Starting phenix.real_space_refine on Wed Mar 20 12:36:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tui_26132/03_2024/7tui_26132_updated.pdb" } resolution = 2.66 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= 0.009 sd= 0.273 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 1 5.49 5 S 99 5.16 5 C 17478 2.51 5 N 4563 2.21 5 O 5239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 886": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1149": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A GLU 1309": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1377": "OE1" <-> "OE2" Residue "A GLU 1500": "OE1" <-> "OE2" Residue "A GLU 1557": "OE1" <-> "OE2" Residue "A GLU 1715": "OE1" <-> "OE2" Residue "B GLU 762": "OE1" <-> "OE2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B GLU 963": "OE1" <-> "OE2" Residue "B GLU 973": "OE1" <-> "OE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B GLU 986": "OE1" <-> "OE2" Residue "B GLU 1125": "OE1" <-> "OE2" Residue "B PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1490": "OE1" <-> "OE2" Residue "B GLU 1627": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1433, 11295 Classifications: {'peptide': 1433} Link IDs: {'PTRANS': 56, 'TRANS': 1376} Chain breaks: 3 Chain: "B" Number of atoms: 16085 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2034, 16075 Unusual residues: {'FMN': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B2037 "'] Classifications: {'peptide': 2033, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 107, 'TRANS': 1924, None: 1} Not linked: pdbres="GLU B2037 " pdbres="FMN B2101 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 2034, 16075 Unusual residues: {'FMN': 1} Inner-chain residues flagged as termini: ['pdbres="GLU B2037 "'] Classifications: {'peptide': 2033, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 107, 'TRANS': 1924, None: 1} Not linked: pdbres="GLU B2037 " pdbres="FMN B2101 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 16433 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 727 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 727 " occ=0.50 Time building chain proxies: 22.50, per 1000 atoms: 0.82 Number of scatterers: 27380 At special positions: 0 Unit cell: (202.91, 157.59, 170.98, 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 99 16.00 P 1 15.00 O 5239 8.00 N 4563 7.00 C 17478 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: 11.24 Conformation dependent library (CDL) restraints added in 7.8 seconds 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 145 helices and 29 sheets defined 39.8% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.521A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 54 through 64 Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 326 through 347 Processing helix chain 'A' and resid 354 through 381 removed outlier: 3.514A pdb=" N ALA A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.621A pdb=" N ARG A 409 " --> pdb=" O TRP A 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.662A pdb=" N ARG A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 455 removed outlier: 3.603A pdb=" N LYS A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 463 through 482 removed outlier: 3.663A pdb=" N GLN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 630 through 632 No H-bonds generated for 'chain 'A' and resid 630 through 632' Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 691 through 702 removed outlier: 3.521A pdb=" N LEU A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 745 through 756 removed outlier: 3.578A pdb=" N ALA A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.611A pdb=" N SER A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 891 removed outlier: 4.535A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 888 " --> pdb=" O ALA A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.567A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 909 " --> pdb=" O ILE A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 977 removed outlier: 3.910A pdb=" N ILE A 953 " --> pdb=" O GLU A 949 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASN A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 975 " --> pdb=" O ASP A 971 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASN A 976 " --> pdb=" O ASN A 972 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.657A pdb=" N GLN A1003 " --> pdb=" O ASP A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1016 No H-bonds generated for 'chain 'A' and resid 1014 through 1016' Processing helix chain 'A' and resid 1032 through 1040 Processing helix chain 'A' and resid 1046 through 1055 Processing helix chain 'A' and resid 1085 through 1098 removed outlier: 4.367A pdb=" N LYS A1089 " --> pdb=" O GLU A1085 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N GLU A1094 " --> pdb=" O SER A1090 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1109 No H-bonds generated for 'chain 'A' and resid 1107 through 1109' Processing helix chain 'A' and resid 1115 through 1117 No H-bonds generated for 'chain 'A' and resid 1115 through 1117' Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 7.503A pdb=" N GLU A1149 " --> pdb=" O HIS A1145 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1209 through 1224 Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1260 Processing helix chain 'A' and resid 1273 through 1276 Processing helix chain 'A' and resid 1281 through 1289 Processing helix chain 'A' and resid 1303 through 1306 removed outlier: 3.640A pdb=" N THR A1306 " --> pdb=" O ALA A1303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1303 through 1306' Processing helix chain 'A' and resid 1309 through 1319 Processing helix chain 'A' and resid 1336 through 1344 Processing helix chain 'A' and resid 1351 through 1356 Processing helix chain 'A' and resid 1389 through 1395 Processing helix chain 'A' and resid 1423 through 1428 Processing helix chain 'A' and resid 1440 through 1442 No H-bonds generated for 'chain 'A' and resid 1440 through 1442' Processing helix chain 'A' and resid 1444 through 1476 removed outlier: 3.533A pdb=" N GLN A1457 " --> pdb=" O LYS A1453 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A1470 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A1474 " --> pdb=" O GLN A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1512 removed outlier: 3.541A pdb=" N LEU A1490 " --> pdb=" O MET A1486 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU A1495 " --> pdb=" O LYS A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 removed outlier: 4.329A pdb=" N PHE A1533 " --> pdb=" O ALA A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1539 No H-bonds generated for 'chain 'A' and resid 1537 through 1539' Processing helix chain 'A' and resid 1551 through 1567 removed outlier: 3.698A pdb=" N LYS A1555 " --> pdb=" O VAL A1551 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A1558 " --> pdb=" O ASP A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1585 removed outlier: 3.673A pdb=" N THR A1585 " --> pdb=" O LYS A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 Processing helix chain 'A' and resid 1620 through 1622 No H-bonds generated for 'chain 'A' and resid 1620 through 1622' Processing helix chain 'A' and resid 1662 through 1664 No H-bonds generated for 'chain 'A' and resid 1662 through 1664' Processing helix chain 'A' and resid 1671 through 1698 removed outlier: 3.508A pdb=" N THR A1679 " --> pdb=" O GLU A1675 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1719 Processing helix chain 'A' and resid 1737 through 1739 No H-bonds generated for 'chain 'A' and resid 1737 through 1739' Processing helix chain 'B' and resid 22 through 38 removed outlier: 6.129A pdb=" N PHE B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B 28 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 31 " --> pdb=" O TYR B 28 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 36 " --> pdb=" O ASP B 33 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 37 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 94 through 103 removed outlier: 3.694A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 171 through 192 removed outlier: 5.895A pdb=" N ASP B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 215 through 218 No H-bonds generated for 'chain 'B' and resid 215 through 218' Processing helix chain 'B' and resid 221 through 242 Proline residue: B 226 - end of helix Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 264 through 272 removed outlier: 4.542A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 300 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.560A pdb=" N GLN B 342 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 383 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.610A pdb=" N ASP B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 4.034A pdb=" N LYS B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 478 No H-bonds generated for 'chain 'B' and resid 475 through 478' Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.933A pdb=" N PHE B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 530 through 534' Processing helix chain 'B' and resid 571 through 574 No H-bonds generated for 'chain 'B' and resid 571 through 574' Processing helix chain 'B' and resid 591 through 600 removed outlier: 4.049A pdb=" N SER B 597 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 614 through 627 Processing helix chain 'B' and resid 643 through 659 Proline residue: B 651 - end of helix Processing helix chain 'B' and resid 675 through 683 removed outlier: 3.929A pdb=" N GLU B 680 " --> pdb=" O GLU B 676 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 681 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 709 Processing helix chain 'B' and resid 735 through 738 No H-bonds generated for 'chain 'B' and resid 735 through 738' Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 761 through 769 Proline residue: B 766 - end of helix Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 816 through 821 removed outlier: 4.763A pdb=" N GLU B 820 " --> pdb=" O GLN B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 847 through 858 Processing helix chain 'B' and resid 864 through 885 removed outlier: 4.194A pdb=" N LEU B 868 " --> pdb=" O LYS B 864 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ASP B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP B 876 " --> pdb=" O ASN B 872 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N HIS B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 903 No H-bonds generated for 'chain 'B' and resid 901 through 903' Processing helix chain 'B' and resid 906 through 917 Processing helix chain 'B' and resid 928 through 944 Processing helix chain 'B' and resid 958 through 961 Processing helix chain 'B' and resid 964 through 974 Processing helix chain 'B' and resid 976 through 978 No H-bonds generated for 'chain 'B' and resid 976 through 978' Processing helix chain 'B' and resid 985 through 996 Processing helix chain 'B' and resid 1011 through 1018 removed outlier: 4.387A pdb=" N GLU B1014 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE B1015 " --> pdb=" O ARG B1012 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS B1018 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 3.839A pdb=" N GLU B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1131 Processing helix chain 'B' and resid 1137 through 1143 Processing helix chain 'B' and resid 1157 through 1161 Processing helix chain 'B' and resid 1173 through 1176 No H-bonds generated for 'chain 'B' and resid 1173 through 1176' Processing helix chain 'B' and resid 1185 through 1187 No H-bonds generated for 'chain 'B' and resid 1185 through 1187' Processing helix chain 'B' and resid 1242 through 1255 Processing helix chain 'B' and resid 1280 through 1285 Processing helix chain 'B' and resid 1310 through 1323 removed outlier: 3.693A pdb=" N ILE B1313 " --> pdb=" O ASP B1310 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B1314 " --> pdb=" O PHE B1311 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP B1317 " --> pdb=" O VAL B1314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B1318 " --> pdb=" O ILE B1315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B1321 " --> pdb=" O LYS B1318 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B1323 " --> pdb=" O ILE B1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 1425 through 1432 Processing helix chain 'B' and resid 1498 through 1506 Processing helix chain 'B' and resid 1537 through 1543 Processing helix chain 'B' and resid 1548 through 1550 No H-bonds generated for 'chain 'B' and resid 1548 through 1550' Processing helix chain 'B' and resid 1553 through 1558 Processing helix chain 'B' and resid 1568 through 1578 Processing helix chain 'B' and resid 1665 through 1670 Processing helix chain 'B' and resid 1672 through 1689 Processing helix chain 'B' and resid 1693 through 1698 Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 4.042A pdb=" N ASN B1719 " --> pdb=" O ALA B1715 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B1720 " --> pdb=" O ILE B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1762 through 1772 Proline residue: B1767 - end of helix Processing helix chain 'B' and resid 1814 through 1827 Processing helix chain 'B' and resid 1856 through 1859 No H-bonds generated for 'chain 'B' and resid 1856 through 1859' Processing helix chain 'B' and resid 1867 through 1870 No H-bonds generated for 'chain 'B' and resid 1867 through 1870' Processing helix chain 'B' and resid 1892 through 1902 removed outlier: 3.749A pdb=" N VAL B1901 " --> pdb=" O THR B1897 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B1902 " --> pdb=" O LEU B1898 " (cutoff:3.500A) Processing helix chain 'B' and resid 1904 through 1907 No H-bonds generated for 'chain 'B' and resid 1904 through 1907' Processing helix chain 'B' and resid 1912 through 1916 Processing helix chain 'B' and resid 1927 through 1931 removed outlier: 3.695A pdb=" N GLU B1930 " --> pdb=" O HIS B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1941 removed outlier: 6.212A pdb=" N LEU B1940 " --> pdb=" O ALA B1936 " (cutoff:3.500A) Processing helix chain 'B' and resid 1991 through 1997 removed outlier: 5.625A pdb=" N GLY B1996 " --> pdb=" O GLN B1992 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2016 removed outlier: 5.188A pdb=" N GLN B2015 " --> pdb=" O GLU B2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 2025 through 2031 removed outlier: 4.514A pdb=" N ILE B2029 " --> pdb=" O LYS B2025 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.578A pdb=" N GLN A 77 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU A 46 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 399 through 401 removed outlier: 6.593A pdb=" N ALA A 770 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR A 684 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 772 " --> pdb=" O THR A 684 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 496 through 502 Processing sheet with id= D, first strand: chain 'A' and resid 651 through 654 removed outlier: 4.138A pdb=" N MET A 923 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A 867 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1059 through 1066 Processing sheet with id= F, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 4.226A pdb=" N GLY A1101 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1187 " --> pdb=" O GLY A1101 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1118 through 1125 Processing sheet with id= H, first strand: chain 'A' and resid 1133 through 1135 Processing sheet with id= I, first strand: chain 'A' and resid 1242 through 1244 removed outlier: 6.528A pdb=" N VAL A1325 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET A1387 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL A1020 " --> pdb=" O MET A1387 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1577 through 1579 removed outlier: 7.593A pdb=" N ALA A1642 " --> pdb=" O GLY A1541 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A1543 " --> pdb=" O ALA A1642 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER A1644 " --> pdb=" O ALA A1543 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A1653 " --> pdb=" O GLY A1649 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A1405 " --> pdb=" O VAL A1658 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1660 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A1403 " --> pdb=" O VAL A1660 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1727 through 1729 Processing sheet with id= L, first strand: chain 'B' and resid 6 through 11 Processing sheet with id= M, first strand: chain 'B' and resid 256 through 259 removed outlier: 3.993A pdb=" N TRP B 256 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 148 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 485 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE B 149 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 487 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG B 511 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ASP B 488 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE B 513 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 325 through 329 removed outlier: 6.168A pdb=" N SER B 367 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 355 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 555 through 558 Processing sheet with id= P, first strand: chain 'B' and resid 579 through 581 removed outlier: 6.543A pdb=" N VAL B 786 " --> pdb=" O MET B 580 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 605 through 607 removed outlier: 6.689A pdb=" N GLY B 635 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 636 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 666 " --> pdb=" O ILE B 636 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU B 638 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 668 " --> pdb=" O LEU B 638 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N HIS B 689 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ILE B 668 " --> pdb=" O HIS B 689 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLY B 691 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU B 692 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 716 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 830 through 834 Processing sheet with id= S, first strand: chain 'B' and resid 1113 through 1115 removed outlier: 6.204A pdb=" N GLU B1183 " --> pdb=" O PRO B1191 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B1185 " --> pdb=" O LEU B1189 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B1189 " --> pdb=" O ILE B1185 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1146 through 1148 Processing sheet with id= U, first strand: chain 'B' and resid 1203 through 1209 Processing sheet with id= V, first strand: chain 'B' and resid 1595 through 1597 removed outlier: 6.599A pdb=" N GLN B1395 " --> pdb=" O LEU B1339 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASN B1341 " --> pdb=" O THR B1393 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR B1393 " --> pdb=" O ASN B1341 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1359 through 1361 removed outlier: 3.513A pdb=" N TYR B1383 " --> pdb=" O SER B1359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET B1390 " --> pdb=" O ILE B1382 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B1384 " --> pdb=" O PRO B1388 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1416 through 1418 Processing sheet with id= Y, first strand: chain 'B' and resid 1529 through 1531 removed outlier: 3.766A pdb=" N LYS B1622 " --> pdb=" O ILE B1644 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B1644 " --> pdb=" O LYS B1622 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ASN B1630 " --> pdb=" O PRO B1636 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1649 through 1651 Processing sheet with id= AA, first strand: chain 'B' and resid 1703 through 1707 Processing sheet with id= AB, first strand: chain 'B' and resid 1840 through 1844 removed outlier: 5.778A pdb=" N ALA B1889 " --> pdb=" O ILE B1876 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B1876 " --> pdb=" O ALA B1889 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASP B1891 " --> pdb=" O LEU B1874 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B1874 " --> pdb=" O ASP B1891 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 1453 through 1457 911 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.10 Time building geometry restraints manager: 12.01 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: 8866 1.34 - 1.46: 5491 1.46 - 1.58: 13449 1.58 - 1.70: 3 1.70 - 1.81: 170 Bond restraints: 27979 Sorted by residual: bond pdb=" CB PRO A1132 " pdb=" CG PRO A1132 " ideal model delta sigma weight residual 1.492 1.595 -0.103 5.00e-02 4.00e+02 4.21e+00 bond pdb=" CB PRO B2006 " pdb=" CG PRO B2006 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.72e+00 bond pdb=" CG LEU B2009 " pdb=" CD2 LEU B2009 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" C TYR B 765 " pdb=" N PRO B 766 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.17e+00 bond pdb=" CB ILE A1102 " pdb=" CG2 ILE A1102 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 ... (remaining 27974 not shown) Histogram of bond angle deviations from ideal: 94.38 - 102.39: 114 102.39 - 110.40: 6792 110.40 - 118.42: 14897 118.42 - 126.43: 15698 126.43 - 134.44: 408 Bond angle restraints: 37909 Sorted by residual: angle pdb=" C LEU B1969 " pdb=" N MET B1970 " pdb=" CA MET B1970 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" CA PRO A1132 " pdb=" N PRO A1132 " pdb=" CD PRO A1132 " ideal model delta sigma weight residual 112.00 103.18 8.82 1.40e+00 5.10e-01 3.97e+01 angle pdb=" C GLU B2034 " pdb=" CA GLU B2034 " pdb=" CB GLU B2034 " ideal model delta sigma weight residual 117.23 109.28 7.95 1.36e+00 5.41e-01 3.42e+01 angle pdb=" N LYS B 743 " pdb=" CA LYS B 743 " pdb=" C LYS B 743 " ideal model delta sigma weight residual 114.64 106.04 8.60 1.52e+00 4.33e-01 3.20e+01 angle pdb=" C LYS A1298 " pdb=" N THR A1299 " pdb=" CA THR A1299 " ideal model delta sigma weight residual 122.26 116.89 5.37 1.10e+00 8.26e-01 2.39e+01 ... (remaining 37904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.95: 15743 18.95 - 37.91: 967 37.91 - 56.86: 115 56.86 - 75.81: 19 75.81 - 94.77: 14 Dihedral angle restraints: 16858 sinusoidal: 6799 harmonic: 10059 Sorted by residual: dihedral pdb=" CA MET B1810 " pdb=" C MET B1810 " pdb=" N PRO B1811 " pdb=" CA PRO B1811 " ideal model delta harmonic sigma weight residual -180.00 -147.05 -32.95 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA TYR B1929 " pdb=" C TYR B1929 " pdb=" N GLU B1930 " pdb=" CA GLU B1930 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LYS B1982 " pdb=" C LYS B1982 " pdb=" N LYS B1983 " pdb=" CA LYS B1983 " ideal model delta harmonic sigma weight residual -180.00 -148.77 -31.23 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 16855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3091 0.051 - 0.102: 950 0.102 - 0.154: 157 0.154 - 0.205: 17 0.205 - 0.256: 7 Chirality restraints: 4222 Sorted by residual: chirality pdb=" CB ILE B1786 " pdb=" CA ILE B1786 " pdb=" CG1 ILE B1786 " pdb=" CG2 ILE B1786 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR A 709 " pdb=" CA THR A 709 " pdb=" OG1 THR A 709 " pdb=" CG2 THR A 709 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO B1477 " pdb=" N PRO B1477 " pdb=" C PRO B1477 " pdb=" CB PRO B1477 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4219 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A1131 " 0.070 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A1132 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A1132 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1132 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B2005 " 0.051 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO B2006 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B2006 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B2006 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1120 " -0.050 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO B1121 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B1121 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B1121 " -0.043 5.00e-02 4.00e+02 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 370 2.61 - 3.18: 24943 3.18 - 3.75: 44353 3.75 - 4.33: 63081 4.33 - 4.90: 100332 Nonbonded interactions: 233079 Sorted by model distance: nonbonded pdb=" OG1 THR B1535 " pdb=" OE1 GLU B1537 " model vdw 2.034 2.440 nonbonded pdb=" O LEU B2002 " pdb=" OG1 THR B2003 " model vdw 2.098 2.440 nonbonded pdb=" OD1 ASP A1076 " pdb=" OH TYR A1092 " model vdw 2.100 2.440 nonbonded pdb=" OD2 ASP A1013 " pdb=" OG SER A1506 " model vdw 2.102 2.440 nonbonded pdb=" O PHE A 35 " pdb=" OG1 THR A 41 " model vdw 2.103 2.440 ... (remaining 233074 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.980 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 86.780 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.140 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 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 : 0.005 0.103 27979 Z= 0.322 Angle : 0.870 15.108 37909 Z= 0.506 Chirality : 0.049 0.256 4222 Planarity : 0.006 0.101 4878 Dihedral : 12.343 94.768 10398 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.83 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.61 % Twisted General : 0.06 % 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: -2.00 (0.14), residues: 3459 helix: -0.73 (0.14), residues: 1355 sheet: -1.69 (0.25), residues: 420 loop : -1.68 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 719 HIS 0.015 0.002 HIS B 842 PHE 0.029 0.002 PHE B1421 TYR 0.039 0.002 TYR B1777 ARG 0.015 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 436 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 GLU cc_start: 0.7001 (mp0) cc_final: 0.6771 (mp0) REVERT: A 888 ILE cc_start: 0.7949 (mt) cc_final: 0.7715 (OUTLIER) REVERT: A 1138 GLU cc_start: 0.7538 (pt0) cc_final: 0.7319 (pt0) REVERT: A 1261 LYS cc_start: 0.5438 (mttp) cc_final: 0.4694 (ttmt) REVERT: B 387 MET cc_start: 0.2826 (tpp) cc_final: 0.2539 (mmt) REVERT: B 1160 ASP cc_start: 0.7657 (m-30) cc_final: 0.7390 (m-30) REVERT: B 1607 THR cc_start: 0.8226 (t) cc_final: 0.8022 (m) REVERT: B 1791 MET cc_start: 0.4435 (mpp) cc_final: 0.4148 (mpp) outliers start: 0 outliers final: 1 residues processed: 436 average time/residue: 1.5759 time to fit residues: 789.4346 Evaluate side-chains 266 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 271 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 164 optimal weight: 0.0970 chunk 201 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1080 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN A1556 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN B 415 HIS B 474 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 HIS ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B1370 GLN B1567 HIS B1669 ASN ** B1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1868 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27979 Z= 0.261 Angle : 0.688 13.029 37909 Z= 0.355 Chirality : 0.047 0.255 4222 Planarity : 0.005 0.074 4878 Dihedral : 5.643 93.450 3728 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.74 % Favored : 92.85 % Rotamer: Outliers : 1.90 % Allowed : 9.93 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.61 % Twisted General : 0.03 % 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: -1.68 (0.14), residues: 3459 helix: -0.33 (0.14), residues: 1351 sheet: -1.66 (0.24), residues: 449 loop : -1.56 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 719 HIS 0.010 0.001 HIS B 842 PHE 0.036 0.002 PHE B1516 TYR 0.032 0.002 TYR B1777 ARG 0.010 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 310 time to evaluate : 3.105 Fit side-chains revert: symmetry clash REVERT: A 334 LYS cc_start: 0.5935 (tptt) cc_final: 0.5216 (mmtp) REVERT: A 352 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7747 (mp) REVERT: A 439 MET cc_start: 0.8494 (ptm) cc_final: 0.8100 (ptp) REVERT: A 647 LYS cc_start: 0.7410 (tttt) cc_final: 0.7206 (tttp) REVERT: A 668 SER cc_start: 0.7545 (m) cc_final: 0.7315 (t) REVERT: A 799 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8225 (tm) REVERT: A 944 ARG cc_start: 0.7484 (ptp-110) cc_final: 0.7169 (ttm110) REVERT: A 1052 MET cc_start: 0.8600 (mmm) cc_final: 0.8147 (mmm) REVERT: A 1116 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7757 (mttp) REVERT: A 1261 LYS cc_start: 0.5455 (mttp) cc_final: 0.4629 (ttmt) REVERT: A 1626 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: B 387 MET cc_start: 0.3020 (tpp) cc_final: 0.2280 (mpp) REVERT: B 1160 ASP cc_start: 0.7640 (m-30) cc_final: 0.7369 (m-30) REVERT: B 1607 THR cc_start: 0.8182 (t) cc_final: 0.7889 (m) REVERT: B 1617 MET cc_start: 0.5702 (mpt) cc_final: 0.5097 (mtt) REVERT: B 1773 GLU cc_start: 0.4283 (mt-10) cc_final: 0.3479 (mt-10) outliers start: 57 outliers final: 17 residues processed: 337 average time/residue: 1.4954 time to fit residues: 588.4878 Evaluate side-chains 288 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1626 GLU Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1696 ILE Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1438 LEU Chi-restraints excluded: chain B residue 1810 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 0.0980 chunk 97 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 340 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 312 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1450 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 HIS B1827 GLN B1868 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 27979 Z= 0.222 Angle : 0.639 12.441 37909 Z= 0.329 Chirality : 0.045 0.240 4222 Planarity : 0.005 0.052 4878 Dihedral : 5.438 92.196 3728 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.45 % Favored : 93.23 % Rotamer: Outliers : 2.10 % Allowed : 12.20 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.48 (0.14), residues: 3459 helix: -0.06 (0.14), residues: 1350 sheet: -1.61 (0.24), residues: 463 loop : -1.53 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 648 HIS 0.008 0.001 HIS B 842 PHE 0.032 0.002 PHE B1516 TYR 0.029 0.002 TYR B1777 ARG 0.007 0.001 ARG B1072 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 291 time to evaluate : 3.179 Fit side-chains revert: symmetry clash REVERT: A 334 LYS cc_start: 0.5976 (tptt) cc_final: 0.5206 (mmtt) REVERT: A 338 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7908 (tptm) REVERT: A 352 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7791 (mp) REVERT: A 712 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.6270 (mtm110) REVERT: A 799 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8206 (tm) REVERT: A 1043 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7134 (pm20) REVERT: A 1052 MET cc_start: 0.8612 (mmm) cc_final: 0.8000 (mmm) REVERT: A 1261 LYS cc_start: 0.5490 (mttp) cc_final: 0.4673 (ttmt) REVERT: A 1707 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7411 (tttt) REVERT: B 329 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6911 (mtp180) REVERT: B 387 MET cc_start: 0.3177 (tpp) cc_final: 0.2429 (mpp) REVERT: B 815 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.7232 (Cg_endo) REVERT: B 850 MET cc_start: 0.7516 (mmm) cc_final: 0.7299 (mmm) REVERT: B 1160 ASP cc_start: 0.7618 (m-30) cc_final: 0.7353 (m-30) REVERT: B 1387 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7597 (mttm) REVERT: B 1617 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5248 (mtt) REVERT: B 1773 GLU cc_start: 0.4226 (mt-10) cc_final: 0.3546 (mt-10) REVERT: B 1791 MET cc_start: 0.5022 (mpt) cc_final: 0.4342 (mpp) outliers start: 63 outliers final: 24 residues processed: 326 average time/residue: 1.4339 time to fit residues: 548.1084 Evaluate side-chains 290 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 329 ARG Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1387 LYS Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1631 VAL Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1810 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 334 optimal weight: 0.0060 chunk 165 optimal weight: 6.9990 chunk 299 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN A 782 ASN A 918 GLN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 818 GLN ** B 842 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN B1066 HIS B1184 ASN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1839 ASN B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27979 Z= 0.288 Angle : 0.669 12.381 37909 Z= 0.345 Chirality : 0.047 0.238 4222 Planarity : 0.005 0.050 4878 Dihedral : 5.526 91.294 3728 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.00 % Favored : 92.68 % Rotamer: Outliers : 3.37 % Allowed : 13.03 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.61 % 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: -1.50 (0.14), residues: 3459 helix: -0.14 (0.14), residues: 1355 sheet: -1.72 (0.24), residues: 462 loop : -1.45 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 648 HIS 0.009 0.001 HIS A1145 PHE 0.034 0.002 PHE B1516 TYR 0.026 0.002 TYR B1777 ARG 0.014 0.001 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 277 time to evaluate : 2.713 Fit side-chains REVERT: A 334 LYS cc_start: 0.6060 (tptt) cc_final: 0.5230 (mmtt) REVERT: A 352 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 396 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 439 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8165 (ptp) REVERT: A 712 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6229 (mtm110) REVERT: A 799 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8230 (tm) REVERT: A 1043 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: A 1116 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7757 (mttp) REVERT: A 1261 LYS cc_start: 0.5588 (mttp) cc_final: 0.4664 (ttmt) REVERT: A 1518 LYS cc_start: 0.6199 (pmtt) cc_final: 0.5361 (mmtt) REVERT: A 1526 LEU cc_start: 0.8003 (tp) cc_final: 0.7714 (tt) REVERT: A 1635 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 1707 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7452 (tppt) REVERT: B 325 MET cc_start: 0.0886 (OUTLIER) cc_final: -0.0974 (mmp) REVERT: B 387 MET cc_start: 0.3100 (tpp) cc_final: 0.2368 (mpp) REVERT: B 685 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6568 (pp) REVERT: B 815 PRO cc_start: 0.7689 (Cg_exo) cc_final: 0.7387 (Cg_endo) REVERT: B 1160 ASP cc_start: 0.7703 (m-30) cc_final: 0.7489 (m-30) REVERT: B 1387 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7616 (mttm) REVERT: B 1617 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5280 (mtt) REVERT: B 1773 GLU cc_start: 0.4551 (mt-10) cc_final: 0.3677 (mt-10) outliers start: 101 outliers final: 41 residues processed: 347 average time/residue: 1.4721 time to fit residues: 594.8569 Evaluate side-chains 318 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 264 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1043 GLU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1164 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1672 SER Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 403 CYS Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 865 ASN Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1387 LYS Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1631 VAL Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1810 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 249 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 170 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN B 842 HIS ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27979 Z= 0.181 Angle : 0.609 12.163 37909 Z= 0.312 Chirality : 0.044 0.234 4222 Planarity : 0.004 0.046 4878 Dihedral : 5.291 90.446 3728 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.63 % Favored : 93.08 % Rotamer: Outliers : 2.27 % Allowed : 14.90 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.32 (0.14), residues: 3459 helix: 0.08 (0.14), residues: 1357 sheet: -1.60 (0.24), residues: 468 loop : -1.43 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 648 HIS 0.007 0.001 HIS B 842 PHE 0.041 0.002 PHE B 62 TYR 0.025 0.001 TYR B1777 ARG 0.010 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 292 time to evaluate : 3.219 Fit side-chains REVERT: A 334 LYS cc_start: 0.6047 (tptt) cc_final: 0.5263 (mmtt) REVERT: A 396 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7816 (pp) REVERT: A 712 ARG cc_start: 0.6614 (ptp90) cc_final: 0.6272 (mtm110) REVERT: A 799 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8196 (tm) REVERT: A 1261 LYS cc_start: 0.5287 (mttp) cc_final: 0.4533 (ttmt) REVERT: A 1354 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 1635 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8319 (tp) REVERT: A 1707 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7392 (tppt) REVERT: B 325 MET cc_start: 0.0482 (OUTLIER) cc_final: -0.0739 (mmp) REVERT: B 387 MET cc_start: 0.3112 (tpp) cc_final: 0.2228 (mpp) REVERT: B 584 MET cc_start: 0.7622 (mtm) cc_final: 0.7213 (mtm) REVERT: B 685 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6443 (pp) REVERT: B 815 PRO cc_start: 0.7452 (Cg_exo) cc_final: 0.7164 (Cg_endo) REVERT: B 850 MET cc_start: 0.7470 (mmm) cc_final: 0.7267 (mmm) REVERT: B 1160 ASP cc_start: 0.7678 (m-30) cc_final: 0.7441 (m-30) REVERT: B 1617 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4537 (mtt) REVERT: B 1773 GLU cc_start: 0.4326 (mt-10) cc_final: 0.3547 (mt-10) REVERT: B 1791 MET cc_start: 0.5139 (mpt) cc_final: 0.4400 (mpp) outliers start: 68 outliers final: 27 residues processed: 340 average time/residue: 1.4823 time to fit residues: 588.9047 Evaluate side-chains 289 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1083 ILE Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1446 VAL Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1631 VAL Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 334 optimal weight: 30.0000 chunk 277 optimal weight: 0.0670 chunk 154 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27979 Z= 0.190 Angle : 0.603 9.298 37909 Z= 0.308 Chirality : 0.044 0.346 4222 Planarity : 0.004 0.045 4878 Dihedral : 5.157 90.725 3728 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.74 % Favored : 93.00 % Rotamer: Outliers : 2.93 % Allowed : 15.33 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.22 (0.14), residues: 3459 helix: 0.19 (0.14), residues: 1357 sheet: -1.55 (0.24), residues: 470 loop : -1.39 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 648 HIS 0.005 0.001 HIS A 11 PHE 0.032 0.002 PHE B 62 TYR 0.021 0.001 TYR B1777 ARG 0.010 0.001 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 279 time to evaluate : 3.236 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: -0.2098 (OUTLIER) cc_final: -0.3389 (m-70) REVERT: A 334 LYS cc_start: 0.6016 (tptt) cc_final: 0.5275 (mmtt) REVERT: A 352 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 396 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7794 (pp) REVERT: A 712 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6380 (mtm110) REVERT: A 799 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8211 (tm) REVERT: A 901 MET cc_start: 0.7536 (tpt) cc_final: 0.6910 (tpt) REVERT: A 944 ARG cc_start: 0.7449 (ptp-110) cc_final: 0.7118 (ttm110) REVERT: A 1116 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7647 (mttp) REVERT: A 1261 LYS cc_start: 0.5314 (mttp) cc_final: 0.4550 (ttmt) REVERT: A 1354 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7074 (mm-30) REVERT: A 1518 LYS cc_start: 0.6173 (pmtt) cc_final: 0.5359 (mmtt) REVERT: A 1635 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8348 (tp) REVERT: A 1707 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7432 (tmtt) REVERT: B 325 MET cc_start: 0.0404 (OUTLIER) cc_final: -0.0801 (mmp) REVERT: B 387 MET cc_start: 0.3186 (tpp) cc_final: 0.2226 (tpp) REVERT: B 584 MET cc_start: 0.7571 (mtm) cc_final: 0.7277 (mtm) REVERT: B 685 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6659 (pp) REVERT: B 815 PRO cc_start: 0.7317 (Cg_exo) cc_final: 0.6979 (Cg_endo) REVERT: B 1160 ASP cc_start: 0.7684 (m-30) cc_final: 0.7449 (m-30) REVERT: B 1617 MET cc_start: 0.5354 (OUTLIER) cc_final: 0.3733 (mtt) REVERT: B 1791 MET cc_start: 0.4950 (mpt) cc_final: 0.3952 (mpp) outliers start: 88 outliers final: 36 residues processed: 339 average time/residue: 1.4948 time to fit residues: 593.7122 Evaluate side-chains 312 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 265 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1617 MET Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 0.0030 chunk 37 optimal weight: 0.0770 chunk 190 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 chunk 333 optimal weight: 0.0070 chunk 208 optimal weight: 0.2980 chunk 203 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 27979 Z= 0.161 Angle : 0.580 9.690 37909 Z= 0.297 Chirality : 0.043 0.225 4222 Planarity : 0.004 0.048 4878 Dihedral : 4.966 88.885 3728 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.54 % Favored : 93.20 % Rotamer: Outliers : 2.00 % Allowed : 16.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.08 (0.14), residues: 3459 helix: 0.29 (0.14), residues: 1375 sheet: -1.32 (0.25), residues: 450 loop : -1.38 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 648 HIS 0.020 0.001 HIS A 39 PHE 0.039 0.001 PHE B1449 TYR 0.020 0.001 TYR B1777 ARG 0.012 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 291 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: -0.2212 (OUTLIER) cc_final: -0.2692 (m90) REVERT: A 334 LYS cc_start: 0.6022 (tptt) cc_final: 0.5279 (mmtt) REVERT: A 396 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7750 (pp) REVERT: A 439 MET cc_start: 0.8112 (ptm) cc_final: 0.7708 (mtp) REVERT: A 712 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6527 (mtm110) REVERT: A 799 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8190 (tm) REVERT: A 944 ARG cc_start: 0.7437 (ptp-110) cc_final: 0.7136 (ttm110) REVERT: A 1052 MET cc_start: 0.8592 (mmm) cc_final: 0.8059 (mmm) REVERT: A 1261 LYS cc_start: 0.4967 (mttp) cc_final: 0.4597 (ptpt) REVERT: A 1518 LYS cc_start: 0.5990 (pmtt) cc_final: 0.5248 (mmtt) REVERT: A 1635 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8311 (tp) REVERT: B 325 MET cc_start: 0.0357 (OUTLIER) cc_final: -0.0682 (mmp) REVERT: B 387 MET cc_start: 0.3184 (tpp) cc_final: 0.2274 (mpp) REVERT: B 584 MET cc_start: 0.7422 (mtm) cc_final: 0.7138 (mtm) REVERT: B 685 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6543 (pp) REVERT: B 1791 MET cc_start: 0.4924 (mpt) cc_final: 0.3963 (mpp) REVERT: B 1892 LEU cc_start: 0.7847 (mt) cc_final: 0.7488 (mt) outliers start: 60 outliers final: 22 residues processed: 328 average time/residue: 1.4675 time to fit residues: 562.0376 Evaluate side-chains 297 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 31 optimal weight: 0.0020 chunk 262 optimal weight: 0.7980 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN B 702 GLN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 27979 Z= 0.214 Angle : 0.603 9.832 37909 Z= 0.308 Chirality : 0.045 0.225 4222 Planarity : 0.004 0.045 4878 Dihedral : 5.000 88.352 3728 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.16 % Favored : 93.58 % Rotamer: Outliers : 2.23 % Allowed : 16.93 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.07 (0.14), residues: 3459 helix: 0.29 (0.14), residues: 1365 sheet: -1.42 (0.24), residues: 462 loop : -1.30 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 648 HIS 0.005 0.001 HIS A 11 PHE 0.037 0.002 PHE B1449 TYR 0.021 0.001 TYR B1777 ARG 0.013 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 284 time to evaluate : 3.209 Fit side-chains REVERT: A 334 LYS cc_start: 0.6163 (tptt) cc_final: 0.5325 (mmtt) REVERT: A 396 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7761 (pp) REVERT: A 712 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6409 (mtm110) REVERT: A 799 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8224 (tm) REVERT: A 944 ARG cc_start: 0.7413 (ptp-110) cc_final: 0.7185 (ttm110) REVERT: A 1220 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: A 1261 LYS cc_start: 0.5351 (mttp) cc_final: 0.4570 (ttmt) REVERT: A 1518 LYS cc_start: 0.6040 (pmtt) cc_final: 0.5317 (mmtt) REVERT: A 1635 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 1728 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6295 (pt0) REVERT: B 325 MET cc_start: 0.0177 (OUTLIER) cc_final: -0.0330 (mmp) REVERT: B 329 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6946 (mtp180) REVERT: B 387 MET cc_start: 0.3211 (tpp) cc_final: 0.2270 (tpp) REVERT: B 584 MET cc_start: 0.7629 (mtm) cc_final: 0.7391 (mtm) REVERT: B 616 MET cc_start: 0.8034 (mmp) cc_final: 0.7829 (mmt) REVERT: B 1773 GLU cc_start: 0.4441 (mt-10) cc_final: 0.3629 (mt-10) REVERT: B 1791 MET cc_start: 0.4866 (mpt) cc_final: 0.3869 (mpp) REVERT: B 1892 LEU cc_start: 0.7825 (mt) cc_final: 0.7459 (mt) outliers start: 67 outliers final: 39 residues processed: 331 average time/residue: 1.4466 time to fit residues: 558.8275 Evaluate side-chains 310 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1368 THR Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1390 MET Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 6.9990 chunk 319 optimal weight: 0.5980 chunk 291 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 293 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A 969 ASN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1546 HIS A1553 ASN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN B 887 GLN ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1437 HIS B1619 ASN B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 27979 Z= 0.317 Angle : 0.690 10.977 37909 Z= 0.353 Chirality : 0.048 0.263 4222 Planarity : 0.005 0.093 4878 Dihedral : 5.388 89.805 3728 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.83 % Favored : 92.91 % Rotamer: Outliers : 2.30 % Allowed : 17.10 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.35 (0.14), residues: 3459 helix: -0.04 (0.14), residues: 1362 sheet: -1.63 (0.23), residues: 475 loop : -1.34 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 648 HIS 0.009 0.001 HIS A 11 PHE 0.033 0.002 PHE B1516 TYR 0.024 0.002 TYR B 602 ARG 0.014 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 292 time to evaluate : 3.110 Fit side-chains revert: symmetry clash REVERT: A 334 LYS cc_start: 0.6241 (tptt) cc_final: 0.5263 (mmtt) REVERT: A 396 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7902 (pp) REVERT: A 469 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7954 (tttm) REVERT: A 712 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6380 (mtm110) REVERT: A 799 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8308 (tm) REVERT: A 1116 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7772 (mttp) REVERT: A 1220 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6750 (mm-30) REVERT: A 1261 LYS cc_start: 0.5609 (mttp) cc_final: 0.4645 (ttmt) REVERT: A 1429 ARG cc_start: 0.4851 (tpt170) cc_final: 0.3863 (mmt-90) REVERT: A 1518 LYS cc_start: 0.6244 (pmtt) cc_final: 0.5465 (mmtt) REVERT: A 1635 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8387 (tp) REVERT: A 1707 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7457 (tmtt) REVERT: B 325 MET cc_start: 0.0727 (OUTLIER) cc_final: 0.0057 (mmp) REVERT: B 387 MET cc_start: 0.3318 (tpp) cc_final: 0.2275 (tpp) REVERT: B 584 MET cc_start: 0.7651 (mtm) cc_final: 0.7416 (mtm) REVERT: B 1665 MET cc_start: 0.8639 (mmp) cc_final: 0.7834 (mmp) REVERT: B 1773 GLU cc_start: 0.4781 (mt-10) cc_final: 0.3841 (mt-10) REVERT: B 1892 LEU cc_start: 0.7863 (mt) cc_final: 0.7496 (mt) outliers start: 69 outliers final: 39 residues processed: 344 average time/residue: 1.4728 time to fit residues: 592.7692 Evaluate side-chains 324 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 276 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 744 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1220 GLU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1628 VAL Chi-restraints excluded: chain A residue 1635 ILE Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1707 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain B residue 1055 ASP Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1704 LEU Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 5.9990 chunk 328 optimal weight: 0.0870 chunk 200 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 228 optimal weight: 0.0020 chunk 344 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 212 optimal weight: 0.0270 chunk 168 optimal weight: 30.0000 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 39 HIS A 339 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1619 ASN B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27979 Z= 0.173 Angle : 0.614 16.408 37909 Z= 0.309 Chirality : 0.044 0.222 4222 Planarity : 0.004 0.073 4878 Dihedral : 5.024 87.669 3728 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.11 % Favored : 93.63 % Rotamer: Outliers : 1.57 % Allowed : 18.33 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.13 (0.14), residues: 3459 helix: 0.21 (0.14), residues: 1370 sheet: -1.50 (0.24), residues: 475 loop : -1.30 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 648 HIS 0.004 0.001 HIS B 728 PHE 0.029 0.001 PHE B1516 TYR 0.022 0.001 TYR B 59 ARG 0.018 0.001 ARG A 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6918 Ramachandran restraints generated. 3459 Oldfield, 0 Emsley, 3459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 3.198 Fit side-chains revert: symmetry clash REVERT: A 334 LYS cc_start: 0.6276 (tptt) cc_final: 0.5373 (mmtt) REVERT: A 396 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7798 (pp) REVERT: A 712 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6375 (mtm110) REVERT: A 799 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8205 (tm) REVERT: A 944 ARG cc_start: 0.7419 (ptp-110) cc_final: 0.7124 (ttm110) REVERT: A 1003 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: A 1052 MET cc_start: 0.8623 (mmm) cc_final: 0.8045 (mmm) REVERT: A 1116 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7640 (mttp) REVERT: A 1261 LYS cc_start: 0.5128 (mttp) cc_final: 0.4651 (ptpt) REVERT: A 1518 LYS cc_start: 0.5909 (pmtt) cc_final: 0.5260 (mmtt) REVERT: B 387 MET cc_start: 0.3128 (tpp) cc_final: 0.2226 (tpp) REVERT: B 399 ARG cc_start: 0.4609 (mtp180) cc_final: 0.4367 (mtm180) REVERT: B 584 MET cc_start: 0.7568 (mtm) cc_final: 0.7323 (mtm) REVERT: B 1791 MET cc_start: 0.4833 (mpt) cc_final: 0.3924 (mpp) REVERT: B 1892 LEU cc_start: 0.7708 (mt) cc_final: 0.7347 (mt) outliers start: 47 outliers final: 26 residues processed: 317 average time/residue: 1.4310 time to fit residues: 531.0280 Evaluate side-chains 294 residues out of total 2999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 712 ARG Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 1003 GLN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 LYS Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1331 TYR Chi-restraints excluded: chain A residue 1332 ASP Chi-restraints excluded: chain A residue 1364 MET Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1647 SER Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1087 VAL Chi-restraints excluded: chain B residue 1329 VAL Chi-restraints excluded: chain B residue 1337 VAL Chi-restraints excluded: chain B residue 1406 CYS Chi-restraints excluded: chain B residue 1699 ASN Chi-restraints excluded: chain B residue 1754 SER Chi-restraints excluded: chain B residue 1877 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 253 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 274 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1619 ASN B1868 ASN ** B1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.239374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172941 restraints weight = 46523.505| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.07 r_work: 0.3831 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27979 Z= 0.203 Angle : 0.626 17.019 37909 Z= 0.315 Chirality : 0.045 0.276 4222 Planarity : 0.004 0.062 4878 Dihedral : 5.018 87.900 3728 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.31 % Favored : 93.40 % Rotamer: Outliers : 1.37 % Allowed : 19.00 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.09 (0.14), residues: 3459 helix: 0.26 (0.14), residues: 1365 sheet: -1.50 (0.24), residues: 472 loop : -1.29 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 648 HIS 0.005 0.001 HIS A 11 PHE 0.030 0.002 PHE B1516 TYR 0.020 0.001 TYR B1777 ARG 0.015 0.001 ARG B1576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11459.80 seconds wall clock time: 203 minutes 24.76 seconds (12204.76 seconds total)