Starting phenix.real_space_refine on Fri Jul 26 20:25:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_18544.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_18544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_18544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_18544.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp8_18544/07_2024/8qp8_18544.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A GLU 173": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "L ARG 354": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} 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: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 6, 'HIS:plan': 12, 'PHE:plan': 9, 'GLU:plan': 14, 'ARG:plan': 11} 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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 11} 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, 'ARG:plan': 5, 'GLN:plan1': 4} 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: 19.41, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 14.45 Conformation dependent library (CDL) restraints added in 5.9 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: 12.92 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: 20.58 Time building geometry restraints manager: 15.66 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: 97.49 - 104.80: 1452 104.80 - 112.12: 18096 112.12 - 119.43: 11785 119.43 - 126.75: 17042 126.75 - 134.06: 1009 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=" 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 angle pdb=" N GLY L 367 " pdb=" CA GLY L 367 " pdb=" C GLY L 367 " ideal model delta sigma weight residual 116.01 109.54 6.47 1.64e+00 3.72e-01 1.56e+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 2.440 nonbonded pdb=" NH1 ARG X 143 " pdb=" O GLY X 146 " model vdw 2.206 2.520 nonbonded pdb=" O GLU U 187 " pdb=" OG1 THR U 190 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR G 290 " pdb=" OD1 ASP C 886 " model vdw 2.224 2.440 ... (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 ========== 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: 6.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 1.350 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 106.950 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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= 0.200 Angle : 0.547 13.053 49384 Z= 0.305 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 : 10.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.037 0.001 TRP A1637 HIS 0.005 0.001 HIS D 89 PHE 0.021 0.001 PHE A1099 TYR 0.017 0.001 TYR A1204 ARG 0.004 0.000 ARG X 138 *********************** 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 fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 3.830 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: 0.5072 (tpt) 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: 0.5442 time to fit residues: 142.6737 Evaluate side-chains 125 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 340 optimal weight: 40.0000 chunk 305 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 315 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 192 optimal weight: 0.0070 chunk 235 optimal weight: 0.7980 chunk 365 optimal weight: 2.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 335 GLN C 583 ASN C 837 GLN ** U 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 443 GLN A1117 HIS A1400 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35743 Z= 0.225 Angle : 0.554 13.806 49384 Z= 0.277 Chirality : 0.041 0.599 5588 Planarity : 0.004 0.051 5711 Dihedral : 16.113 174.073 7111 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.35 % Allowed : 4.27 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3866 helix: 1.75 (0.13), residues: 1626 sheet: -0.30 (0.24), residues: 473 loop : -0.48 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1637 HIS 0.007 0.001 HIS C 627 PHE 0.016 0.001 PHE A1099 TYR 0.017 0.001 TYR A 88 ARG 0.004 0.000 ARG A1678 *********************** 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 141 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 4.065 Fit side-chains REVERT: G 254 TYR cc_start: 0.7144 (m-80) cc_final: 0.6939 (m-80) REVERT: C 934 MET cc_start: 0.8480 (ttp) cc_final: 0.7753 (ttp) REVERT: U 390 MET cc_start: 0.8041 (mmt) cc_final: 0.7661 (mmt) REVERT: A 641 MET cc_start: 0.8068 (tpp) cc_final: 0.7853 (mmm) REVERT: A 1418 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6015 (mmt180) REVERT: N 133 MET cc_start: 0.6291 (tmm) cc_final: 0.5815 (ttp) outliers start: 11 outliers final: 7 residues processed: 138 average time/residue: 0.4493 time to fit residues: 108.1647 Evaluate side-chains 135 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 3.755 ------------------------------------------------------------------------------- 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 1315 VAL Chi-restraints excluded: chain A residue 1418 ARG Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 203 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 304 optimal weight: 0.0060 chunk 249 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 366 optimal weight: 9.9990 chunk 396 optimal weight: 0.3980 chunk 326 optimal weight: 0.8980 chunk 363 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 294 optimal weight: 0.0000 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 837 GLN U 166 ASN U 276 GLN A1400 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35743 Z= 0.119 Angle : 0.474 8.915 49384 Z= 0.239 Chirality : 0.038 0.340 5588 Planarity : 0.004 0.066 5711 Dihedral : 15.964 177.564 7111 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.38 % Allowed : 5.87 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3866 helix: 2.00 (0.13), residues: 1623 sheet: 0.06 (0.25), residues: 455 loop : -0.43 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1515 HIS 0.007 0.001 HIS D 89 PHE 0.013 0.001 PHE A 166 TYR 0.013 0.001 TYR A1204 ARG 0.004 0.000 ARG L 377 *********************** 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 149 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 3.911 Fit side-chains REVERT: U 390 MET cc_start: 0.8051 (mmt) cc_final: 0.7795 (mmt) REVERT: A 641 MET cc_start: 0.8040 (tpp) cc_final: 0.7790 (mmm) REVERT: A 976 MET cc_start: 0.8459 (tpp) cc_final: 0.8179 (tpt) outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 0.4325 time to fit residues: 110.9366 Evaluate side-chains 134 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 4.186 ------------------------------------------------------------------------------- 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 1420 ASN Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 362 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 174 optimal weight: 0.6980 chunk 246 optimal weight: 6.9990 chunk 367 optimal weight: 0.0980 chunk 389 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 335 GLN C 837 GLN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN A1527 ASN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35743 Z= 0.215 Angle : 0.507 9.275 49384 Z= 0.258 Chirality : 0.040 0.365 5588 Planarity : 0.004 0.069 5711 Dihedral : 15.954 178.432 7111 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.80 % Allowed : 7.22 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3866 helix: 1.99 (0.13), residues: 1626 sheet: -0.05 (0.24), residues: 478 loop : -0.40 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1637 HIS 0.004 0.001 HIS C 642 PHE 0.015 0.001 PHE A1099 TYR 0.017 0.001 TYR A 88 ARG 0.005 0.000 ARG L 377 *********************** 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 154 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 3.707 Fit side-chains REVERT: C 934 MET cc_start: 0.8528 (ttp) cc_final: 0.7832 (ttp) REVERT: U 390 MET cc_start: 0.8081 (mmt) cc_final: 0.7766 (mmt) REVERT: A 1048 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7694 (mpp) REVERT: A 1418 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6366 (mmt180) REVERT: N 133 MET cc_start: 0.6279 (tmm) cc_final: 0.5826 (ttp) outliers start: 25 outliers final: 12 residues processed: 150 average time/residue: 0.4451 time to fit residues: 117.1442 Evaluate side-chains 140 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 3.841 ------------------------------------------------------------------------------- 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 949 ILE Chi-restraints excluded: chain U residue 276 GLN Chi-restraints excluded: chain A residue 164 MET 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 1418 ARG Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 324 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 chunk 290 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 332 optimal weight: 20.0000 chunk 269 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 349 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 335 GLN C 583 ASN ** U 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 HIS A1400 ASN A1424 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35743 Z= 0.235 Angle : 0.512 8.533 49384 Z= 0.261 Chirality : 0.040 0.333 5588 Planarity : 0.004 0.070 5711 Dihedral : 15.966 179.702 7111 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.03 % Allowed : 8.18 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3866 helix: 1.89 (0.13), residues: 1628 sheet: -0.19 (0.24), residues: 472 loop : -0.43 (0.15), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1637 HIS 0.005 0.001 HIS A 680 PHE 0.018 0.001 PHE A 166 TYR 0.017 0.001 TYR A 88 ARG 0.005 0.000 ARG L 377 *********************** 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 162 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 3.806 Fit side-chains REVERT: C 934 MET cc_start: 0.8518 (ttp) cc_final: 0.7835 (ttp) REVERT: U 384 MET cc_start: 0.5389 (mmm) cc_final: 0.5009 (mmm) REVERT: U 390 MET cc_start: 0.8103 (mmt) cc_final: 0.7768 (mmt) REVERT: A 641 MET cc_start: 0.7246 (mmm) cc_final: 0.6856 (tpt) REVERT: A 1048 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7864 (mpp) REVERT: A 1734 MET cc_start: 0.8545 (mmp) cc_final: 0.8167 (mmm) REVERT: L 362 MET cc_start: 0.6120 (ptm) cc_final: 0.5908 (ppp) outliers start: 32 outliers final: 19 residues processed: 154 average time/residue: 0.4662 time to fit residues: 126.1920 Evaluate side-chains 148 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 3.767 ------------------------------------------------------------------------------- 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 U residue 276 GLN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain A residue 1022 MET 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 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 131 optimal weight: 4.9990 chunk 350 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 389 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 chunk 180 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 248 GLN C 583 ASN C 768 GLN A1400 ASN D 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35743 Z= 0.134 Angle : 0.474 8.720 49384 Z= 0.240 Chirality : 0.038 0.232 5588 Planarity : 0.004 0.067 5711 Dihedral : 15.896 179.634 7111 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.74 % Allowed : 8.79 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3866 helix: 2.09 (0.13), residues: 1620 sheet: -0.04 (0.24), residues: 458 loop : -0.39 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 PHE 0.014 0.001 PHE A1099 TYR 0.012 0.001 TYR A 431 ARG 0.003 0.000 ARG A 71 *********************** 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 151 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 3.914 Fit side-chains REVERT: U 384 MET cc_start: 0.6059 (mmm) cc_final: 0.5802 (mmm) REVERT: U 390 MET cc_start: 0.8081 (mmt) cc_final: 0.7748 (mmt) REVERT: A 976 MET cc_start: 0.8453 (tpp) cc_final: 0.8225 (tpt) REVERT: A 1048 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7835 (mpp) REVERT: A 1622 MET cc_start: 0.8213 (mmm) cc_final: 0.7939 (mmt) REVERT: N 133 MET cc_start: 0.6176 (tmm) cc_final: 0.5720 (ttp) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.4541 time to fit residues: 116.0587 Evaluate side-chains 143 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 3.649 ------------------------------------------------------------------------------- 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 490 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 768 ASP 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 1420 ASN Chi-restraints excluded: chain A residue 1519 THR Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 375 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 222 optimal weight: 0.8980 chunk 284 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 328 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 388 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 890 HIS U 276 GLN A1400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35743 Z= 0.141 Angle : 0.468 8.680 49384 Z= 0.237 Chirality : 0.038 0.202 5588 Planarity : 0.004 0.064 5711 Dihedral : 15.837 179.930 7111 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.77 % Allowed : 9.14 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3866 helix: 2.17 (0.13), residues: 1620 sheet: 0.11 (0.24), residues: 454 loop : -0.35 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1515 HIS 0.006 0.001 HIS A 680 PHE 0.019 0.001 PHE A 166 TYR 0.013 0.001 TYR A 431 ARG 0.003 0.000 ARG A 71 *********************** 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 152 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 3.622 Fit side-chains REVERT: U 390 MET cc_start: 0.8089 (mmt) cc_final: 0.7745 (mmt) REVERT: A 976 MET cc_start: 0.8405 (tpp) cc_final: 0.8170 (tpt) REVERT: A 1048 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7643 (mpp) REVERT: A 1622 MET cc_start: 0.8209 (mmm) cc_final: 0.7929 (mmt) REVERT: N 133 MET cc_start: 0.6258 (tmm) cc_final: 0.5773 (ttm) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.4368 time to fit residues: 112.2990 Evaluate side-chains 145 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 3.795 ------------------------------------------------------------------------------- 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 490 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 768 ASP 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 A residue 1420 ASN Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 240 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 305 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 166 ASN A1400 ASN D 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35743 Z= 0.146 Angle : 0.472 10.781 49384 Z= 0.238 Chirality : 0.038 0.209 5588 Planarity : 0.004 0.065 5711 Dihedral : 15.816 179.995 7111 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.83 % Allowed : 9.20 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3866 helix: 2.20 (0.13), residues: 1620 sheet: 0.14 (0.25), residues: 454 loop : -0.32 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1515 HIS 0.005 0.001 HIS A 680 PHE 0.013 0.001 PHE A1099 TYR 0.013 0.001 TYR A 431 ARG 0.002 0.000 ARG A 71 *********************** 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 154 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 4.149 Fit side-chains REVERT: U 390 MET cc_start: 0.8091 (mmt) cc_final: 0.7747 (mmt) REVERT: A 271 MET cc_start: 0.6907 (mtt) cc_final: 0.6692 (mtm) REVERT: A 976 MET cc_start: 0.8440 (tpp) cc_final: 0.8195 (tpt) REVERT: A 1048 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7637 (mpp) REVERT: A 1622 MET cc_start: 0.8200 (mmm) cc_final: 0.7905 (mmt) REVERT: N 133 MET cc_start: 0.6233 (tmm) cc_final: 0.5786 (ttm) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.4368 time to fit residues: 115.9093 Evaluate side-chains 148 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 3.769 ------------------------------------------------------------------------------- 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 768 ASP 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 A residue 1420 ASN Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 353 optimal weight: 0.1980 chunk 372 optimal weight: 9.9990 chunk 339 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 217 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 284 optimal weight: 0.0040 chunk 111 optimal weight: 0.9980 chunk 327 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 overall best weight: 2.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 335 GLN C 583 ASN C 596 ASN A 505 ASN A1004 ASN A1400 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35743 Z= 0.286 Angle : 0.543 12.474 49384 Z= 0.274 Chirality : 0.041 0.302 5588 Planarity : 0.004 0.060 5711 Dihedral : 15.914 179.959 7111 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.83 % Allowed : 9.49 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3866 helix: 1.97 (0.13), residues: 1626 sheet: -0.17 (0.24), residues: 479 loop : -0.37 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1515 HIS 0.005 0.001 HIS A 680 PHE 0.018 0.001 PHE A1099 TYR 0.018 0.001 TYR A 431 ARG 0.004 0.000 ARG A 409 *********************** 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 153 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 4.113 Fit side-chains REVERT: C 934 MET cc_start: 0.8557 (ttp) cc_final: 0.7925 (ttp) REVERT: U 390 MET cc_start: 0.8141 (mmt) cc_final: 0.7760 (mmt) REVERT: A 641 MET cc_start: 0.7696 (mmm) cc_final: 0.7475 (tmm) REVERT: A 697 MET cc_start: 0.4484 (tpt) cc_final: 0.4194 (tpt) REVERT: A 1048 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7732 (mpp) REVERT: A 1622 MET cc_start: 0.8207 (mmm) cc_final: 0.7929 (mmt) REVERT: A 1652 MET cc_start: 0.0729 (mmt) cc_final: 0.0438 (mmt) REVERT: A 1734 MET cc_start: 0.8550 (mmp) cc_final: 0.8221 (mmm) REVERT: N 133 MET cc_start: 0.6256 (tmm) cc_final: 0.5801 (ttm) REVERT: L 343 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7286 (tt) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.4480 time to fit residues: 116.5540 Evaluate side-chains 147 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 3.830 ------------------------------------------------------------------------------- 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 628 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 97 HIS 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 768 ASP 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 A residue 1420 ASN Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 237 optimal weight: 0.0070 chunk 382 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 266 optimal weight: 0.1980 chunk 401 optimal weight: 5.9990 chunk 369 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 246 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 335 GLN C 583 ASN U 166 ASN A 495 GLN A1400 ASN A1610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35743 Z= 0.117 Angle : 0.482 12.533 49384 Z= 0.241 Chirality : 0.038 0.234 5588 Planarity : 0.004 0.063 5711 Dihedral : 15.840 179.077 7111 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.74 % Allowed : 9.69 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.14), residues: 3866 helix: 2.15 (0.13), residues: 1615 sheet: 0.15 (0.25), residues: 454 loop : -0.31 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A1515 HIS 0.004 0.001 HIS C 627 PHE 0.013 0.001 PHE A1099 TYR 0.011 0.001 TYR A 431 ARG 0.003 0.000 ARG A 71 ********************** 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 149 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 4.912 Fit side-chains REVERT: G 324 MET cc_start: 0.8474 (mmm) cc_final: 0.8242 (mmm) REVERT: U 390 MET cc_start: 0.8093 (mmt) cc_final: 0.7732 (mmt) REVERT: A 697 MET cc_start: 0.4268 (tpt) cc_final: 0.3994 (tpt) REVERT: A 1048 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7644 (mpp) REVERT: A 1622 MET cc_start: 0.8199 (mmm) cc_final: 0.7910 (mmt) REVERT: A 1652 MET cc_start: 0.0716 (mmt) cc_final: 0.0451 (mmt) REVERT: N 133 MET cc_start: 0.6204 (tmm) cc_final: 0.5793 (ttm) REVERT: L 343 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7291 (tt) outliers start: 23 outliers final: 19 residues processed: 145 average time/residue: 0.4615 time to fit residues: 121.4355 Evaluate side-chains 147 residues out of total 3516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 3.734 ------------------------------------------------------------------------------- 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 628 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 949 ILE Chi-restraints excluded: chain A residue 97 HIS 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 768 ASP 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 1420 ASN Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain L residue 343 LEU Chi-restraints excluded: chain D residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 253 optimal weight: 1.9990 chunk 340 optimal weight: 0.4980 chunk 97 optimal weight: 0.3980 chunk 294 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 134 optimal weight: 0.0670 chunk 328 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 166 ASN A 495 GLN A1400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.075960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.054163 restraints weight = 124496.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055303 restraints weight = 68697.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055746 restraints weight = 48091.068| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35743 Z= 0.135 Angle : 0.478 12.199 49384 Z= 0.238 Chirality : 0.038 0.239 5588 Planarity : 0.004 0.065 5711 Dihedral : 15.799 178.754 7111 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.71 % Allowed : 9.81 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3866 helix: 2.24 (0.13), residues: 1614 sheet: 0.20 (0.25), residues: 454 loop : -0.29 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A1515 HIS 0.004 0.000 HIS C 627 PHE 0.013 0.001 PHE A1099 TYR 0.013 0.001 TYR A 431 ARG 0.002 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5045.73 seconds wall clock time: 93 minutes 23.48 seconds (5603.48 seconds total)