Starting phenix.real_space_refine on Mon Jul 6 09:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.map" model { file = "/net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qp8_18544/07_2026/8qp8_18544.cif" } resolution = 3.5 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= 0.009 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: 5 Type Number sf(0) Gaussians P 189 5.49 5 S 132 5.16 5 C 21299 2.51 5 N 6058 2.21 5 O 6883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 34561 Number of models: 1 Model: "" Number of chains: 16 Chain: "7" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 882 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "6" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 795 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 3, 'rna3p': 33} Chain breaks: 1 Chain: "5" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1496 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 25, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1617 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 61} Chain breaks: 2 Chain: "S" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 294 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 6727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6727 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 50, 'TRANS': 801} Chain: "U" Number of atoms: 3749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3749 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 23, 'TRANS': 432} Chain: "A" Number of atoms: 15169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1918, 15169 Classifications: {'peptide': 1918} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PCIS': 1, 'PTRANS': 112, 'TRANS': 1804} Chain breaks: 6 Unresolved non-hydrogen bonds: 841 Unresolved non-hydrogen angles: 1088 Unresolved non-hydrogen dihedrals: 723 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLU:plan': 14, 'TRP:plan': 6, 'ARG:plan': 11, 'ASN:plan1': 14, 'HIS:plan': 12, 'TYR:plan': 15, 'ASP:plan': 12, 'PHE:plan': 9, 'GLN:plan1': 13} Unresolved non-hydrogen planarities: 514 Chain: "R" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 531 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 12, 'TRP:plan': 2, 'PHE:plan': 7, 'ARG:plan': 11, 'ASN:plan1': 4, 'TYR:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 208 Chain: "N" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1221 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain breaks: 2 Chain: "L" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 390 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 216 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1169 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "X" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 162 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.63, per 1000 atoms: 0.19 Number of scatterers: 34561 At special positions: 0 Unit cell: (211.95, 145.8, 153.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 189 15.00 O 6883 8.00 N 6058 7.00 C 21299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 37 sheets defined 46.2% alpha, 13.6% beta 53 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain '7' and resid 461 through 472 removed outlier: 3.511A pdb=" N SER 7 465 " --> pdb=" O ASP 7 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 308 through 316 Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 354 Processing helix chain 'S' and resid 721 through 735 Processing helix chain 'S' and resid 739 through 758 Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.679A pdb=" N ASP C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN C 125 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.650A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 270 through 293 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 344 removed outlier: 4.414A pdb=" N TRP C 344 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 Processing helix chain 'C' and resid 387 through 399 Proline residue: C 393 - end of helix Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 3.510A pdb=" N HIS C 437 " --> pdb=" O MET C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 5.153A pdb=" N LYS C 446 " --> pdb=" O LYS C 442 " (cutoff:3.500A) Proline residue: C 447 - end of helix Processing helix chain 'C' and resid 459 through 467 removed outlier: 3.854A pdb=" N ASP C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 removed outlier: 3.809A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 710 through 721 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.700A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 777 Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 807 through 823 removed outlier: 3.708A pdb=" N THR C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 853 removed outlier: 4.499A pdb=" N ALA C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG C 853 " --> pdb=" O VAL C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.565A pdb=" N ILE C 935 " --> pdb=" O ARG C 931 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 937 " --> pdb=" O PHE C 933 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 109 removed outlier: 3.650A pdb=" N LEU U 108 " --> pdb=" O CYS U 105 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP U 109 " --> pdb=" O PRO U 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 105 through 109' Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 183 through 185 No H-bonds generated for 'chain 'U' and resid 183 through 185' Processing helix chain 'U' and resid 186 through 194 removed outlier: 3.626A pdb=" N THR U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 198 through 207 removed outlier: 4.506A pdb=" N ASP U 207 " --> pdb=" O ILE U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 245 Processing helix chain 'U' and resid 247 through 256 removed outlier: 3.844A pdb=" N GLU U 256 " --> pdb=" O ASN U 252 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 262 removed outlier: 4.438A pdb=" N ASN U 262 " --> pdb=" O ASP U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 286 removed outlier: 3.902A pdb=" N VAL U 275 " --> pdb=" O MET U 271 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG U 277 " --> pdb=" O LEU U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 308 Processing helix chain 'U' and resid 319 through 335 Processing helix chain 'U' and resid 344 through 351 Processing helix chain 'U' and resid 367 through 374 Processing helix chain 'U' and resid 375 through 377 No H-bonds generated for 'chain 'U' and resid 375 through 377' Processing helix chain 'U' and resid 416 through 420 Processing helix chain 'U' and resid 482 through 485 removed outlier: 3.515A pdb=" N LEU U 485 " --> pdb=" O ARG U 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 482 through 485' Processing helix chain 'U' and resid 486 through 491 removed outlier: 3.521A pdb=" N ALA U 491 " --> pdb=" O GLU U 487 " (cutoff:3.500A) Processing helix chain 'U' and resid 539 through 546 removed outlier: 3.795A pdb=" N ILE U 543 " --> pdb=" O PRO U 540 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR U 544 " --> pdb=" O GLN U 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.319A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.593A pdb=" N LEU A 246 " --> pdb=" O ASN A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.776A pdb=" N GLY A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.962A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.622A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.749A pdb=" N LYS A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 540 through 567 removed outlier: 4.362A pdb=" N PHE A 544 " --> pdb=" O PHE A 540 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 597 through 617 removed outlier: 3.976A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 656 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 696 Processing helix chain 'A' and resid 701 through 722 removed outlier: 3.853A pdb=" N LYS A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 797 Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 removed outlier: 3.538A pdb=" N ALA A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 1001 removed outlier: 3.828A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1014 removed outlier: 3.546A pdb=" N ASN A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1063 removed outlier: 3.681A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1122 through 1126 removed outlier: 4.068A pdb=" N ILE A1125 " --> pdb=" O ASN A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.516A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1274 through 1281 removed outlier: 3.918A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1340 Processing helix chain 'A' and resid 1367 through 1371 Processing helix chain 'A' and resid 1374 through 1399 Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1420 through 1425 removed outlier: 6.818A pdb=" N LYS A1425 " --> pdb=" O LEU A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 Processing helix chain 'A' and resid 1479 through 1486 Processing helix chain 'A' and resid 1490 through 1494 Processing helix chain 'A' and resid 1510 through 1514 removed outlier: 4.553A pdb=" N LYS A1514 " --> pdb=" O GLU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1538 Proline residue: A1530 - end of helix Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1601 through 1605 removed outlier: 3.507A pdb=" N LEU A1604 " --> pdb=" O LEU A1601 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A1605 " --> pdb=" O ASP A1602 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1601 through 1605' Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1721 through 1737 removed outlier: 3.986A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 2071 through 2082 Processing helix chain 'A' and resid 2083 through 2088 Processing helix chain 'A' and resid 2107 through 2116 Processing helix chain 'A' and resid 2167 through 2172 removed outlier: 3.897A pdb=" N GLU A2171 " --> pdb=" O TYR A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2203 Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2254 No H-bonds generated for 'chain 'A' and resid 2252 through 2254' Processing helix chain 'A' and resid 2310 through 2315 Processing helix chain 'R' and resid 395 through 404 Processing helix chain 'R' and resid 431 through 443 Processing helix chain 'R' and resid 461 through 473 Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.814A pdb=" N ARG N 23 " --> pdb=" O GLY N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 95 through 114 Processing helix chain 'N' and resid 116 through 135 Processing helix chain 'N' and resid 137 through 149 removed outlier: 4.378A pdb=" N ASP N 144 " --> pdb=" O GLN N 140 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU N 145 " --> pdb=" O GLN N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 159 removed outlier: 3.642A pdb=" N TRP N 157 " --> pdb=" O THR N 153 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU N 158 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER N 159 " --> pdb=" O GLU N 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 153 through 159' Processing helix chain 'N' and resid 240 through 260 removed outlier: 3.942A pdb=" N GLY N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 281 Processing helix chain 'L' and resid 357 through 366 removed outlier: 4.395A pdb=" N LYS L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'D' and resid 10 through 18 Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.716A pdb=" N MET D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.839A pdb=" N MET D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 191 removed outlier: 8.621A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AA3, first strand: chain 'C' and resid 522 through 526 removed outlier: 4.933A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C 531 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 500 through 502 Processing sheet with id=AA5, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.633A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.633A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 663 through 666 removed outlier: 3.660A pdb=" N ALA C 861 " --> pdb=" O THR C 870 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 859 " --> pdb=" O LYS C 872 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.908A pdb=" N LEU C 827 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE C 906 " --> pdb=" O LEU C 827 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 896 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 674 through 676 removed outlier: 6.596A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ASP C 793 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 142 through 144 removed outlier: 4.376A pdb=" N PHE U 172 " --> pdb=" O ILE U 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 213 through 214 Processing sheet with id=AB3, first strand: chain 'U' and resid 227 through 228 removed outlier: 6.382A pdb=" N GLY U 227 " --> pdb=" O VAL U 295 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'U' and resid 387 through 389 removed outlier: 6.130A pdb=" N SER U 353 " --> pdb=" O THR U 445 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN U 437 " --> pdb=" O LEU U 361 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS U 429 " --> pdb=" O LYS U 440 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 392 through 395 removed outlier: 6.364A pdb=" N LEU U 392 " --> pdb=" O CYS U 454 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS U 456 " --> pdb=" O LEU U 392 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU U 394 " --> pdb=" O LYS U 456 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N TYR U 549 " --> pdb=" O ILE U 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA U 548 " --> pdb=" O VAL U 505 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL U 505 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE U 550 " --> pdb=" O ASN U 503 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN U 503 " --> pdb=" O ILE U 550 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE U 552 " --> pdb=" O ILE U 501 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 392 through 395 removed outlier: 6.364A pdb=" N LEU U 392 " --> pdb=" O CYS U 454 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS U 456 " --> pdb=" O LEU U 392 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU U 394 " --> pdb=" O LYS U 456 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N TYR U 549 " --> pdb=" O ILE U 455 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA U 548 " --> pdb=" O VAL U 505 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL U 505 " --> pdb=" O ALA U 548 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE U 550 " --> pdb=" O ASN U 503 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN U 503 " --> pdb=" O ILE U 550 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE U 552 " --> pdb=" O ILE U 501 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE U 501 " --> pdb=" O LEU U 520 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N TRP U 527 " --> pdb=" O ILE U 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 413 through 415 removed outlier: 6.792A pdb=" N VAL U 414 " --> pdb=" O ASN U 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'U' and resid 458 through 460 Processing sheet with id=AB9, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AC1, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AC2, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AC3, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AC4, first strand: chain 'A' and resid 904 through 910 removed outlier: 3.629A pdb=" N LEU A 901 " --> pdb=" O HIS A 904 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 6.528A pdb=" N PHE A1098 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A1088 " --> pdb=" O HIS A1096 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS A1096 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 6.215A pdb=" N ARG A1224 " --> pdb=" O ASN A1218 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN A1218 " --> pdb=" O ARG A1224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1342 through 1346 Processing sheet with id=AC8, first strand: chain 'A' and resid 1502 through 1503 Processing sheet with id=AC9, first strand: chain 'A' and resid 1552 through 1554 removed outlier: 3.657A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1608 through 1611 removed outlier: 12.731A pdb=" N ILE A1629 " --> pdb=" O GLN A1665 " (cutoff:3.500A) removed outlier: 11.515A pdb=" N GLN A1665 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N LEU A1631 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 11.441A pdb=" N ASP A1663 " --> pdb=" O LEU A1631 " (cutoff:3.500A) removed outlier: 12.096A pdb=" N ALA A1633 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 12.319A pdb=" N TRP A1661 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 11.454A pdb=" N TYR A1635 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS A1659 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A1655 " --> pdb=" O VAL A1639 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.121A pdb=" N TYR A2091 " --> pdb=" O LEU A2225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 2103 through 2104 removed outlier: 5.511A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A2126 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TRP A2177 " --> pdb=" O GLY A2126 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A2128 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N ILE A2212 " --> pdb=" O GLU A2173 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A2175 " --> pdb=" O ILE A2212 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A2214 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP A2177 " --> pdb=" O ILE A2214 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N CYS A2216 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N HIS A2179 " --> pdb=" O CYS A2216 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 2103 through 2104 removed outlier: 5.511A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N PHE A2270 " --> pdb=" O GLU A2141 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ARG A2143 " --> pdb=" O PHE A2270 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N MET A2272 " --> pdb=" O ARG A2143 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A2145 " --> pdb=" O MET A2272 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2229 through 2230 Processing sheet with id=AD6, first strand: chain 'R' and resid 409 through 414 removed outlier: 6.744A pdb=" N LYS R 409 " --> pdb=" O PHE R 426 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE R 426 " --> pdb=" O LYS R 409 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N LYS R 411 " --> pdb=" O TYR R 424 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N TYR R 424 " --> pdb=" O LYS R 411 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE R 413 " --> pdb=" O LYS R 422 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 446 through 447 removed outlier: 3.600A pdb=" N ARG R 450 " --> pdb=" O VAL R 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AD9, first strand: chain 'D' and resid 7 through 8 removed outlier: 4.361A pdb=" N ASP D 62 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 25 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N TYR D 59 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL D 27 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL D 61 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ARG D 29 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.218A pdb=" N MET D 91 " --> pdb=" O VAL D 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 1430 hydrogen bonds defined for protein. 4062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 128 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10517 1.34 - 1.46: 6736 1.46 - 1.58: 17904 1.58 - 1.69: 366 1.69 - 1.81: 220 Bond restraints: 35743 Sorted by residual: bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.606 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O14 IHP A2401 " pdb=" P4 IHP A2401 " ideal model delta sigma weight residual 1.671 1.608 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.607 0.062 2.00e-02 2.50e+03 9.47e+00 ... (remaining 35738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 49002 2.61 - 5.22: 348 5.22 - 7.83: 29 7.83 - 10.44: 4 10.44 - 13.05: 1 Bond angle restraints: 49384 Sorted by residual: angle pdb=" N PRO A1417 " pdb=" CA PRO A1417 " pdb=" C PRO A1417 " ideal model delta sigma weight residual 112.47 99.42 13.05 2.06e+00 2.36e-01 4.01e+01 angle pdb=" N ILE A1419 " pdb=" CA ILE A1419 " pdb=" C ILE A1419 " ideal model delta sigma weight residual 111.17 103.04 8.13 1.38e+00 5.25e-01 3.47e+01 angle pdb=" C ARG L 357 " pdb=" CA ARG L 357 " pdb=" CB ARG L 357 " ideal model delta sigma weight residual 116.54 111.09 5.45 1.15e+00 7.56e-01 2.24e+01 angle pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sigma weight residual 118.80 123.55 -4.75 1.10e+00 8.26e-01 1.86e+01 angle pdb=" C ILE A1416 " pdb=" N PRO A1417 " pdb=" CA PRO A1417 " ideal model delta sigma weight residual 119.84 114.80 5.04 1.25e+00 6.40e-01 1.62e+01 ... (remaining 49379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 21028 35.45 - 70.90: 641 70.90 - 106.35: 70 106.35 - 141.80: 10 141.80 - 177.25: 5 Dihedral angle restraints: 21754 sinusoidal: 10295 harmonic: 11459 Sorted by residual: dihedral pdb=" O4' C 5 23 " pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sinusoidal sigma weight residual 200.00 66.23 133.77 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 54.75 177.25 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual -128.00 47.17 -175.17 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 21751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 5584 1.003 - 2.006: 0 2.006 - 3.008: 0 3.008 - 4.011: 0 4.011 - 5.014: 4 Chirality restraints: 5588 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C1 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O11 IHP A2401 " both_signs ideal model delta sigma weight residual False 2.32 -2.48 4.80 2.00e-01 2.50e+01 5.75e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.36 -4.77 2.00e-01 2.50e+01 5.70e+02 ... (remaining 5585 not shown) Planarity restraints: 5711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1637 " 0.019 2.00e-02 2.50e+03 1.37e-02 4.68e+00 pdb=" CG TRP A1637 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A1637 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A1637 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1637 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1637 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1637 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1637 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1637 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1637 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 697 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 698 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 698 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 698 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1416 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A1417 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1417 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1417 " -0.030 5.00e-02 4.00e+02 ... (remaining 5708 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1263 2.71 - 3.26: 34403 3.26 - 3.80: 59614 3.80 - 4.35: 75459 4.35 - 4.90: 119777 Nonbonded interactions: 290516 Sorted by model distance: nonbonded pdb=" OG SER U 511 " pdb=" OE1 GLU U 512 " model vdw 2.161 3.040 nonbonded pdb=" NH1 ARG X 143 " pdb=" O GLY X 146 " model vdw 2.206 3.120 nonbonded pdb=" O GLU U 187 " pdb=" OG1 THR U 190 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR G 290 " pdb=" OD1 ASP C 886 " model vdw 2.224 3.040 ... (remaining 290511 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: 7.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 38.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.003 0.069 35743 Z= 0.161 Angle : 0.548 13.053 49384 Z= 0.314 Chirality : 0.135 5.014 5588 Planarity : 0.004 0.052 5711 Dihedral : 16.310 177.247 14332 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 0.06 % Allowed : 0.61 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3866 helix: 1.37 (0.13), residues: 1607 sheet: -0.25 (0.25), residues: 464 loop : -0.53 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 138 TYR 0.017 0.001 TYR A1204 PHE 0.021 0.001 PHE A1099 TRP 0.037 0.001 TRP A1637 HIS 0.005 0.001 HIS D 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (35743) covalent geometry : angle 0.54778 / 0.31 (49384) hydrogen bonds : bond 0.15695 / 11.68 ( 1538) hydrogen bonds : angle 6.66313 / 7.31 ( 4286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.322 Fit side-chains REVERT: A 641 MET cc_start: 0.8025 (tpp) cc_final: 0.7762 (mmm) REVERT: A 697 MET cc_start: 0.5728 (tpt) cc_final: 0.5071 (tpt) REVERT: A 976 MET cc_start: 0.8750 (tpt) cc_final: 0.8548 (tpp) REVERT: D 112 MET cc_start: 0.8760 (mmm) cc_final: 0.8154 (tpt) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.2099 time to fit residues: 53.1256 Evaluate side-chains 125 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.0470 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0570 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 335 GLN C 583 ASN ** U 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN A1400 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.076179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.054572 restraints weight = 125277.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055483 restraints weight = 67303.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055752 restraints weight = 50588.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.055906 restraints weight = 46158.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.055961 restraints weight = 41087.674| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.0715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35743 Z= 0.122 Angle : 0.541 18.000 49384 Z= 0.278 Chirality : 0.046 1.381 5588 Planarity : 0.004 0.050 5711 Dihedral : 16.183 174.860 7111 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.19 % Allowed : 3.59 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3866 helix: 1.71 (0.13), residues: 1638 sheet: -0.26 (0.24), residues: 450 loop : -0.51 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 441 TYR 0.015 0.001 TYR A1044 PHE 0.017 0.001 PHE A1099 TRP 0.022 0.001 TRP A1637 HIS 0.007 0.001 HIS C 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (35743) covalent geometry : angle 0.54062 / 0.28 (49384) hydrogen bonds : bond 0.04866 / 3.56 ( 1538) hydrogen bonds : angle 4.78532 / 5.27 ( 4286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 697 MET cc_start: 0.5791 (tpt) cc_final: 0.5313 (tpt) REVERT: A 1652 MET cc_start: 0.1356 (mmt) cc_final: 0.1037 (mmt) REVERT: D 112 MET cc_start: 0.8835 (mmm) cc_final: 0.8115 (tpt) outliers start: 6 outliers final: 5 residues processed: 135 average time/residue: 0.2035 time to fit residues: 47.3466 Evaluate side-chains 133 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 949 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 7 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 380 optimal weight: 0.7980 chunk 364 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 215 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 335 GLN C 837 GLN A 495 GLN A1117 HIS A1400 ASN A1460 HIS ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.075179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053407 restraints weight = 124340.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054354 restraints weight = 67691.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054556 restraints weight = 50706.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054766 restraints weight = 45832.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054879 restraints weight = 41762.823| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35743 Z= 0.167 Angle : 0.526 11.296 49384 Z= 0.275 Chirality : 0.041 0.361 5588 Planarity : 0.004 0.048 5711 Dihedral : 16.097 174.296 7111 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.64 % Allowed : 5.77 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3866 helix: 1.73 (0.13), residues: 1637 sheet: -0.44 (0.24), residues: 452 loop : -0.49 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1418 TYR 0.017 0.001 TYR A 88 PHE 0.018 0.001 PHE A1099 TRP 0.018 0.001 TRP A1515 HIS 0.007 0.001 HIS D 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (35743) covalent geometry : angle 0.52571 / 0.27 (49384) hydrogen bonds : bond 0.04544 / 3.41 ( 1538) hydrogen bonds : angle 4.55631 / 5.05 ( 4286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: C 934 MET cc_start: 0.8498 (ttp) cc_final: 0.7817 (ttp) REVERT: A 271 MET cc_start: 0.6911 (mtt) cc_final: 0.6703 (mtm) REVERT: A 697 MET cc_start: 0.5570 (tpt) cc_final: 0.5322 (tpt) REVERT: A 1652 MET cc_start: 0.1321 (mmt) cc_final: 0.1049 (mmt) REVERT: A 1734 MET cc_start: 0.8497 (mmp) cc_final: 0.8026 (mmm) REVERT: N 133 MET cc_start: 0.6262 (tmm) cc_final: 0.5702 (ttp) REVERT: D 82 MET cc_start: 0.6812 (mmm) cc_final: 0.6552 (mmm) outliers start: 20 outliers final: 8 residues processed: 146 average time/residue: 0.1970 time to fit residues: 49.8294 Evaluate side-chains 137 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 280 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 215 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 335 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 278 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 14 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 335 GLN C 583 ASN A1004 ASN A1352 HIS A1400 ASN A1424 GLN A1527 ASN A1563 HIS ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.073870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051776 restraints weight = 124833.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052765 restraints weight = 72470.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053156 restraints weight = 51853.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053258 restraints weight = 43538.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053327 restraints weight = 41978.711| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35743 Z= 0.268 Angle : 0.616 13.797 49384 Z= 0.322 Chirality : 0.045 0.555 5588 Planarity : 0.005 0.046 5711 Dihedral : 16.172 176.801 7111 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.06 % Allowed : 7.70 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3866 helix: 1.48 (0.13), residues: 1618 sheet: -0.60 (0.24), residues: 475 loop : -0.59 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 283 TYR 0.024 0.002 TYR A 88 PHE 0.026 0.002 PHE C 339 TRP 0.019 0.002 TRP A1515 HIS 0.007 0.002 HIS C 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (35743) covalent geometry : angle 0.61568 / 0.32 (49384) hydrogen bonds : bond 0.04756 / 3.61 ( 1538) hydrogen bonds : angle 4.67095 / 5.17 ( 4286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: C 934 MET cc_start: 0.8563 (ttp) cc_final: 0.8214 (ttp) REVERT: U 390 MET cc_start: 0.8062 (mmt) cc_final: 0.7708 (mmt) REVERT: A 641 MET cc_start: 0.7826 (mmm) cc_final: 0.7503 (mmm) REVERT: A 976 MET cc_start: 0.8507 (tpp) cc_final: 0.8259 (tpt) REVERT: A 1048 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7577 (mpp) REVERT: A 1652 MET cc_start: 0.0762 (mmt) cc_final: 0.0533 (mmt) REVERT: A 1734 MET cc_start: 0.8519 (mmp) cc_final: 0.8080 (mmm) REVERT: L 362 MET cc_start: 0.5768 (ptm) cc_final: 0.5503 (ppp) outliers start: 33 outliers final: 18 residues processed: 153 average time/residue: 0.1925 time to fit residues: 51.3442 Evaluate side-chains 144 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 280 MET Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 236 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 13 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 353 optimal weight: 6.9990 chunk 299 optimal weight: 0.0000 chunk 185 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 281 optimal weight: 0.8980 chunk 385 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 166 ASN ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.074776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052720 restraints weight = 124507.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053731 restraints weight = 69260.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.054156 restraints weight = 49469.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054302 restraints weight = 43111.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.054356 restraints weight = 41081.637| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35743 Z= 0.140 Angle : 0.515 9.828 49384 Z= 0.270 Chirality : 0.041 0.393 5588 Planarity : 0.004 0.052 5711 Dihedral : 16.102 178.329 7111 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.80 % Allowed : 9.27 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3866 helix: 1.65 (0.13), residues: 1623 sheet: -0.43 (0.24), residues: 451 loop : -0.52 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 283 TYR 0.013 0.001 TYR A 431 PHE 0.015 0.001 PHE A1099 TRP 0.023 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (35743) covalent geometry : angle 0.51549 / 0.27 (49384) hydrogen bonds : bond 0.04247 / 3.22 ( 1538) hydrogen bonds : angle 4.46455 / 4.96 ( 4286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.947 Fit side-chains revert: symmetry clash REVERT: C 934 MET cc_start: 0.8533 (ttp) cc_final: 0.7889 (ttp) REVERT: U 354 MET cc_start: 0.7612 (ttp) cc_final: 0.7357 (ttp) REVERT: U 384 MET cc_start: 0.5404 (mmm) cc_final: 0.4818 (mmm) REVERT: U 390 MET cc_start: 0.8104 (mmt) cc_final: 0.7703 (mmt) REVERT: A 641 MET cc_start: 0.7765 (mmm) cc_final: 0.7529 (mmm) REVERT: A 1048 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: A 1622 MET cc_start: 0.8166 (mmm) cc_final: 0.7906 (mmt) REVERT: A 1652 MET cc_start: 0.0749 (mmt) cc_final: 0.0545 (mmt) REVERT: A 1734 MET cc_start: 0.8497 (mmp) cc_final: 0.8057 (mmm) REVERT: N 133 MET cc_start: 0.6087 (tmm) cc_final: 0.5484 (ttm) REVERT: D 82 MET cc_start: 0.7205 (mmm) cc_final: 0.6874 (mmm) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 0.1885 time to fit residues: 47.9095 Evaluate side-chains 139 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 3 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 368 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 400 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 332 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 335 GLN C 743 ASN U 166 ASN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN D 13 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.073423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050905 restraints weight = 125251.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052731 restraints weight = 68205.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.052798 restraints weight = 43040.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.052925 restraints weight = 38844.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052951 restraints weight = 36900.682| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 35743 Z= 0.243 Angle : 0.576 11.386 49384 Z= 0.302 Chirality : 0.043 0.428 5588 Planarity : 0.005 0.054 5711 Dihedral : 16.127 178.273 7111 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.15 % Allowed : 9.53 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3866 helix: 1.53 (0.13), residues: 1621 sheet: -0.61 (0.24), residues: 471 loop : -0.58 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 283 TYR 0.021 0.002 TYR A 88 PHE 0.019 0.002 PHE A1099 TRP 0.023 0.002 TRP A1515 HIS 0.006 0.001 HIS C 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (35743) covalent geometry : angle 0.57645 / 0.30 (49384) hydrogen bonds : bond 0.04524 / 3.43 ( 1538) hydrogen bonds : angle 4.55286 / 5.05 ( 4286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 1.054 Fit side-chains REVERT: C 934 MET cc_start: 0.8616 (ttp) cc_final: 0.8023 (ttp) REVERT: A 641 MET cc_start: 0.7780 (mmm) cc_final: 0.7532 (mmm) REVERT: A 697 MET cc_start: 0.4611 (tpt) cc_final: 0.4311 (tpt) REVERT: A 1048 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7569 (mpp) REVERT: A 1622 MET cc_start: 0.8143 (mmm) cc_final: 0.7885 (mmt) REVERT: A 1734 MET cc_start: 0.8533 (mmp) cc_final: 0.8103 (mmm) REVERT: N 133 MET cc_start: 0.6268 (tmm) cc_final: 0.5601 (ttm) REVERT: D 82 MET cc_start: 0.7068 (mmm) cc_final: 0.6745 (mmm) outliers start: 36 outliers final: 23 residues processed: 156 average time/residue: 0.1862 time to fit residues: 51.2187 Evaluate side-chains 150 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 284 optimal weight: 0.0370 chunk 189 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 381 optimal weight: 0.8980 chunk 362 optimal weight: 40.0000 chunk 354 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 333 optimal weight: 7.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 248 GLN C 768 GLN ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN A 680 HIS A1296 GLN A1400 ASN D 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053095 restraints weight = 124664.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054187 restraints weight = 69225.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054554 restraints weight = 48850.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054667 restraints weight = 43029.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054713 restraints weight = 40920.939| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35743 Z= 0.109 Angle : 0.499 8.920 49384 Z= 0.262 Chirality : 0.040 0.324 5588 Planarity : 0.004 0.055 5711 Dihedral : 16.070 179.652 7111 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.74 % Allowed : 10.33 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3866 helix: 1.73 (0.13), residues: 1624 sheet: -0.43 (0.24), residues: 456 loop : -0.47 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 357 TYR 0.017 0.001 TYR A1204 PHE 0.014 0.001 PHE A1099 TRP 0.031 0.001 TRP A1515 HIS 0.004 0.001 HIS C 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (35743) covalent geometry : angle 0.49942 / 0.26 (49384) hydrogen bonds : bond 0.04044 / 3.08 ( 1538) hydrogen bonds : angle 4.34475 / 4.82 ( 4286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.969 Fit side-chains REVERT: C 934 MET cc_start: 0.8492 (ttp) cc_final: 0.7843 (ttp) REVERT: U 384 MET cc_start: 0.5329 (mmm) cc_final: 0.4776 (mmm) REVERT: A 976 MET cc_start: 0.8451 (tpp) cc_final: 0.8181 (tpt) REVERT: A 1048 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: A 1652 MET cc_start: 0.0754 (mmt) cc_final: 0.0404 (mmt) REVERT: A 1718 TRP cc_start: 0.4664 (m-10) cc_final: 0.4284 (m100) REVERT: A 1734 MET cc_start: 0.8511 (mmp) cc_final: 0.8088 (mmm) REVERT: N 133 MET cc_start: 0.6227 (tmm) cc_final: 0.5603 (ttm) REVERT: D 82 MET cc_start: 0.7114 (mmm) cc_final: 0.6882 (mmm) outliers start: 23 outliers final: 17 residues processed: 146 average time/residue: 0.1811 time to fit residues: 46.4817 Evaluate side-chains 145 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 184 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 23 optimal weight: 40.0000 chunk 180 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 chunk 52 optimal weight: 0.0980 chunk 294 optimal weight: 0.0040 chunk 400 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 258 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 335 GLN ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN D 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.074943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053092 restraints weight = 124314.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054104 restraints weight = 68176.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054315 restraints weight = 48703.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054491 restraints weight = 47257.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054519 restraints weight = 42268.533| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35743 Z= 0.122 Angle : 0.493 8.348 49384 Z= 0.258 Chirality : 0.040 0.314 5588 Planarity : 0.004 0.058 5711 Dihedral : 16.010 179.747 7111 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.93 % Allowed : 10.39 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3866 helix: 1.80 (0.13), residues: 1624 sheet: -0.37 (0.24), residues: 456 loop : -0.43 (0.15), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 357 TYR 0.016 0.001 TYR A1204 PHE 0.014 0.001 PHE A1099 TRP 0.032 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (35743) covalent geometry : angle 0.49301 / 0.26 (49384) hydrogen bonds : bond 0.03972 / 3.03 ( 1538) hydrogen bonds : angle 4.27639 / 4.74 ( 4286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.178 Fit side-chains REVERT: C 934 MET cc_start: 0.8506 (ttp) cc_final: 0.7855 (ttp) REVERT: U 384 MET cc_start: 0.5460 (mmm) cc_final: 0.4997 (mmm) REVERT: A 697 MET cc_start: 0.4559 (tpt) cc_final: 0.4237 (tpt) REVERT: A 976 MET cc_start: 0.8427 (tpp) cc_final: 0.8154 (tpt) REVERT: A 1048 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7663 (mpp) REVERT: A 1734 MET cc_start: 0.8403 (mmp) cc_final: 0.7939 (mmm) REVERT: N 133 MET cc_start: 0.6119 (tmm) cc_final: 0.5594 (ttm) REVERT: D 82 MET cc_start: 0.7153 (mmm) cc_final: 0.6921 (mmm) REVERT: D 101 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7351 (mtmm) outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 0.1864 time to fit residues: 48.5432 Evaluate side-chains 150 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain G residue 335 GLN Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 400 optimal weight: 20.0000 chunk 357 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 396 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.053039 restraints weight = 124303.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054088 restraints weight = 69333.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054527 restraints weight = 48939.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054618 restraints weight = 42284.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054704 restraints weight = 41084.386| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35743 Z= 0.125 Angle : 0.493 8.023 49384 Z= 0.258 Chirality : 0.040 0.318 5588 Planarity : 0.004 0.057 5711 Dihedral : 15.997 179.599 7111 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.90 % Allowed : 10.46 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3866 helix: 1.83 (0.13), residues: 1625 sheet: -0.35 (0.24), residues: 456 loop : -0.42 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 357 TYR 0.015 0.001 TYR A1204 PHE 0.015 0.001 PHE A1099 TRP 0.035 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (35743) covalent geometry : angle 0.49336 / 0.26 (49384) hydrogen bonds : bond 0.03933 / 3.00 ( 1538) hydrogen bonds : angle 4.25079 / 4.70 ( 4286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.010 Fit side-chains REVERT: C 934 MET cc_start: 0.8497 (ttp) cc_final: 0.7845 (ttp) REVERT: U 384 MET cc_start: 0.5376 (mmm) cc_final: 0.4985 (mmm) REVERT: A 697 MET cc_start: 0.4487 (tpt) cc_final: 0.4190 (tpt) REVERT: A 976 MET cc_start: 0.8414 (tpp) cc_final: 0.8142 (tpt) REVERT: A 1048 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7637 (mpp) REVERT: A 1622 MET cc_start: 0.8164 (mmm) cc_final: 0.7839 (mmt) REVERT: A 1718 TRP cc_start: 0.5047 (m-10) cc_final: 0.4479 (m100) REVERT: A 1734 MET cc_start: 0.8405 (mmp) cc_final: 0.7939 (mmm) REVERT: N 133 MET cc_start: 0.6113 (tmm) cc_final: 0.5604 (ttm) REVERT: D 82 MET cc_start: 0.7153 (mmm) cc_final: 0.6936 (mmm) REVERT: D 101 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7341 (mtmm) outliers start: 28 outliers final: 21 residues processed: 151 average time/residue: 0.1854 time to fit residues: 49.1429 Evaluate side-chains 150 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 20 optimal weight: 40.0000 chunk 126 optimal weight: 4.9990 chunk 28 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 193 optimal weight: 0.5980 chunk 401 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.074967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052976 restraints weight = 125003.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054140 restraints weight = 69666.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054456 restraints weight = 48713.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054647 restraints weight = 42346.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054664 restraints weight = 40675.699| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35743 Z= 0.128 Angle : 0.499 14.354 49384 Z= 0.258 Chirality : 0.040 0.321 5588 Planarity : 0.004 0.057 5711 Dihedral : 15.976 179.419 7111 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.90 % Allowed : 10.52 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3866 helix: 1.85 (0.13), residues: 1627 sheet: -0.30 (0.24), residues: 458 loop : -0.42 (0.15), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 357 TYR 0.014 0.001 TYR A 431 PHE 0.015 0.001 PHE A1099 TRP 0.041 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (35743) covalent geometry : angle 0.49889 / 0.26 (49384) hydrogen bonds : bond 0.03903 / 2.98 ( 1538) hydrogen bonds : angle 4.22160 / 4.66 ( 4286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7732 Ramachandran restraints generated. 3866 Oldfield, 0 Emsley, 3866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.407 Fit side-chains REVERT: C 934 MET cc_start: 0.8505 (ttp) cc_final: 0.7853 (ttp) REVERT: U 384 MET cc_start: 0.5308 (mmm) cc_final: 0.4976 (mmm) REVERT: A 697 MET cc_start: 0.4410 (tpt) cc_final: 0.4113 (tpt) REVERT: A 1048 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7647 (mpp) REVERT: A 1622 MET cc_start: 0.8164 (mmm) cc_final: 0.7844 (mmt) REVERT: A 1718 TRP cc_start: 0.5087 (m-10) cc_final: 0.4528 (m100) REVERT: A 1734 MET cc_start: 0.8404 (mmp) cc_final: 0.7933 (mmm) REVERT: N 133 MET cc_start: 0.6112 (tmm) cc_final: 0.5619 (ttm) REVERT: D 82 MET cc_start: 0.7149 (mmm) cc_final: 0.6941 (mmm) REVERT: D 101 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7465 (mtmm) outliers start: 28 outliers final: 22 residues processed: 148 average time/residue: 0.1950 time to fit residues: 51.1769 Evaluate side-chains 150 residues out of total 3516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 322 ASP Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 947 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 973 CYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 9 optimal weight: 0.0050 chunk 398 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 108 optimal weight: 0.0050 chunk 281 optimal weight: 0.5980 chunk 280 optimal weight: 2.9990 chunk 352 optimal weight: 0.0980 chunk 293 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 583 ASN C 890 HIS ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.075966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054243 restraints weight = 124258.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.055424 restraints weight = 67749.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.055855 restraints weight = 46749.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055917 restraints weight = 40777.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.055973 restraints weight = 39165.393| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 35743 Z= 0.090 Angle : 0.474 10.283 49384 Z= 0.246 Chirality : 0.038 0.319 5588 Planarity : 0.004 0.056 5711 Dihedral : 15.903 178.431 7111 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.71 % Allowed : 10.74 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3866 helix: 1.96 (0.13), residues: 1628 sheet: -0.23 (0.25), residues: 431 loop : -0.35 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 357 TYR 0.011 0.001 TYR A1660 PHE 0.013 0.001 PHE A1099 TRP 0.040 0.001 TRP A1515 HIS 0.004 0.001 HIS A 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (35743) covalent geometry : angle 0.47374 / 0.25 (49384) hydrogen bonds : bond 0.03664 / 2.81 ( 1538) hydrogen bonds : angle 4.09427 / 4.52 ( 4286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.41 seconds wall clock time: 80 minutes 27.36 seconds (4827.36 seconds total)