REVERT: D 485 MET cc_start: 0.6635 (mmm) cc_final: 0.6294 (mmm) REVERT: D 725 MET cc_start: 0.6977 (ppp) cc_final: 0.6682 (ppp) REVERT: D 738 ARG cc_start: 0.3705 (ttm170) cc_final: 0.3337 (ttm110) REVERT: D 743 MET cc_start: 0.3137 (ppp) cc_final: 0.2377 (tmm) REVERT: D 983 LYS cc_start: 0.5035 (mtmm) cc_final: 0.4315 (tttt) REVERT: D 1040 MET cc_start: 0.0883 (mpp) cc_final: 0.0430 (ptp) REVERT: D 1143 ASP cc_start: 0.6822 (m-30) cc_final: 0.6465 (m-30) REVERT: D 1274 PHE cc_start: 0.4881 (t80) cc_final: 0.4457 (t80) REVERT: D 1371 ARG cc_start: 0.5004 (ptt-90) cc_final: 0.4139 (tmm160) REVERT: E 41 GLU cc_start: 0.3299 (tt0) cc_final: 0.2957 (tt0) REVERT: F 277 MET cc_start: 0.3307 (mtt) cc_final: 0.2925 (mtp) outliers start: 132 outliers final: 116 residues processed: 374 average time/residue: 0.1913 time to fit residues: 121.6781 Evaluate side-chains 363 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 242 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1023 HIS Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 500 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 402 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 chunk 307 optimal weight: 7.9990 chunk 260 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.083791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.062924 restraints weight = 222634.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064076 restraints weight = 142901.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063762 restraints weight = 99670.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.064094 restraints weight = 87298.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064142 restraints weight = 76393.762| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 35313 Z= 0.114 Angle : 0.611 10.094 48229 Z= 0.323 Chirality : 0.043 0.291 5478 Planarity : 0.005 0.065 5839 Dihedral : 17.343 176.613 5867 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.17 % Favored : 92.81 % Rotamer: Outliers : 4.02 % Allowed : 24.35 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.81 (0.13), residues: 4003 helix: -1.68 (0.13), residues: 1428 sheet: -1.60 (0.24), residues: 423 loop : -2.05 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1330 TYR 0.032 0.001 TYR C1149 PHE 0.018 0.001 PHE C1323 TRP 0.028 0.001 TRP A 650 HIS 0.010 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (35308) covalent geometry : angle 0.61070 / 0.32 (48229) hydrogen bonds : bond 0.04038 / 2.79 ( 937) hydrogen bonds : angle 5.61209 / 3.86 ( 2563) metal coordination : bond 0.00129 / 0.05 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8006 Ramachandran restraints generated. 4003 Oldfield, 0 Emsley, 4003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 263 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.6611 (mmm) cc_final: 0.6028 (tpp) REVERT: A 93 GLN cc_start: 0.5917 (mp-120) cc_final: 0.5626 (mm-40) REVERT: A 157 THR cc_start: 0.5175 (m) cc_final: 0.4688 (t) REVERT: A 645 MET cc_start: 0.2092 (ppp) cc_final: 0.1891 (ppp) REVERT: B 142 MET cc_start: 0.2391 (pmm) cc_final: 0.1972 (pmm) REVERT: C 92 TYR cc_start: 0.6401 (OUTLIER) cc_final: 0.4706 (p90) REVERT: C 215 TYR cc_start: 0.4071 (m-80) cc_final: 0.3094 (m-80) REVERT: C 244 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6208 (pm20) REVERT: C 378 ARG cc_start: 0.5421 (mtp180) cc_final: 0.4918 (mmm160) REVERT: C 477 GLU cc_start: 0.5693 (mm-30) cc_final: 0.4949 (tm-30) REVERT: C 492 MET cc_start: 0.3166 (mtt) cc_final: 0.2490 (mtp) REVERT: C 504 GLU cc_start: 0.6119 (tp30) cc_final: 0.5862 (mm-30) REVERT: C 515 MET cc_start: 0.4909 (ttp) cc_final: 0.4462 (ttp) REVERT: C 517 GLN cc_start: 0.6159 (tp40) cc_final: 0.5809 (tt0) REVERT: C 678 ARG cc_start: 0.6600 (mmm160) cc_final: 0.6348 (mmp80) REVERT: C 844 LYS cc_start: 0.5671 (ptmt) cc_final: 0.5281 (tptt) REVERT: C 899 GLU cc_start: 0.7313 (tt0) cc_final: 0.6998 (tp30) REVERT: C 1034 ARG cc_start: 0.6587 (tpt170) cc_final: 0.6096 (tpt170) REVERT: C 1116 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.6898 (m-70) REVERT: C 1119 MET cc_start: 0.7024 (tpp) cc_final: 0.6804 (tpt) REVERT: C 1197 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7029 (mt-10) REVERT: C 1265 PHE cc_start: 0.5334 (t80) cc_final: 0.4438 (m-80) REVERT: C 1304 MET cc_start: 0.5462 (mmt) cc_final: 0.5207 (mmm) REVERT: C 1338 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: D 44 ILE cc_start: 0.7187 (mm) cc_final: 0.6940 (tp) REVERT: D 130 MET cc_start: 0.6995 (tpp) cc_final: 0.6160 (mmm) REVERT: D 248 ASP cc_start: 0.6749 (t0) cc_final: 0.6398 (t0) REVERT: D 466 MET cc_start: 0.7296 (mtp) cc_final: 0.6507 (mtp) REVERT: D 472 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7025 (pp) REVERT: D 485 MET cc_start: 0.6661 (mmm) cc_final: 0.6262 (mmm) REVERT: D 725 MET cc_start: 0.7333 (ppp) cc_final: 0.6986 (ppp) REVERT: D 738 ARG cc_start: 0.3583 (ttm170) cc_final: 0.3212 (ttm110) REVERT: D 983 LYS cc_start: 0.4972 (mtmm) cc_final: 0.4331 (tttt) REVERT: D 1040 MET cc_start: 0.0753 (mpp) cc_final: 0.0324 (ptp) REVERT: D 1143 ASP cc_start: 0.6810 (m-30) cc_final: 0.6467 (m-30) REVERT: D 1274 PHE cc_start: 0.4896 (t80) cc_final: 0.4467 (t80) REVERT: D 1371 ARG cc_start: 0.4926 (ptt-90) cc_final: 0.4046 (tmm160) REVERT: E 41 GLU cc_start: 0.3302 (tt0) cc_final: 0.2957 (tt0) REVERT: F 277 MET cc_start: 0.3311 (mtt) cc_final: 0.2925 (mtp) REVERT: G 112 PHE cc_start: 0.4427 (t80) cc_final: 0.4114 (t80) outliers start: 139 outliers final: 124 residues processed: 391 average time/residue: 0.1838 time to fit residues: 123.3702 Evaluate side-chains 374 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 246 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 92 TYR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 818 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 823 VAL Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1050 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1116 HIS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1338 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 366 CYS Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 753 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 796 LEU Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain D residue 843 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 895 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 950 ILE Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1246 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 395 THR Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 526 THR Chi-restraints excluded: chain F residue 580 PHE Chi-restraints excluded: chain F residue 583 THR Chi-restraints excluded: chain G residue 35 LYS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain I residue 141 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 193 GLU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 254 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 220 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 1 optimal weight: 30.0000 chunk 114 optimal weight: 0.6980 chunk 335 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 310 optimal weight: 0.0030 chunk 304 optimal weight: 0.0010 chunk 360 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 605 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.083704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062835 restraints weight = 222420.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.063862 restraints weight = 144009.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063917 restraints weight = 97745.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.064192 restraints weight = 79889.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064163 restraints weight = 76190.520| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35313 Z= 0.120 Angle : 0.622 10.019 48229 Z= 0.327 Chirality : 0.044 0.295 5478 Planarity : 0.005 0.064 5839 Dihedral : 17.325 177.101 5867 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.08 % Rotamer: Outliers : 4.27 % Allowed : 24.26 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.73 (0.13), residues: 4003 helix: -1.62 (0.13), residues: 1413 sheet: -1.57 (0.25), residues: 411 loop : -2.00 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 678 TYR 0.039 0.001 TYR C1149 PHE 0.024 0.001 PHE B 231 TRP 0.028 0.001 TRP A 650 HIS 0.010 0.001 HIS C 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (35308) covalent geometry : angle 0.62185 / 0.33 (48229) hydrogen bonds : bond 0.04027 / 2.79 ( 937) hydrogen bonds : angle 5.60478 / 3.85 ( 2563) metal coordination : bond 0.00156 / 0.07 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6374.45 seconds wall clock time: 110 minutes 51.82 seconds (6651.82 seconds total)