Starting phenix.real_space_refine on Sun Mar 24 23:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3u_25671/03_2024/7t3u_25671_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 18 5.49 5 S 119 5.16 5 C 27584 2.51 5 N 8231 2.21 5 O 8541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44501 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 12132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2020, 12132 Classifications: {'peptide': 2020} Incomplete info: {'truncation_to_alanine': 1232} Link IDs: {'PTRANS': 56, 'TRANS': 1963} Chain breaks: 27 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 4452 Unresolved non-hydrogen angles: 5693 Unresolved non-hydrogen dihedrals: 3672 Unresolved non-hydrogen chiralities: 423 Planarities with less than four sites: {'GLN:plan1': 73, 'ARG:plan': 64, 'TYR:plan': 41, 'ASN:plan1': 73, 'TRP:plan': 12, 'ASP:plan': 77, 'PHE:plan': 60, 'GLU:plan': 94, 'HIS:plan': 47} Unresolved non-hydrogen planarities: 2428 Chain: "B" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1662, 10375 Classifications: {'peptide': 1662} Incomplete info: {'truncation_to_alanine': 914} Link IDs: {'PTRANS': 41, 'TRANS': 1620} Chain breaks: 23 Unresolved chain link angles: 24 Unresolved non-hydrogen bonds: 3327 Unresolved non-hydrogen angles: 4248 Unresolved non-hydrogen dihedrals: 2736 Unresolved non-hydrogen chiralities: 318 Planarities with less than four sites: {'GLN:plan1': 56, 'HIS:plan': 38, 'TYR:plan': 32, 'ASN:plan1': 45, 'TRP:plan': 6, 'ASP:plan': 58, 'PHE:plan': 46, 'GLU:plan': 76, 'ARG:plan': 50} Unresolved non-hydrogen planarities: 1831 Chain: "C" Number of atoms: 9741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1575, 9741 Classifications: {'peptide': 1575} Incomplete info: {'truncation_to_alanine': 889} Link IDs: {'PTRANS': 40, 'TRANS': 1534} Chain breaks: 19 Unresolved chain link angles: 23 Unresolved non-hydrogen bonds: 3242 Unresolved non-hydrogen angles: 4121 Unresolved non-hydrogen dihedrals: 2665 Unresolved non-hydrogen chiralities: 299 Planarities with less than four sites: {'GLN:plan1': 55, 'HIS:plan': 38, 'TYR:plan': 29, 'ASN:plan1': 47, 'TRP:plan': 4, 'ASP:plan': 60, 'PHE:plan': 44, 'GLU:plan': 73, 'ARG:plan': 51} Unresolved non-hydrogen planarities: 1781 Chain: "D" Number of atoms: 12073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2012, 12073 Classifications: {'peptide': 2012} Incomplete info: {'truncation_to_alanine': 1230} Link IDs: {'PTRANS': 56, 'TRANS': 1955} Chain breaks: 27 Unresolved chain link angles: 40 Unresolved non-hydrogen bonds: 4446 Unresolved non-hydrogen angles: 5685 Unresolved non-hydrogen dihedrals: 3668 Unresolved non-hydrogen chiralities: 422 Planarities with less than four sites: {'GLN:plan1': 73, 'ARG:plan': 64, 'TYR:plan': 41, 'ASN:plan1': 72, 'TRP:plan': 12, 'ASP:plan': 77, 'PHE:plan': 60, 'GLU:plan': 94, 'HIS:plan': 47} Unresolved non-hydrogen planarities: 2425 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11509 SG CYS A2538 110.486 132.912 90.143 1.00 61.07 S ATOM 11534 SG CYS A2541 111.392 130.302 87.522 1.00 56.20 S ATOM 21884 SG CYS B2538 121.500 106.522 89.963 1.00 41.02 S ATOM 21909 SG CYS B2541 124.217 107.618 87.436 1.00 40.94 S ATOM 31625 SG CYS C2538 147.600 117.341 89.938 1.00 52.35 S ATOM 31650 SG CYS C2541 146.663 120.200 87.489 1.00 58.20 S ATOM 43698 SG CYS D2538 136.800 143.535 89.954 1.00 65.83 S ATOM 43723 SG CYS D2541 133.997 142.564 87.449 1.00 57.15 S Time building chain proxies: 24.08, per 1000 atoms: 0.54 Number of scatterers: 44501 At special positions: 0 Unit cell: (258.336, 255.852, 173.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 119 16.00 P 18 15.00 O 8541 8.00 N 8231 7.00 C 27584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 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: 20.57 Conformation dependent library (CDL) restraints added in 10.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2701 " pdb="ZN ZN A2701 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A2701 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2541 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2538 " pdb=" ZN B2701 " pdb="ZN ZN B2701 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2701 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2538 " pdb=" ZN C2701 " pdb="ZN ZN C2701 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2701 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2538 " pdb=" ZN D2701 " pdb="ZN ZN D2701 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2701 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2538 " Number of angles added : 4 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 372 helices and 32 sheets defined 63.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.91 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 87 through 110 Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 466 through 484 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 514 through 526 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 568 through 577 removed outlier: 4.245A pdb=" N GLN A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 592 through 600 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.531A pdb=" N LEU A 637 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 720 through 740 Processing helix chain 'A' and resid 745 through 754 removed outlier: 4.807A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 854 through 872 removed outlier: 3.676A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 890 removed outlier: 3.943A pdb=" N ARG A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 997 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.832A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1122 removed outlier: 3.924A pdb=" N TYR A1107 " --> pdb=" O ASP A1103 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A1108 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A1116 " --> pdb=" O SER A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 Processing helix chain 'A' and resid 1189 through 1200 Processing helix chain 'A' and resid 1202 through 1211 Processing helix chain 'A' and resid 1219 through 1234 Processing helix chain 'A' and resid 1240 through 1253 removed outlier: 3.852A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A1250 " --> pdb=" O LEU A1246 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N HIS A1251 " --> pdb=" O HIS A1247 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A1252 " --> pdb=" O LYS A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1267 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1280 through 1293 Processing helix chain 'A' and resid 1297 through 1307 Processing helix chain 'A' and resid 1320 through 1328 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1361 through 1375 Processing helix chain 'A' and resid 1381 through 1390 Processing helix chain 'A' and resid 1393 through 1400 Processing helix chain 'A' and resid 1407 through 1416 Processing helix chain 'A' and resid 1440 through 1446 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 4.383A pdb=" N LEU A1469 " --> pdb=" O LYS A1466 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER A1470 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A1472 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU A1473 " --> pdb=" O SER A1470 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A1475 " --> pdb=" O VAL A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1495 No H-bonds generated for 'chain 'A' and resid 1492 through 1495' Processing helix chain 'A' and resid 1497 through 1504 removed outlier: 5.882A pdb=" N LEU A1502 " --> pdb=" O VAL A1498 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLN A1503 " --> pdb=" O VAL A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1509 No H-bonds generated for 'chain 'A' and resid 1506 through 1509' Processing helix chain 'A' and resid 1517 through 1527 Processing helix chain 'A' and resid 1590 through 1622 Proline residue: A1608 - end of helix removed outlier: 4.187A pdb=" N GLN A1611 " --> pdb=" O PRO A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing helix chain 'A' and resid 1633 through 1637 Processing helix chain 'A' and resid 1642 through 1654 Processing helix chain 'A' and resid 1659 through 1672 Processing helix chain 'A' and resid 1681 through 1694 removed outlier: 3.927A pdb=" N GLN A1685 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU A1686 " --> pdb=" O ARG A1682 " (cutoff:3.500A) Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1759 Processing helix chain 'A' and resid 1766 through 1778 Processing helix chain 'A' and resid 1780 through 1793 removed outlier: 4.026A pdb=" N GLU A1783 " --> pdb=" O LYS A1780 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A1786 " --> pdb=" O GLU A1783 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A1791 " --> pdb=" O VAL A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1881 Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1886 through 1893 Processing helix chain 'A' and resid 1904 through 1912 Processing helix chain 'A' and resid 1934 through 1948 removed outlier: 3.973A pdb=" N CYS A1948 " --> pdb=" O LEU A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1953 through 1960 Processing helix chain 'A' and resid 1966 through 1975 Processing helix chain 'A' and resid 1988 through 2004 removed outlier: 3.602A pdb=" N MET A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2013 through 2019 removed outlier: 4.138A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2033 Processing helix chain 'A' and resid 2046 through 2063 removed outlier: 4.042A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2070 Processing helix chain 'A' and resid 2113 through 2118 Processing helix chain 'A' and resid 2142 through 2145 Processing helix chain 'A' and resid 2149 through 2157 Processing helix chain 'A' and resid 2168 through 2190 removed outlier: 4.077A pdb=" N ASP A2173 " --> pdb=" O SER A2169 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2199 Processing helix chain 'A' and resid 2202 through 2221 Processing helix chain 'A' and resid 2262 through 2275 Processing helix chain 'A' and resid 2280 through 2302 Processing helix chain 'A' and resid 2319 through 2335 Processing helix chain 'A' and resid 2338 through 2345 removed outlier: 3.811A pdb=" N TYR A2341 " --> pdb=" O GLU A2338 " (cutoff:3.500A) Processing helix chain 'A' and resid 2348 through 2351 No H-bonds generated for 'chain 'A' and resid 2348 through 2351' Processing helix chain 'A' and resid 2354 through 2363 Processing helix chain 'A' and resid 2366 through 2389 Processing helix chain 'A' and resid 2458 through 2467 Processing helix chain 'A' and resid 2475 through 2478 Processing helix chain 'A' and resid 2490 through 2504 Processing helix chain 'A' and resid 2508 through 2536 removed outlier: 4.336A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE A2516 " --> pdb=" O ILE A2512 " (cutoff:3.500A) Processing helix chain 'A' and resid 2546 through 2548 No H-bonds generated for 'chain 'A' and resid 2546 through 2548' Processing helix chain 'A' and resid 2555 through 2558 No H-bonds generated for 'chain 'A' and resid 2555 through 2558' Processing helix chain 'A' and resid 2565 through 2575 Processing helix chain 'A' and resid 2585 through 2595 Processing helix chain 'A' and resid 2608 through 2610 No H-bonds generated for 'chain 'A' and resid 2608 through 2610' Processing helix chain 'B' and resid 437 through 461 Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 515 through 526 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 547 through 563 Processing helix chain 'B' and resid 568 through 576 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 592 through 600 removed outlier: 3.806A pdb=" N HIS B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 646 through 655 Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 720 through 739 removed outlier: 3.911A pdb=" N VAL B 725 " --> pdb=" O HIS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 754 removed outlier: 3.980A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 764 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 814 through 818 Processing helix chain 'B' and resid 829 through 845 removed outlier: 4.491A pdb=" N ASN B 832 " --> pdb=" O LYS B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 873 Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 962 through 997 removed outlier: 3.869A pdb=" N GLU B 997 " --> pdb=" O VAL B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1034 removed outlier: 3.912A pdb=" N ALA B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1053 through 1064 Processing helix chain 'B' and resid 1068 through 1092 removed outlier: 3.699A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG B1085 " --> pdb=" O HIS B1081 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN B1086 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1122 Processing helix chain 'B' and resid 1170 through 1182 Processing helix chain 'B' and resid 1189 through 1199 Processing helix chain 'B' and resid 1202 through 1210 Processing helix chain 'B' and resid 1219 through 1236 Processing helix chain 'B' and resid 1240 through 1249 removed outlier: 3.934A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1259 through 1267 Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'B' and resid 1280 through 1291 Processing helix chain 'B' and resid 1297 through 1306 Processing helix chain 'B' and resid 1320 through 1331 removed outlier: 5.800A pdb=" N ASP B1330 " --> pdb=" O THR B1326 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASP B1331 " --> pdb=" O ASN B1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 1341 through 1351 Processing helix chain 'B' and resid 1361 through 1377 Processing helix chain 'B' and resid 1381 through 1390 Processing helix chain 'B' and resid 1393 through 1401 Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1436 through 1452 removed outlier: 3.983A pdb=" N ALA B1449 " --> pdb=" O THR B1445 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG B1450 " --> pdb=" O LEU B1446 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B1451 " --> pdb=" O ASP B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1462 through 1470 Processing helix chain 'B' and resid 1472 through 1479 Processing helix chain 'B' and resid 1492 through 1509 removed outlier: 3.931A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B1498 " --> pdb=" O HIS B1494 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B1507 " --> pdb=" O GLN B1503 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B1508 " --> pdb=" O SER B1504 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B1509 " --> pdb=" O THR B1505 " (cutoff:3.500A) Processing helix chain 'B' and resid 1518 through 1531 Processing helix chain 'B' and resid 1591 through 1626 Proline residue: B1608 - end of helix removed outlier: 3.778A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Proline residue: B1624 - end of helix Processing helix chain 'B' and resid 1633 through 1639 Processing helix chain 'B' and resid 1642 through 1654 Processing helix chain 'B' and resid 1659 through 1672 Processing helix chain 'B' and resid 1680 through 1694 Processing helix chain 'B' and resid 1720 through 1730 Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1761 Processing helix chain 'B' and resid 1766 through 1775 Processing helix chain 'B' and resid 1786 through 1799 removed outlier: 3.784A pdb=" N ARG B1792 " --> pdb=" O VAL B1788 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1796 " --> pdb=" O ARG B1792 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1884 Proline residue: B1872 - end of helix removed outlier: 3.520A pdb=" N CYS B1881 " --> pdb=" O LEU B1877 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASN B1883 " --> pdb=" O LEU B1879 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N HIS B1884 " --> pdb=" O LEU B1880 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1891 Processing helix chain 'B' and resid 1903 through 1915 Processing helix chain 'B' and resid 1934 through 1948 Processing helix chain 'B' and resid 1955 through 1960 Processing helix chain 'B' and resid 1966 through 1975 removed outlier: 3.517A pdb=" N THR B1971 " --> pdb=" O ILE B1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1984 removed outlier: 3.713A pdb=" N LYS B1983 " --> pdb=" O SER B1979 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B1984 " --> pdb=" O PRO B1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1979 through 1984' Processing helix chain 'B' and resid 1987 through 2002 Processing helix chain 'B' and resid 2011 through 2019 removed outlier: 3.690A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2033 removed outlier: 3.658A pdb=" N TYR B2033 " --> pdb=" O ILE B2029 " (cutoff:3.500A) Processing helix chain 'B' and resid 2046 through 2063 removed outlier: 4.297A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2070 Processing helix chain 'B' and resid 2113 through 2120 Processing helix chain 'B' and resid 2142 through 2145 Processing helix chain 'B' and resid 2149 through 2158 Processing helix chain 'B' and resid 2168 through 2190 removed outlier: 3.990A pdb=" N ASP B2173 " --> pdb=" O SER B2169 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2199 Processing helix chain 'B' and resid 2202 through 2221 Processing helix chain 'B' and resid 2262 through 2275 Processing helix chain 'B' and resid 2280 through 2302 Processing helix chain 'B' and resid 2319 through 2335 Processing helix chain 'B' and resid 2338 through 2345 removed outlier: 3.832A pdb=" N TYR B2341 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B2342 " --> pdb=" O LEU B2339 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B2343 " --> pdb=" O PHE B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2348 through 2351 No H-bonds generated for 'chain 'B' and resid 2348 through 2351' Processing helix chain 'B' and resid 2353 through 2364 Processing helix chain 'B' and resid 2366 through 2390 Processing helix chain 'B' and resid 2458 through 2467 Processing helix chain 'B' and resid 2475 through 2478 Processing helix chain 'B' and resid 2490 through 2504 Processing helix chain 'B' and resid 2511 through 2536 removed outlier: 4.064A pdb=" N ILE B2516 " --> pdb=" O ILE B2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 2546 through 2548 No H-bonds generated for 'chain 'B' and resid 2546 through 2548' Processing helix chain 'B' and resid 2555 through 2558 No H-bonds generated for 'chain 'B' and resid 2555 through 2558' Processing helix chain 'B' and resid 2565 through 2575 Processing helix chain 'B' and resid 2580 through 2582 No H-bonds generated for 'chain 'B' and resid 2580 through 2582' Processing helix chain 'B' and resid 2585 through 2595 Processing helix chain 'C' and resid 438 through 461 removed outlier: 4.477A pdb=" N ASP C 447 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 461 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 484 Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 514 through 526 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 547 through 563 Processing helix chain 'C' and resid 568 through 577 removed outlier: 4.050A pdb=" N GLN C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 591 through 600 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 612 through 625 Processing helix chain 'C' and resid 628 through 638 Processing helix chain 'C' and resid 646 through 657 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 720 through 740 removed outlier: 3.512A pdb=" N ASN C 724 " --> pdb=" O ALA C 720 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 725 " --> pdb=" O HIS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 754 Processing helix chain 'C' and resid 757 through 764 Processing helix chain 'C' and resid 771 through 783 Processing helix chain 'C' and resid 812 through 816 removed outlier: 3.563A pdb=" N TYR C 815 " --> pdb=" O ILE C 812 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP C 816 " --> pdb=" O LYS C 813 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 812 through 816' Processing helix chain 'C' and resid 831 through 845 Processing helix chain 'C' and resid 854 through 873 Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 962 through 997 removed outlier: 3.570A pdb=" N GLU C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 993 " --> pdb=" O TYR C 989 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C 994 " --> pdb=" O LEU C 990 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 997 " --> pdb=" O VAL C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1036 Processing helix chain 'C' and resid 1053 through 1063 Processing helix chain 'C' and resid 1068 through 1081 Processing helix chain 'C' and resid 1084 through 1094 Processing helix chain 'C' and resid 1102 through 1122 Processing helix chain 'C' and resid 1169 through 1182 Processing helix chain 'C' and resid 1189 through 1200 Processing helix chain 'C' and resid 1202 through 1211 Processing helix chain 'C' and resid 1219 through 1235 Processing helix chain 'C' and resid 1240 through 1248 Processing helix chain 'C' and resid 1258 through 1268 removed outlier: 4.196A pdb=" N GLU C1262 " --> pdb=" O LEU C1258 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C1268 " --> pdb=" O MET C1264 " (cutoff:3.500A) Processing helix chain 'C' and resid 1272 through 1277 removed outlier: 4.061A pdb=" N GLU C1277 " --> pdb=" O GLN C1273 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1293 Processing helix chain 'C' and resid 1297 through 1304 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 5.813A pdb=" N ASP C1330 " --> pdb=" O THR C1326 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASP C1331 " --> pdb=" O ASN C1327 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C1332 " --> pdb=" O ALA C1328 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1352 Processing helix chain 'C' and resid 1361 through 1376 Processing helix chain 'C' and resid 1381 through 1390 Processing helix chain 'C' and resid 1393 through 1401 Processing helix chain 'C' and resid 1407 through 1419 Processing helix chain 'C' and resid 1590 through 1622 Proline residue: C1608 - end of helix Processing helix chain 'C' and resid 1624 through 1627 removed outlier: 3.961A pdb=" N LEU C1627 " --> pdb=" O PRO C1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1624 through 1627' Processing helix chain 'C' and resid 1633 through 1638 Processing helix chain 'C' and resid 1642 through 1654 Processing helix chain 'C' and resid 1659 through 1674 Processing helix chain 'C' and resid 1681 through 1694 removed outlier: 4.007A pdb=" N LEU C1686 " --> pdb=" O ARG C1682 " (cutoff:3.500A) Processing helix chain 'C' and resid 1720 through 1731 Processing helix chain 'C' and resid 1733 through 1739 removed outlier: 4.333A pdb=" N ASP C1739 " --> pdb=" O LYS C1735 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1760 Processing helix chain 'C' and resid 1766 through 1778 Processing helix chain 'C' and resid 1780 through 1797 removed outlier: 3.809A pdb=" N GLU C1783 " --> pdb=" O LYS C1780 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C1785 " --> pdb=" O SER C1782 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE C1786 " --> pdb=" O GLU C1783 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C1788 " --> pdb=" O PHE C1785 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS C1790 " --> pdb=" O LYS C1787 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP C1791 " --> pdb=" O VAL C1788 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS C1794 " --> pdb=" O ASP C1791 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG C1795 " --> pdb=" O ARG C1792 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN C1797 " --> pdb=" O LYS C1794 " (cutoff:3.500A) Processing helix chain 'C' and resid 1868 through 1881 removed outlier: 3.509A pdb=" N GLN C1871 " --> pdb=" O LEU C1868 " (cutoff:3.500A) Proline residue: C1872 - end of helix removed outlier: 3.838A pdb=" N LEU C1880 " --> pdb=" O LEU C1877 " (cutoff:3.500A) Processing helix chain 'C' and resid 1886 through 1893 Processing helix chain 'C' and resid 1903 through 1915 Processing helix chain 'C' and resid 1934 through 1948 removed outlier: 3.923A pdb=" N CYS C1948 " --> pdb=" O LEU C1944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1957 through 1960 No H-bonds generated for 'chain 'C' and resid 1957 through 1960' Processing helix chain 'C' and resid 1966 through 1975 removed outlier: 3.723A pdb=" N THR C1971 " --> pdb=" O ILE C1967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1984 removed outlier: 4.090A pdb=" N LYS C1983 " --> pdb=" O SER C1979 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C1984 " --> pdb=" O PRO C1980 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1979 through 1984' Processing helix chain 'C' and resid 1987 through 2003 Processing helix chain 'C' and resid 2011 through 2019 removed outlier: 3.567A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2033 Processing helix chain 'C' and resid 2046 through 2063 removed outlier: 4.080A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) Processing helix chain 'C' and resid 2066 through 2070 Processing helix chain 'C' and resid 2113 through 2119 Processing helix chain 'C' and resid 2142 through 2145 Processing helix chain 'C' and resid 2149 through 2157 Processing helix chain 'C' and resid 2168 through 2190 removed outlier: 4.002A pdb=" N ASP C2173 " --> pdb=" O SER C2169 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2199 Processing helix chain 'C' and resid 2202 through 2221 Processing helix chain 'C' and resid 2262 through 2275 Processing helix chain 'C' and resid 2280 through 2302 Processing helix chain 'C' and resid 2319 through 2335 Processing helix chain 'C' and resid 2343 through 2351 removed outlier: 4.945A pdb=" N ILE C2349 " --> pdb=" O PHE C2346 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C2351 " --> pdb=" O LEU C2348 " (cutoff:3.500A) Processing helix chain 'C' and resid 2354 through 2364 Processing helix chain 'C' and resid 2366 through 2389 Processing helix chain 'C' and resid 2458 through 2467 Processing helix chain 'C' and resid 2475 through 2478 Processing helix chain 'C' and resid 2490 through 2504 Processing helix chain 'C' and resid 2508 through 2536 removed outlier: 4.240A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C2516 " --> pdb=" O ILE C2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 2546 through 2548 No H-bonds generated for 'chain 'C' and resid 2546 through 2548' Processing helix chain 'C' and resid 2555 through 2558 No H-bonds generated for 'chain 'C' and resid 2555 through 2558' Processing helix chain 'C' and resid 2565 through 2575 removed outlier: 3.520A pdb=" N LEU C2569 " --> pdb=" O MET C2565 " (cutoff:3.500A) Processing helix chain 'C' and resid 2580 through 2582 No H-bonds generated for 'chain 'C' and resid 2580 through 2582' Processing helix chain 'C' and resid 2585 through 2595 Processing helix chain 'C' and resid 2608 through 2610 No H-bonds generated for 'chain 'C' and resid 2608 through 2610' Processing helix chain 'D' and resid 52 through 55 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 88 through 110 removed outlier: 4.654A pdb=" N LYS D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 514 through 526 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 547 through 563 Processing helix chain 'D' and resid 568 through 583 removed outlier: 4.118A pdb=" N GLN D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY D 579 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 600 Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 638 Processing helix chain 'D' and resid 646 through 657 Processing helix chain 'D' and resid 708 through 717 Processing helix chain 'D' and resid 720 through 740 Processing helix chain 'D' and resid 745 through 754 removed outlier: 3.655A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 764 Processing helix chain 'D' and resid 771 through 782 Processing helix chain 'D' and resid 812 through 819 removed outlier: 4.498A pdb=" N ASP D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 845 removed outlier: 3.829A pdb=" N ASN D 832 " --> pdb=" O LYS D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 873 removed outlier: 4.144A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D 860 " --> pdb=" O LYS D 856 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 861 " --> pdb=" O ASN D 857 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 862 " --> pdb=" O LYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 891 Processing helix chain 'D' and resid 962 through 997 Processing helix chain 'D' and resid 1026 through 1036 removed outlier: 3.568A pdb=" N PHE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1063 Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.831A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG D1085 " --> pdb=" O HIS D1081 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN D1086 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1122 Processing helix chain 'D' and resid 1169 through 1182 Processing helix chain 'D' and resid 1189 through 1200 Processing helix chain 'D' and resid 1202 through 1211 Processing helix chain 'D' and resid 1219 through 1235 Processing helix chain 'D' and resid 1240 through 1253 removed outlier: 3.621A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS D1251 " --> pdb=" O HIS D1247 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU D1252 " --> pdb=" O LYS D1248 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1267 Processing helix chain 'D' and resid 1272 through 1276 Processing helix chain 'D' and resid 1280 through 1291 Processing helix chain 'D' and resid 1297 through 1307 Processing helix chain 'D' and resid 1320 through 1332 removed outlier: 5.947A pdb=" N ASP D1330 " --> pdb=" O THR D1326 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP D1331 " --> pdb=" O ASN D1327 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D1332 " --> pdb=" O ALA D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1339 through 1350 Processing helix chain 'D' and resid 1361 through 1375 Processing helix chain 'D' and resid 1382 through 1390 Processing helix chain 'D' and resid 1393 through 1401 Processing helix chain 'D' and resid 1407 through 1416 Processing helix chain 'D' and resid 1437 through 1445 Processing helix chain 'D' and resid 1448 through 1452 Processing helix chain 'D' and resid 1463 through 1480 removed outlier: 3.604A pdb=" N VAL D1471 " --> pdb=" O TYR D1467 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D1473 " --> pdb=" O LEU D1469 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN D1477 " --> pdb=" O LEU D1473 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D1478 " --> pdb=" O ASP D1474 " (cutoff:3.500A) Processing helix chain 'D' and resid 1486 through 1488 No H-bonds generated for 'chain 'D' and resid 1486 through 1488' Processing helix chain 'D' and resid 1492 through 1497 removed outlier: 3.989A pdb=" N THR D1496 " --> pdb=" O GLN D1492 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1492 through 1497' Processing helix chain 'D' and resid 1501 through 1503 No H-bonds generated for 'chain 'D' and resid 1501 through 1503' Processing helix chain 'D' and resid 1505 through 1507 No H-bonds generated for 'chain 'D' and resid 1505 through 1507' Processing helix chain 'D' and resid 1516 through 1523 removed outlier: 4.399A pdb=" N SER D1521 " --> pdb=" O HIS D1518 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL D1522 " --> pdb=" O LYS D1519 " (cutoff:3.500A) Processing helix chain 'D' and resid 1528 through 1531 No H-bonds generated for 'chain 'D' and resid 1528 through 1531' Processing helix chain 'D' and resid 1591 through 1622 Proline residue: D1608 - end of helix Processing helix chain 'D' and resid 1624 through 1626 No H-bonds generated for 'chain 'D' and resid 1624 through 1626' Processing helix chain 'D' and resid 1633 through 1639 Processing helix chain 'D' and resid 1642 through 1654 Processing helix chain 'D' and resid 1659 through 1673 removed outlier: 3.767A pdb=" N LEU D1673 " --> pdb=" O LEU D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1680 through 1694 Processing helix chain 'D' and resid 1720 through 1731 Processing helix chain 'D' and resid 1733 through 1743 Processing helix chain 'D' and resid 1747 through 1761 Processing helix chain 'D' and resid 1766 through 1778 Processing helix chain 'D' and resid 1780 through 1799 removed outlier: 5.019A pdb=" N PHE D1786 " --> pdb=" O GLU D1783 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP D1791 " --> pdb=" O VAL D1788 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS D1794 " --> pdb=" O ASP D1791 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D1795 " --> pdb=" O ARG D1792 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D1797 " --> pdb=" O LYS D1794 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN D1798 " --> pdb=" O ARG D1795 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1884 Proline residue: D1872 - end of helix removed outlier: 5.783A pdb=" N ASN D1883 " --> pdb=" O LEU D1879 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS D1884 " --> pdb=" O LEU D1880 " (cutoff:3.500A) Processing helix chain 'D' and resid 1886 through 1893 Processing helix chain 'D' and resid 1904 through 1915 Processing helix chain 'D' and resid 1934 through 1948 removed outlier: 3.588A pdb=" N THR D1940 " --> pdb=" O LEU D1936 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS D1948 " --> pdb=" O LEU D1944 " (cutoff:3.500A) Processing helix chain 'D' and resid 1957 through 1960 No H-bonds generated for 'chain 'D' and resid 1957 through 1960' Processing helix chain 'D' and resid 1966 through 1974 removed outlier: 3.825A pdb=" N ILE D1974 " --> pdb=" O ILE D1970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2004 removed outlier: 3.558A pdb=" N MET D2004 " --> pdb=" O LEU D2000 " (cutoff:3.500A) Processing helix chain 'D' and resid 2012 through 2019 removed outlier: 3.790A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2033 Processing helix chain 'D' and resid 2046 through 2063 removed outlier: 4.156A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) Processing helix chain 'D' and resid 2065 through 2070 Processing helix chain 'D' and resid 2113 through 2120 Processing helix chain 'D' and resid 2142 through 2146 Processing helix chain 'D' and resid 2149 through 2157 Processing helix chain 'D' and resid 2168 through 2190 removed outlier: 4.089A pdb=" N ASP D2173 " --> pdb=" O SER D2169 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2192 through 2199 Processing helix chain 'D' and resid 2202 through 2221 Processing helix chain 'D' and resid 2262 through 2275 Processing helix chain 'D' and resid 2280 through 2302 Processing helix chain 'D' and resid 2319 through 2335 Processing helix chain 'D' and resid 2338 through 2351 removed outlier: 3.521A pdb=" N ILE D2343 " --> pdb=" O PHE D2340 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D2351 " --> pdb=" O LEU D2348 " (cutoff:3.500A) Processing helix chain 'D' and resid 2353 through 2363 Processing helix chain 'D' and resid 2366 through 2390 Processing helix chain 'D' and resid 2458 through 2467 Processing helix chain 'D' and resid 2476 through 2478 No H-bonds generated for 'chain 'D' and resid 2476 through 2478' Processing helix chain 'D' and resid 2490 through 2504 Processing helix chain 'D' and resid 2508 through 2536 removed outlier: 4.257A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE D2516 " --> pdb=" O ILE D2512 " (cutoff:3.500A) Processing helix chain 'D' and resid 2546 through 2548 No H-bonds generated for 'chain 'D' and resid 2546 through 2548' Processing helix chain 'D' and resid 2555 through 2561 Processing helix chain 'D' and resid 2565 through 2576 Processing helix chain 'D' and resid 2580 through 2582 No H-bonds generated for 'chain 'D' and resid 2580 through 2582' Processing helix chain 'D' and resid 2585 through 2595 Processing helix chain 'D' and resid 2608 through 2610 No H-bonds generated for 'chain 'D' and resid 2608 through 2610' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.866A pdb=" N ASN A 222 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 17 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 57 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 429 through 433 removed outlier: 3.650A pdb=" N VAL A 241 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 252 through 257 Processing sheet with id= F, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= G, first strand: chain 'A' and resid 367 through 370 Processing sheet with id= H, first strand: chain 'A' and resid 397 through 399 Processing sheet with id= I, first strand: chain 'A' and resid 667 through 670 Processing sheet with id= J, first strand: chain 'A' and resid 2121 through 2124 Processing sheet with id= K, first strand: chain 'A' and resid 2396 through 2398 Processing sheet with id= L, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.752A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 693 through 695 removed outlier: 4.101A pdb=" N LEU B 694 " --> pdb=" O LYS B 706 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 706 " --> pdb=" O LEU B 694 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 2121 through 2124 Processing sheet with id= O, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id= P, first strand: chain 'C' and resid 667 through 671 Processing sheet with id= Q, first strand: chain 'C' and resid 2121 through 2124 Processing sheet with id= R, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id= S, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.836A pdb=" N PHE D 25 " --> pdb=" O GLU D 39 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 57 through 61 Processing sheet with id= U, first strand: chain 'D' and resid 132 through 135 Processing sheet with id= V, first strand: chain 'D' and resid 163 through 165 Processing sheet with id= W, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= X, first strand: chain 'D' and resid 242 through 245 Processing sheet with id= Y, first strand: chain 'D' and resid 252 through 257 Processing sheet with id= Z, first strand: chain 'D' and resid 283 through 286 Processing sheet with id= AA, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= AB, first strand: chain 'D' and resid 368 through 370 Processing sheet with id= AC, first strand: chain 'D' and resid 397 through 400 Processing sheet with id= AD, first strand: chain 'D' and resid 667 through 670 removed outlier: 4.061A pdb=" N ARG D 667 " --> pdb=" O THR D 695 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 2121 through 2124 Processing sheet with id= AF, first strand: chain 'D' and resid 2396 through 2398 3083 hydrogen bonds defined for protein. 8586 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: 22.11 Time building geometry restraints manager: 21.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16062 1.34 - 1.46: 9276 1.46 - 1.58: 19274 1.58 - 1.70: 22 1.70 - 1.82: 184 Bond restraints: 44818 Sorted by residual: bond pdb=" O4 I3P D2702 " pdb=" P4 I3P D2702 " ideal model delta sigma weight residual 1.697 1.648 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O4 I3P A2702 " pdb=" P4 I3P A2702 " ideal model delta sigma weight residual 1.697 1.648 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" O5 I3P A2702 " pdb=" P5 I3P A2702 " ideal model delta sigma weight residual 1.695 1.648 0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" O5 I3P D2702 " pdb=" P5 I3P D2702 " ideal model delta sigma weight residual 1.695 1.648 0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" O1 I3P D2702 " pdb=" P1 I3P D2702 " ideal model delta sigma weight residual 1.691 1.647 0.044 2.00e-02 2.50e+03 4.84e+00 ... (remaining 44813 not shown) Histogram of bond angle deviations from ideal: 98.73 - 106.96: 620 106.96 - 115.19: 27121 115.19 - 123.43: 33250 123.43 - 131.66: 501 131.66 - 139.89: 32 Bond angle restraints: 61524 Sorted by residual: angle pdb=" C ASP B 742 " pdb=" CA ASP B 742 " pdb=" CB ASP B 742 " ideal model delta sigma weight residual 117.23 111.38 5.85 1.36e+00 5.41e-01 1.85e+01 angle pdb=" N VAL A2577 " pdb=" CA VAL A2577 " pdb=" C VAL A2577 " ideal model delta sigma weight residual 113.20 109.74 3.46 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CA GLN A2066 " pdb=" CB GLN A2066 " pdb=" CG GLN A2066 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 angle pdb=" N ILE B2479 " pdb=" CA ILE B2479 " pdb=" C ILE B2479 " ideal model delta sigma weight residual 112.96 109.84 3.12 1.00e+00 1.00e+00 9.71e+00 angle pdb=" N ILE C1869 " pdb=" CA ILE C1869 " pdb=" C ILE C1869 " ideal model delta sigma weight residual 112.29 109.48 2.81 9.40e-01 1.13e+00 8.93e+00 ... (remaining 61519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.48: 25732 22.48 - 44.96: 895 44.96 - 67.45: 118 67.45 - 89.93: 27 89.93 - 112.41: 16 Dihedral angle restraints: 26788 sinusoidal: 5531 harmonic: 21257 Sorted by residual: dihedral pdb=" CB CYS A2455 " pdb=" SG CYS A2455 " pdb=" SG CYS A2461 " pdb=" CB CYS A2461 " ideal model delta sinusoidal sigma weight residual 93.00 161.52 -68.52 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS B2455 " pdb=" SG CYS B2455 " pdb=" SG CYS B2461 " pdb=" CB CYS B2461 " ideal model delta sinusoidal sigma weight residual 93.00 160.38 -67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS D2455 " pdb=" SG CYS D2455 " pdb=" SG CYS D2461 " pdb=" CB CYS D2461 " ideal model delta sinusoidal sigma weight residual 93.00 159.71 -66.71 1 1.00e+01 1.00e-02 5.80e+01 ... (remaining 26785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 6907 0.059 - 0.117: 992 0.117 - 0.176: 38 0.176 - 0.234: 0 0.234 - 0.293: 12 Chirality restraints: 7949 Sorted by residual: chirality pdb=" C3' ATP B2702 " pdb=" C2' ATP B2702 " pdb=" C4' ATP B2702 " pdb=" O3' ATP B2702 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C3' ATP A2703 " pdb=" C2' ATP A2703 " pdb=" C4' ATP A2703 " pdb=" O3' ATP A2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C3' ATP D2703 " pdb=" C2' ATP D2703 " pdb=" C4' ATP D2703 " pdb=" O3' ATP D2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 7946 not shown) Planarity restraints: 8238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D2279 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO D2280 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D2280 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D2280 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2279 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A2280 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2280 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2280 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A2066 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" CD GLN A2066 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN A2066 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 GLN A2066 " -0.011 2.00e-02 2.50e+03 ... (remaining 8235 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 390 2.55 - 3.14: 39178 3.14 - 3.73: 71911 3.73 - 4.31: 82851 4.31 - 4.90: 138512 Nonbonded interactions: 332842 Sorted by model distance: nonbonded pdb=" OD1 ASP B1968 " pdb=" OG SER B2019 " model vdw 1.968 2.440 nonbonded pdb=" O LEU C2155 " pdb=" OG1 THR C2159 " model vdw 1.988 2.440 nonbonded pdb=" O VAL C2575 " pdb=" OH TYR C2583 " model vdw 1.991 2.440 nonbonded pdb=" O LEU D2155 " pdb=" OG1 THR D2159 " model vdw 2.040 2.440 nonbonded pdb=" O VAL D2575 " pdb=" OH TYR D2583 " model vdw 2.061 2.440 ... (remaining 332837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 289 or resid 304 through 1308 or resid 1319 thro \ ugh 1417 or resid 1436 through 1913 or resid 1926 or resid 1932 through 1975 or \ resid 1987 through 2611 or resid 2701 through 2704)) selection = (chain 'D' and (resid 5 through 1913 or resid 1916 or resid 1932 through 2006 or \ resid 2012 through 2611 or resid 2701 through 2704)) } ncs_group { reference = (chain 'B' and (resid 437 through 1305 or resid 1319 through 1420 or (resid 1589 \ through 1731 and (name N or name CA or name C or name O or name CB )) or (resid \ 1732 through 1740 and (name N or name CA or name C or name O or name CB )) or ( \ resid 1751 through 1754 and (name N or name CA or name C or name O or name CB )) \ or resid 1755 or (resid 1756 through 1762 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1763 through 1764 or (resid 1765 through 1800 and ( \ name N or name CA or name C or name O or name CB )) or resid 1865 through 2611 o \ r resid 2701 through 2703)) selection = (chain 'C' and (resid 437 through 486 or resid 503 through 1099 or resid 1101 th \ rough 1776 or resid 1783 through 1893 or resid 1902 through 2611 or resid 2701 t \ hrough 2703)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 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: 0.040 Extract box with map and model: 25.600 Check model and map are aligned: 0.820 Set scattering table: 0.450 Process input model: 137.270 Find NCS groups from input model: 4.390 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:3.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 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 : 0.002 0.049 44818 Z= 0.134 Angle : 0.454 8.610 61524 Z= 0.259 Chirality : 0.037 0.293 7949 Planarity : 0.003 0.053 8238 Dihedral : 12.943 112.409 12776 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.11), residues: 7069 helix: 2.54 (0.08), residues: 4695 sheet: -1.06 (0.31), residues: 313 loop : -1.44 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2566 HIS 0.006 0.001 HIS B2063 PHE 0.012 0.001 PHE C2340 TYR 0.015 0.001 TYR A1947 ARG 0.005 0.000 ARG C2007 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 977 time to evaluate : 4.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1992 LEU cc_start: 0.7922 (mp) cc_final: 0.7549 (tt) REVERT: A 2200 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7066 (mtt90) REVERT: A 2326 TYR cc_start: 0.7586 (t80) cc_final: 0.7194 (t80) REVERT: A 2540 ILE cc_start: 0.8398 (mm) cc_final: 0.7968 (mm) REVERT: B 1736 LEU cc_start: 0.7596 (tp) cc_final: 0.7203 (mp) REVERT: B 1925 LEU cc_start: 0.6569 (mt) cc_final: 0.5975 (pp) REVERT: B 1952 CYS cc_start: 0.8214 (t) cc_final: 0.7650 (t) REVERT: B 2012 ASN cc_start: 0.8326 (m110) cc_final: 0.8104 (m110) REVERT: B 2195 TYR cc_start: 0.8086 (t80) cc_final: 0.7552 (t80) REVERT: B 2204 TRP cc_start: 0.7692 (m100) cc_final: 0.7345 (m100) REVERT: B 2269 ILE cc_start: 0.8823 (mm) cc_final: 0.8508 (mm) REVERT: B 2326 TYR cc_start: 0.7955 (t80) cc_final: 0.7567 (t80) REVERT: B 2554 SER cc_start: 0.8371 (t) cc_final: 0.8000 (p) REVERT: C 2128 ARG cc_start: 0.6681 (mmm-85) cc_final: 0.6273 (mmm-85) REVERT: C 2182 MET cc_start: 0.7269 (mtp) cc_final: 0.6919 (mtp) REVERT: C 2557 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6231 (tm-30) REVERT: D 1744 THR cc_start: 0.8039 (t) cc_final: 0.7618 (p) REVERT: D 1783 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7386 (tt0) REVERT: D 1791 ASP cc_start: 0.7515 (m-30) cc_final: 0.7264 (t70) REVERT: D 1882 GLU cc_start: 0.7667 (tp30) cc_final: 0.7339 (tp30) REVERT: D 1890 ASN cc_start: 0.7330 (m-40) cc_final: 0.6983 (p0) REVERT: D 1901 TYR cc_start: 0.5807 (m-10) cc_final: 0.5215 (m-80) REVERT: D 1999 LEU cc_start: 0.8039 (tp) cc_final: 0.7819 (tp) REVERT: D 2017 LEU cc_start: 0.8651 (mt) cc_final: 0.8438 (mt) REVERT: D 2063 HIS cc_start: 0.7670 (m-70) cc_final: 0.7468 (m170) REVERT: D 2164 GLN cc_start: 0.7492 (mm-40) cc_final: 0.7198 (tp40) outliers start: 0 outliers final: 0 residues processed: 977 average time/residue: 0.5207 time to fit residues: 846.9853 Evaluate side-chains 715 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 715 time to evaluate : 4.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 613 optimal weight: 3.9990 chunk 550 optimal weight: 30.0000 chunk 305 optimal weight: 0.5980 chunk 187 optimal weight: 0.8980 chunk 371 optimal weight: 20.0000 chunk 293 optimal weight: 20.0000 chunk 569 optimal weight: 20.0000 chunk 220 optimal weight: 40.0000 chunk 346 optimal weight: 2.9990 chunk 423 optimal weight: 40.0000 chunk 659 optimal weight: 50.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1797 GLN A2063 HIS A2135 GLN A2210 ASN A2216 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2468 HIS A2472 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2468 HIS ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1897 ASN C1902 ASN C1939 GLN C1953 HIS C1962 HIS C2210 ASN C2292 ASN C2468 HIS D1798 GLN ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.118 44818 Z= 0.713 Angle : 0.850 17.548 61524 Z= 0.435 Chirality : 0.048 0.288 7949 Planarity : 0.005 0.065 8238 Dihedral : 6.198 85.831 7595 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 5.71 % Allowed : 15.62 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.11), residues: 7069 helix: 1.87 (0.08), residues: 4718 sheet: -1.17 (0.32), residues: 287 loop : -1.49 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C2601 HIS 0.013 0.002 HIS A1884 PHE 0.034 0.003 PHE C2390 TYR 0.034 0.003 TYR B2195 ARG 0.010 0.001 ARG D2471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 714 time to evaluate : 5.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1731 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8110 (mm-30) REVERT: A 1777 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: A 1783 GLU cc_start: 0.8522 (tp30) cc_final: 0.7746 (tp30) REVERT: A 2183 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 2201 MET cc_start: 0.9093 (tpp) cc_final: 0.8472 (tpp) REVERT: B 1730 LYS cc_start: 0.7887 (pttp) cc_final: 0.7667 (pttp) REVERT: B 1746 ASN cc_start: 0.6576 (t0) cc_final: 0.6254 (t0) REVERT: B 1765 ASN cc_start: 0.8588 (t0) cc_final: 0.7937 (t0) REVERT: B 1871 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8511 (tp40) REVERT: B 1906 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 2163 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: B 2166 SER cc_start: 0.8878 (m) cc_final: 0.8551 (m) REVERT: B 2191 MET cc_start: 0.7388 (mmm) cc_final: 0.6924 (mtm) REVERT: B 2269 ILE cc_start: 0.9089 (mm) cc_final: 0.8884 (mm) REVERT: B 2554 SER cc_start: 0.9059 (t) cc_final: 0.8748 (p) REVERT: C 2191 MET cc_start: 0.7674 (mpp) cc_final: 0.7389 (mpp) REVERT: C 2264 LEU cc_start: 0.7846 (pp) cc_final: 0.7484 (pp) REVERT: D 1726 CYS cc_start: 0.8938 (p) cc_final: 0.8697 (p) REVERT: D 1727 ARG cc_start: 0.8412 (tpt-90) cc_final: 0.8019 (tpp80) REVERT: D 1744 THR cc_start: 0.7353 (t) cc_final: 0.7135 (p) REVERT: D 1785 PHE cc_start: 0.8824 (t80) cc_final: 0.7688 (t80) REVERT: D 1890 ASN cc_start: 0.7591 (m-40) cc_final: 0.6844 (p0) REVERT: D 1902 ASN cc_start: 0.7673 (t0) cc_final: 0.7195 (t0) REVERT: D 1960 VAL cc_start: 0.7439 (m) cc_final: 0.7148 (p) REVERT: D 2026 VAL cc_start: 0.8093 (p) cc_final: 0.7790 (t) REVERT: D 2063 HIS cc_start: 0.7680 (m-70) cc_final: 0.7337 (m-70) outliers start: 136 outliers final: 90 residues processed: 807 average time/residue: 0.4881 time to fit residues: 674.1248 Evaluate side-chains 722 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 629 time to evaluate : 5.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1905 CYS Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain B residue 1719 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1741 ILE Chi-restraints excluded: chain B residue 1871 GLN Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1924 LEU Chi-restraints excluded: chain B residue 1955 ASN Chi-restraints excluded: chain B residue 2009 ASP Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2163 GLU Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2451 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2135 GLN Chi-restraints excluded: chain C residue 2152 LYS Chi-restraints excluded: chain C residue 2158 THR Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1798 GLN Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1911 LEU Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1975 LEU Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2283 ASN Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2584 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 366 optimal weight: 0.9990 chunk 204 optimal weight: 40.0000 chunk 548 optimal weight: 50.0000 chunk 448 optimal weight: 50.0000 chunk 181 optimal weight: 0.9990 chunk 660 optimal weight: 30.0000 chunk 713 optimal weight: 0.0970 chunk 588 optimal weight: 50.0000 chunk 654 optimal weight: 40.0000 chunk 225 optimal weight: 80.0000 chunk 529 optimal weight: 50.0000 overall best weight: 14.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1773 HIS A1774 ASN ** A1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2063 HIS A2164 GLN A2210 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1790 HIS B1797 GLN B1889 GLN ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1995 ASN B2210 ASN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 ASN C2051 HIS ** C2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2119 ASN C2123 GLN ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2323 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2579 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.218 44818 Z= 1.598 Angle : 1.443 25.581 61524 Z= 0.742 Chirality : 0.068 0.363 7949 Planarity : 0.008 0.100 8238 Dihedral : 7.826 78.136 7595 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.13 % Favored : 89.67 % Rotamer: Outliers : 12.59 % Allowed : 21.87 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.49 (0.10), residues: 7069 helix: -0.23 (0.07), residues: 4647 sheet: -2.10 (0.32), residues: 246 loop : -2.39 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP C2601 HIS 0.024 0.004 HIS A2153 PHE 0.064 0.006 PHE A2539 TYR 0.052 0.005 TYR D2381 ARG 0.025 0.002 ARG A2271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 605 time to evaluate : 4.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1775 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7291 (tp) REVERT: A 1777 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: A 1783 GLU cc_start: 0.8574 (tp30) cc_final: 0.8210 (tp30) REVERT: A 1898 LYS cc_start: 0.8992 (ptpt) cc_final: 0.8667 (tptt) REVERT: A 1939 GLN cc_start: 0.9626 (OUTLIER) cc_final: 0.8961 (mm-40) REVERT: A 2181 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: A 2183 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 2201 MET cc_start: 0.8874 (tpp) cc_final: 0.8304 (tpp) REVERT: A 2211 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 2374 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8494 (mp) REVERT: A 2597 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8817 (mttt) REVERT: B 1740 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 1753 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7403 (t) REVERT: B 1765 ASN cc_start: 0.8827 (t0) cc_final: 0.8378 (t0) REVERT: B 1871 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: B 1910 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8120 (t80) REVERT: B 1939 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: B 1975 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8074 (tt) REVERT: B 2021 ARG cc_start: 0.8413 (mmm160) cc_final: 0.8201 (mmm160) REVERT: B 2181 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: B 2199 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7753 (tpt90) REVERT: B 2270 LEU cc_start: 0.9084 (mt) cc_final: 0.8815 (mp) REVERT: B 2351 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8465 (ttp-110) REVERT: B 2526 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: B 2554 SER cc_start: 0.9077 (t) cc_final: 0.8824 (p) REVERT: B 2593 MET cc_start: 0.8418 (mtt) cc_final: 0.8182 (mtt) REVERT: C 1901 TYR cc_start: 0.3949 (m-80) cc_final: 0.3392 (m-80) REVERT: C 1939 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: C 2056 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7773 (tt) REVERT: C 2135 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 2154 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8830 (mtm110) REVERT: C 2191 MET cc_start: 0.7543 (mpp) cc_final: 0.6448 (mpp) REVERT: C 2611 VAL cc_start: 0.7925 (t) cc_final: 0.7718 (p) REVERT: D 1785 PHE cc_start: 0.8806 (t80) cc_final: 0.8098 (t80) REVERT: D 2021 ARG cc_start: 0.7487 (mmm160) cc_final: 0.7269 (mmm160) REVERT: D 2155 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9238 (tt) REVERT: D 2497 ASP cc_start: 0.8138 (m-30) cc_final: 0.7842 (m-30) outliers start: 300 outliers final: 208 residues processed: 834 average time/residue: 0.4885 time to fit residues: 705.0210 Evaluate side-chains 797 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 569 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1724 THR Chi-restraints excluded: chain A residue 1731 GLU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1928 TYR Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1939 GLN Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 1997 SER Chi-restraints excluded: chain A residue 2004 MET Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2143 ILE Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2157 THR Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2274 TYR Chi-restraints excluded: chain A residue 2275 TYR Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2291 THR Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2329 THR Chi-restraints excluded: chain A residue 2334 LEU Chi-restraints excluded: chain A residue 2342 SER Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2518 ASP Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2550 ASN Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2558 HIS Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1740 LEU Chi-restraints excluded: chain B residue 1741 ILE Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1753 SER Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1790 HIS Chi-restraints excluded: chain B residue 1871 GLN Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1887 ASP Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1910 PHE Chi-restraints excluded: chain B residue 1939 GLN Chi-restraints excluded: chain B residue 1955 ASN Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1967 ILE Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2140 VAL Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2181 GLU Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2331 VAL Chi-restraints excluded: chain B residue 2351 ARG Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain B residue 2532 GLU Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2543 LEU Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1939 GLN Chi-restraints excluded: chain C residue 1940 THR Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1952 CYS Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2056 LEU Chi-restraints excluded: chain C residue 2058 LEU Chi-restraints excluded: chain C residue 2067 LEU Chi-restraints excluded: chain C residue 2119 ASN Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2135 GLN Chi-restraints excluded: chain C residue 2150 GLU Chi-restraints excluded: chain C residue 2154 ARG Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2158 THR Chi-restraints excluded: chain C residue 2188 LEU Chi-restraints excluded: chain C residue 2202 THR Chi-restraints excluded: chain C residue 2207 ILE Chi-restraints excluded: chain C residue 2284 ILE Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2301 VAL Chi-restraints excluded: chain C residue 2324 VAL Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2390 PHE Chi-restraints excluded: chain C residue 2391 LEU Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2536 THR Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2559 ILE Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2598 ASN Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1760 LEU Chi-restraints excluded: chain D residue 1783 GLU Chi-restraints excluded: chain D residue 1791 ASP Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1988 LEU Chi-restraints excluded: chain D residue 1993 LYS Chi-restraints excluded: chain D residue 2023 GLN Chi-restraints excluded: chain D residue 2028 VAL Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2175 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2282 LEU Chi-restraints excluded: chain D residue 2283 ASN Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2328 LEU Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2330 SER Chi-restraints excluded: chain D residue 2331 VAL Chi-restraints excluded: chain D residue 2332 LEU Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2343 ILE Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2372 THR Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2391 LEU Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2498 LEU Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2507 ILE Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2533 ILE Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2558 HIS Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2584 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 652 optimal weight: 40.0000 chunk 496 optimal weight: 0.8980 chunk 342 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 315 optimal weight: 0.8980 chunk 443 optimal weight: 50.0000 chunk 662 optimal weight: 5.9990 chunk 701 optimal weight: 0.9990 chunk 346 optimal weight: 0.6980 chunk 628 optimal weight: 50.0000 chunk 189 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2164 GLN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 ASN B2216 ASN B2323 HIS B2468 HIS ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1883 ASN C2051 HIS C2066 GLN C2323 HIS ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 HIS ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44818 Z= 0.189 Angle : 0.542 10.038 61524 Z= 0.290 Chirality : 0.039 0.238 7949 Planarity : 0.004 0.068 8238 Dihedral : 5.814 65.794 7595 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.61 % Allowed : 27.88 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.10), residues: 7069 helix: 1.30 (0.08), residues: 4712 sheet: -1.95 (0.29), residues: 317 loop : -1.93 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B2184 HIS 0.017 0.001 HIS C2051 PHE 0.021 0.002 PHE C1910 TYR 0.033 0.002 TYR C2054 ARG 0.008 0.001 ARG A2524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 679 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1777 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7747 (mmm) REVERT: A 1783 GLU cc_start: 0.8237 (tp30) cc_final: 0.7717 (tp30) REVERT: A 1898 LYS cc_start: 0.8772 (ptpt) cc_final: 0.8350 (mmtm) REVERT: A 2014 GLU cc_start: 0.6474 (pm20) cc_final: 0.6132 (pm20) REVERT: A 2063 HIS cc_start: 0.7692 (m-70) cc_final: 0.7419 (m170) REVERT: A 2183 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 2556 GLU cc_start: 0.8482 (tp30) cc_final: 0.8267 (tp30) REVERT: A 2597 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8652 (mttp) REVERT: B 1975 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7986 (tt) REVERT: B 2153 HIS cc_start: 0.8351 (t-90) cc_final: 0.8134 (t-90) REVERT: B 2199 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7666 (tpm170) REVERT: B 2201 MET cc_start: 0.7452 (ttt) cc_final: 0.7222 (ttt) REVERT: B 2270 LEU cc_start: 0.8830 (mt) cc_final: 0.8594 (mp) REVERT: B 2526 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: B 2554 SER cc_start: 0.9014 (t) cc_final: 0.8717 (p) REVERT: B 2593 MET cc_start: 0.8226 (mtt) cc_final: 0.7975 (mtt) REVERT: C 1875 ARG cc_start: 0.6194 (tpm170) cc_final: 0.5920 (tpt170) REVERT: C 1901 TYR cc_start: 0.3259 (m-80) cc_final: 0.2821 (m-10) REVERT: C 2133 MET cc_start: 0.8035 (mmm) cc_final: 0.7746 (mmm) REVERT: C 2154 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8808 (ttp80) REVERT: C 2188 LEU cc_start: 0.8673 (tt) cc_final: 0.8449 (tt) REVERT: C 2191 MET cc_start: 0.7206 (mpp) cc_final: 0.6734 (mpp) REVERT: D 1785 PHE cc_start: 0.8771 (t80) cc_final: 0.7657 (t80) REVERT: D 1960 VAL cc_start: 0.7942 (m) cc_final: 0.7730 (p) REVERT: D 2017 LEU cc_start: 0.8136 (mp) cc_final: 0.7895 (mt) REVERT: D 2033 TYR cc_start: 0.7330 (t80) cc_final: 0.7078 (t80) outliers start: 86 outliers final: 54 residues processed: 736 average time/residue: 0.5064 time to fit residues: 635.2130 Evaluate side-chains 668 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 610 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1777 MET Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1953 HIS Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2288 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 2273 ILE Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2354 THR Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1955 ASN Chi-restraints excluded: chain C residue 2056 LEU Chi-restraints excluded: chain C residue 2154 ARG Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1993 LYS Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2506 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 584 optimal weight: 50.0000 chunk 398 optimal weight: 10.0000 chunk 10 optimal weight: 50.0000 chunk 522 optimal weight: 10.0000 chunk 289 optimal weight: 50.0000 chunk 598 optimal weight: 50.0000 chunk 485 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 358 optimal weight: 0.0980 chunk 629 optimal weight: 50.0000 chunk 177 optimal weight: 1.9990 overall best weight: 8.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1955 ASN A2164 GLN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1798 GLN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.129 44818 Z= 0.968 Angle : 0.994 18.731 61524 Z= 0.509 Chirality : 0.052 0.281 7949 Planarity : 0.006 0.084 8238 Dihedral : 6.480 69.798 7595 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.62 % Favored : 91.30 % Rotamer: Outliers : 10.41 % Allowed : 26.78 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.10), residues: 7069 helix: 0.75 (0.08), residues: 4684 sheet: -2.17 (0.31), residues: 275 loop : -2.18 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A2204 HIS 0.014 0.003 HIS A2153 PHE 0.042 0.004 PHE C2390 TYR 0.047 0.003 TYR C2054 ARG 0.009 0.001 ARG B1886 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 572 time to evaluate : 4.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1731 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 1775 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7737 (tp) REVERT: A 1783 GLU cc_start: 0.8344 (tp30) cc_final: 0.7879 (tp30) REVERT: A 1898 LYS cc_start: 0.8898 (ptpt) cc_final: 0.8506 (mmtm) REVERT: A 1955 ASN cc_start: 0.9303 (OUTLIER) cc_final: 0.9064 (m-40) REVERT: A 2066 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8542 (tp40) REVERT: A 2181 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8349 (tp30) REVERT: A 2211 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 2374 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8601 (mp) REVERT: A 2524 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7795 (ttp-170) REVERT: B 1760 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8010 (mp) REVERT: B 1975 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 2199 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7898 (tpt90) REVERT: B 2270 LEU cc_start: 0.8945 (mt) cc_final: 0.8745 (mp) REVERT: B 2526 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: B 2593 MET cc_start: 0.8313 (mtt) cc_final: 0.7985 (mtt) REVERT: C 1901 TYR cc_start: 0.3051 (m-80) cc_final: 0.2701 (m-10) REVERT: C 1939 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: C 2181 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: C 2191 MET cc_start: 0.7469 (mpp) cc_final: 0.6284 (mpp) REVERT: D 1785 PHE cc_start: 0.8812 (t80) cc_final: 0.7749 (t80) REVERT: D 1896 ASN cc_start: 0.7952 (m110) cc_final: 0.7461 (p0) REVERT: D 2001 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 2033 TYR cc_start: 0.7490 (t80) cc_final: 0.7250 (t80) REVERT: D 2063 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7108 (t-90) REVERT: D 2203 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8353 (tt) REVERT: D 2319 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: D 2592 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7762 (tm130) outliers start: 248 outliers final: 193 residues processed: 763 average time/residue: 0.5104 time to fit residues: 670.3998 Evaluate side-chains 759 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 550 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1741 ILE Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1928 TYR Chi-restraints excluded: chain A residue 1930 ASN Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2143 ILE Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2198 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2222 PHE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2274 TYR Chi-restraints excluded: chain A residue 2275 TYR Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2278 ILE Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2526 GLU Chi-restraints excluded: chain A residue 2537 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2609 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1734 THR Chi-restraints excluded: chain B residue 1735 LYS Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1798 GLN Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1940 THR Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 1955 ASN Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1961 THR Chi-restraints excluded: chain B residue 1973 LEU Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2526 GLU Chi-restraints excluded: chain B residue 2543 LEU Chi-restraints excluded: chain B residue 2558 HIS Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain C residue 1879 LEU Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1939 GLN Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1945 THR Chi-restraints excluded: chain C residue 1989 VAL Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2056 LEU Chi-restraints excluded: chain C residue 2124 ILE Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2150 GLU Chi-restraints excluded: chain C residue 2158 THR Chi-restraints excluded: chain C residue 2181 GLU Chi-restraints excluded: chain C residue 2189 ARG Chi-restraints excluded: chain C residue 2265 ILE Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2338 GLU Chi-restraints excluded: chain C residue 2353 GLU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2382 LEU Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2485 LYS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1865 THR Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1959 ILE Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2001 LEU Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2203 LEU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2215 ILE Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2319 GLU Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2330 SER Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2478 ASP Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2499 LEU Chi-restraints excluded: chain D residue 2503 ILE Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2509 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2536 THR Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2553 VAL Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2592 GLN Chi-restraints excluded: chain D residue 2609 SER Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 236 optimal weight: 70.0000 chunk 631 optimal weight: 50.0000 chunk 138 optimal weight: 0.7980 chunk 412 optimal weight: 50.0000 chunk 173 optimal weight: 4.9990 chunk 702 optimal weight: 0.8980 chunk 583 optimal weight: 50.0000 chunk 325 optimal weight: 0.5980 chunk 58 optimal weight: 50.0000 chunk 232 optimal weight: 50.0000 chunk 368 optimal weight: 50.0000 overall best weight: 11.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1955 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1790 HIS ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2323 HIS ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2179 HIS C2337 HIS ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.8513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.183 44818 Z= 1.281 Angle : 1.210 21.714 61524 Z= 0.621 Chirality : 0.059 0.323 7949 Planarity : 0.007 0.081 8238 Dihedral : 7.309 86.409 7595 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.69 % Favored : 89.26 % Rotamer: Outliers : 12.97 % Allowed : 26.70 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.01 % 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: -1.49 (0.10), residues: 7069 helix: -0.14 (0.07), residues: 4644 sheet: -2.43 (0.31), residues: 245 loop : -2.57 (0.13), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A2204 HIS 0.015 0.003 HIS D1884 PHE 0.054 0.004 PHE A2539 TYR 0.058 0.004 TYR C2054 ARG 0.012 0.001 ARG C2128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 560 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1775 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8035 (tt) REVERT: A 1783 GLU cc_start: 0.8433 (tp30) cc_final: 0.8103 (tp30) REVERT: A 1898 LYS cc_start: 0.8984 (ptpt) cc_final: 0.8665 (mmtm) REVERT: A 2066 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.8884 (tp40) REVERT: A 2181 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: A 2211 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8681 (mp) REVERT: A 2352 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7486 (mt-10) REVERT: B 1753 SER cc_start: 0.7774 (OUTLIER) cc_final: 0.7362 (t) REVERT: B 1760 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7981 (mp) REVERT: B 1939 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8346 (tm-30) REVERT: B 1975 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 2021 ARG cc_start: 0.8366 (mmm160) cc_final: 0.8087 (mmm160) REVERT: B 2199 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7989 (tpt90) REVERT: B 2351 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8505 (ttp-110) REVERT: B 2593 MET cc_start: 0.8386 (mtt) cc_final: 0.8114 (mtt) REVERT: B 2604 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.7983 (tpp80) REVERT: C 1938 ILE cc_start: 0.7515 (mt) cc_final: 0.7189 (pt) REVERT: C 2016 ILE cc_start: 0.8069 (mm) cc_final: 0.7742 (mt) REVERT: C 2181 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: C 2191 MET cc_start: 0.7540 (mpp) cc_final: 0.6392 (mpp) REVERT: D 1777 MET cc_start: 0.7669 (ppp) cc_final: 0.7022 (tpp) REVERT: D 1785 PHE cc_start: 0.8845 (t80) cc_final: 0.7806 (t80) REVERT: D 1901 TYR cc_start: 0.7684 (m-80) cc_final: 0.7112 (m-80) REVERT: D 2001 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8567 (mm) REVERT: D 2021 ARG cc_start: 0.7512 (mmm160) cc_final: 0.7186 (mmm160) REVERT: D 2063 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7308 (t-90) REVERT: D 2155 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9280 (tt) REVERT: D 2203 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8339 (tt) REVERT: D 2497 ASP cc_start: 0.8252 (m-30) cc_final: 0.8005 (m-30) REVERT: D 2550 ASN cc_start: 0.8725 (t0) cc_final: 0.8514 (t0) outliers start: 309 outliers final: 248 residues processed: 810 average time/residue: 0.5393 time to fit residues: 761.4149 Evaluate side-chains 807 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 545 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1731 GLU Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1741 ILE Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1800 THR Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2055 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2143 ILE Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2157 THR Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2168 VAL Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2181 GLU Chi-restraints excluded: chain A residue 2198 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2222 PHE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2275 TYR Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2471 ARG Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2518 ASP Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2590 VAL Chi-restraints excluded: chain A residue 2609 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1731 GLU Chi-restraints excluded: chain B residue 1734 THR Chi-restraints excluded: chain B residue 1735 LYS Chi-restraints excluded: chain B residue 1753 SER Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1765 ASN Chi-restraints excluded: chain B residue 1770 LYS Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1790 HIS Chi-restraints excluded: chain B residue 1798 GLN Chi-restraints excluded: chain B residue 1869 ILE Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1939 GLN Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 1955 ASN Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1961 THR Chi-restraints excluded: chain B residue 1973 LEU Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2067 LEU Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2122 SER Chi-restraints excluded: chain B residue 2132 SER Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2175 SER Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2330 SER Chi-restraints excluded: chain B residue 2331 VAL Chi-restraints excluded: chain B residue 2351 ARG Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2508 VAL Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2532 GLU Chi-restraints excluded: chain B residue 2543 LEU Chi-restraints excluded: chain B residue 2558 HIS Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain C residue 1881 CYS Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1894 CYS Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1945 THR Chi-restraints excluded: chain C residue 1973 LEU Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 1989 VAL Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2150 GLU Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2158 THR Chi-restraints excluded: chain C residue 2178 LEU Chi-restraints excluded: chain C residue 2181 GLU Chi-restraints excluded: chain C residue 2189 ARG Chi-restraints excluded: chain C residue 2284 ILE Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2294 ILE Chi-restraints excluded: chain C residue 2301 VAL Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2329 THR Chi-restraints excluded: chain C residue 2330 SER Chi-restraints excluded: chain C residue 2338 GLU Chi-restraints excluded: chain C residue 2353 GLU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2485 LYS Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2519 THR Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2532 GLU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2536 THR Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2594 ILE Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1760 LEU Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1865 THR Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1908 LEU Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1933 ASN Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 1993 LYS Chi-restraints excluded: chain D residue 2001 LEU Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2067 LEU Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2175 SER Chi-restraints excluded: chain D residue 2203 LEU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2215 ILE Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2294 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2330 SER Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2368 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2476 VAL Chi-restraints excluded: chain D residue 2478 ASP Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2509 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2536 THR Chi-restraints excluded: chain D residue 2553 VAL Chi-restraints excluded: chain D residue 2558 HIS Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2577 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2592 GLN Chi-restraints excluded: chain D residue 2609 SER Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 677 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 400 optimal weight: 40.0000 chunk 512 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 591 optimal weight: 50.0000 chunk 392 optimal weight: 50.0000 chunk 699 optimal weight: 0.8980 chunk 437 optimal weight: 20.0000 chunk 426 optimal weight: 50.0000 chunk 323 optimal weight: 3.9990 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1955 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1751 GLN B1790 HIS B1798 GLN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1871 GLN ** C1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.8545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.104 44818 Z= 0.701 Angle : 0.830 14.774 61524 Z= 0.426 Chirality : 0.046 0.285 7949 Planarity : 0.005 0.075 8238 Dihedral : 6.331 75.302 7595 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.51 % Favored : 92.47 % Rotamer: Outliers : 10.71 % Allowed : 29.30 % Favored : 59.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.10), residues: 7069 helix: 0.51 (0.08), residues: 4688 sheet: -2.55 (0.29), residues: 276 loop : -2.42 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D2601 HIS 0.011 0.002 HIS B1790 PHE 0.029 0.003 PHE C2390 TYR 0.025 0.002 TYR C2583 ARG 0.006 0.001 ARG B2062 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 586 time to evaluate : 5.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1775 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 1783 GLU cc_start: 0.8323 (tp30) cc_final: 0.8011 (tp30) REVERT: A 1898 LYS cc_start: 0.8964 (ptpt) cc_final: 0.8594 (mmtm) REVERT: A 1955 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.9020 (m-40) REVERT: A 2066 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8695 (tp-100) REVERT: A 2211 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8646 (mp) REVERT: A 2351 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7962 (ttt-90) REVERT: A 2374 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 1753 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7126 (t) REVERT: B 1760 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8049 (mp) REVERT: B 1939 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B 1975 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8398 (tt) REVERT: B 2021 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7923 (mmm160) REVERT: B 2199 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7778 (tpm170) REVERT: C 1903 LEU cc_start: 0.7833 (pp) cc_final: 0.7629 (pp) REVERT: C 1938 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7014 (pt) REVERT: C 2023 GLN cc_start: 0.6254 (tp-100) cc_final: 0.5368 (pm20) REVERT: C 2191 MET cc_start: 0.7357 (mpp) cc_final: 0.6973 (mpp) REVERT: D 1727 ARG cc_start: 0.7140 (ptm160) cc_final: 0.6878 (ptm-80) REVERT: D 1777 MET cc_start: 0.7727 (ppp) cc_final: 0.7142 (tpp) REVERT: D 1785 PHE cc_start: 0.8836 (t80) cc_final: 0.8140 (t80) REVERT: D 1901 TYR cc_start: 0.7403 (m-80) cc_final: 0.6699 (m-80) REVERT: D 2001 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (mm) REVERT: D 2033 TYR cc_start: 0.7395 (t80) cc_final: 0.7161 (t80) REVERT: D 2063 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7229 (t-90) REVERT: D 2155 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9285 (tt) REVERT: D 2203 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8343 (tt) REVERT: D 2497 ASP cc_start: 0.8171 (m-30) cc_final: 0.7872 (m-30) outliers start: 255 outliers final: 208 residues processed: 792 average time/residue: 0.4806 time to fit residues: 657.6707 Evaluate side-chains 789 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 566 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1741 ILE Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2143 ILE Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2157 THR Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2198 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2290 LEU Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2351 ARG Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2374 LEU Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2471 ARG Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2546 ASP Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2609 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1731 GLU Chi-restraints excluded: chain B residue 1735 LYS Chi-restraints excluded: chain B residue 1738 CYS Chi-restraints excluded: chain B residue 1743 SER Chi-restraints excluded: chain B residue 1753 SER Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1765 ASN Chi-restraints excluded: chain B residue 1770 LYS Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1790 HIS Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1939 GLN Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1973 LEU Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1984 TYR Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2173 ASP Chi-restraints excluded: chain B residue 2175 SER Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2222 PHE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2386 VAL Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2503 ILE Chi-restraints excluded: chain B residue 2508 VAL Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2558 HIS Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1894 CYS Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1938 ILE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1971 THR Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 1989 VAL Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2150 GLU Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2189 ARG Chi-restraints excluded: chain C residue 2265 ILE Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2338 GLU Chi-restraints excluded: chain C residue 2353 GLU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2382 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2390 PHE Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2485 LYS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2537 THR Chi-restraints excluded: chain C residue 2563 HIS Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2609 SER Chi-restraints excluded: chain D residue 1724 THR Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1865 THR Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1889 GLN Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2001 LEU Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2203 LEU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2215 ILE Chi-restraints excluded: chain D residue 2219 ILE Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2368 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2464 THR Chi-restraints excluded: chain D residue 2476 VAL Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2499 LEU Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2523 LEU Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2536 THR Chi-restraints excluded: chain D residue 2549 ASP Chi-restraints excluded: chain D residue 2553 VAL Chi-restraints excluded: chain D residue 2558 HIS Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2608 MET Chi-restraints excluded: chain D residue 2609 SER Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 432 optimal weight: 50.0000 chunk 279 optimal weight: 50.0000 chunk 417 optimal weight: 50.0000 chunk 210 optimal weight: 50.0000 chunk 137 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 444 optimal weight: 10.0000 chunk 476 optimal weight: 0.4980 chunk 345 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 550 optimal weight: 50.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1751 GLN ** B1953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1871 GLN C1956 GLN ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2598 ASN ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1900 ASN ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2550 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.8623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 44818 Z= 0.485 Angle : 0.693 14.540 61524 Z= 0.357 Chirality : 0.042 0.300 7949 Planarity : 0.004 0.075 8238 Dihedral : 5.792 65.138 7595 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 9.45 % Allowed : 30.39 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.10), residues: 7069 helix: 1.07 (0.08), residues: 4709 sheet: -2.50 (0.30), residues: 267 loop : -2.26 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D2601 HIS 0.010 0.001 HIS B1790 PHE 0.023 0.002 PHE C2177 TYR 0.026 0.002 TYR C2583 ARG 0.007 0.001 ARG B2062 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 598 time to evaluate : 5.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1775 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7868 (tt) REVERT: A 1783 GLU cc_start: 0.8338 (tp30) cc_final: 0.8049 (tp30) REVERT: A 1898 LYS cc_start: 0.8970 (ptpt) cc_final: 0.8555 (mmtm) REVERT: A 2066 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8584 (tp40) REVERT: A 2211 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 2351 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7863 (ttt-90) REVERT: A 2352 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7201 (mm-30) REVERT: B 1753 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7004 (t) REVERT: B 1760 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 1767 GLU cc_start: 0.8628 (tt0) cc_final: 0.8215 (pt0) REVERT: B 1939 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: B 1975 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 1984 TYR cc_start: 0.7054 (m-80) cc_final: 0.6691 (m-80) REVERT: B 2021 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7922 (mmm160) REVERT: B 2199 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7722 (tpm170) REVERT: B 2275 TYR cc_start: 0.7450 (t80) cc_final: 0.7099 (m-80) REVERT: B 2604 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7903 (tpp-160) REVERT: C 1903 LEU cc_start: 0.7896 (pp) cc_final: 0.7603 (pp) REVERT: C 1938 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7278 (pt) REVERT: C 2023 GLN cc_start: 0.6333 (tp-100) cc_final: 0.5507 (pm20) REVERT: C 2071 LEU cc_start: 0.6777 (mp) cc_final: 0.6401 (mt) REVERT: C 2191 MET cc_start: 0.7273 (mpp) cc_final: 0.6113 (mpp) REVERT: D 1727 ARG cc_start: 0.7064 (ptm160) cc_final: 0.6738 (ptm-80) REVERT: D 1777 MET cc_start: 0.7751 (ppp) cc_final: 0.7098 (tpp) REVERT: D 1785 PHE cc_start: 0.8839 (t80) cc_final: 0.8103 (t80) REVERT: D 1890 ASN cc_start: 0.7526 (m-40) cc_final: 0.6769 (p0) REVERT: D 1901 TYR cc_start: 0.7389 (m-80) cc_final: 0.6789 (m-80) REVERT: D 1960 VAL cc_start: 0.8024 (m) cc_final: 0.7716 (p) REVERT: D 2001 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8351 (mm) REVERT: D 2033 TYR cc_start: 0.7223 (t80) cc_final: 0.6853 (t80) REVERT: D 2063 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7119 (t-90) REVERT: D 2155 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9296 (tt) REVERT: D 2203 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8313 (tt) REVERT: D 2497 ASP cc_start: 0.8063 (m-30) cc_final: 0.7695 (m-30) REVERT: D 2550 ASN cc_start: 0.8625 (t0) cc_final: 0.8394 (t0) outliers start: 225 outliers final: 190 residues processed: 778 average time/residue: 0.5026 time to fit residues: 678.0279 Evaluate side-chains 781 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 578 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1741 ILE Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2066 GLN Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2157 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2198 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2222 PHE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2288 LEU Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2351 ARG Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2471 ARG Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2537 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2609 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1735 LYS Chi-restraints excluded: chain B residue 1743 SER Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1753 SER Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1770 LYS Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1869 ILE Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1939 GLN Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1973 LEU Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2173 ASP Chi-restraints excluded: chain B residue 2175 SER Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2508 VAL Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2558 HIS Chi-restraints excluded: chain C residue 1894 CYS Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1938 ILE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1962 HIS Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 1989 VAL Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2189 ARG Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2330 SER Chi-restraints excluded: chain C residue 2338 GLU Chi-restraints excluded: chain C residue 2353 GLU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2382 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2499 LEU Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2532 GLU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2563 HIS Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2609 SER Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 1989 VAL Chi-restraints excluded: chain D residue 2001 LEU Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2169 SER Chi-restraints excluded: chain D residue 2203 LEU Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2215 ILE Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2476 VAL Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2499 LEU Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2509 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2553 VAL Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2609 SER Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 636 optimal weight: 50.0000 chunk 670 optimal weight: 4.9990 chunk 611 optimal weight: 20.0000 chunk 652 optimal weight: 40.0000 chunk 392 optimal weight: 50.0000 chunk 284 optimal weight: 8.9990 chunk 512 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 589 optimal weight: 50.0000 chunk 616 optimal weight: 50.0000 chunk 649 optimal weight: 50.0000 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1955 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1751 GLN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1751 GLN ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2467 ASN ** D2472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.9066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.112 44818 Z= 0.831 Angle : 0.920 16.436 61524 Z= 0.471 Chirality : 0.049 0.311 7949 Planarity : 0.005 0.079 8238 Dihedral : 6.333 67.032 7595 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.31 % Favored : 90.68 % Rotamer: Outliers : 11.50 % Allowed : 29.30 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 7069 helix: 0.72 (0.08), residues: 4659 sheet: -2.65 (0.30), residues: 252 loop : -2.40 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A2204 HIS 0.011 0.002 HIS D1884 PHE 0.035 0.003 PHE C2172 TYR 0.031 0.003 TYR D2381 ARG 0.010 0.001 ARG C2021 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 570 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1775 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7728 (tp) REVERT: A 1783 GLU cc_start: 0.8411 (tp30) cc_final: 0.8201 (tp30) REVERT: A 1898 LYS cc_start: 0.8958 (ptpt) cc_final: 0.8570 (mmtm) REVERT: A 1955 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.9041 (m-40) REVERT: A 2211 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8676 (mp) REVERT: A 2351 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7998 (ttt-90) REVERT: A 2352 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7390 (mm-30) REVERT: B 1753 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7215 (t) REVERT: B 1760 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 1914 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.7282 (tmm) REVERT: B 1939 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: B 1975 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 2021 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7937 (mmm160) REVERT: B 2199 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7828 (tpm170) REVERT: B 2275 TYR cc_start: 0.7561 (t80) cc_final: 0.7002 (m-80) REVERT: B 2353 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 1959 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.6056 (mt) REVERT: C 2016 ILE cc_start: 0.8206 (mm) cc_final: 0.7782 (mt) REVERT: C 2071 LEU cc_start: 0.7023 (mp) cc_final: 0.6786 (mt) REVERT: C 2191 MET cc_start: 0.7485 (mpp) cc_final: 0.6305 (mpp) REVERT: D 1777 MET cc_start: 0.7701 (ppp) cc_final: 0.6896 (tpp) REVERT: D 1785 PHE cc_start: 0.8872 (t80) cc_final: 0.8114 (t80) REVERT: D 1901 TYR cc_start: 0.7669 (m-80) cc_final: 0.7104 (m-80) REVERT: D 2001 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8338 (mm) REVERT: D 2033 TYR cc_start: 0.7417 (t80) cc_final: 0.7153 (t80) REVERT: D 2063 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7163 (t-90) REVERT: D 2155 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9286 (tt) REVERT: D 2203 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8332 (tt) REVERT: D 2288 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7897 (mp) REVERT: D 2497 ASP cc_start: 0.8173 (m-30) cc_final: 0.7915 (m-30) REVERT: D 2550 ASN cc_start: 0.8641 (t0) cc_final: 0.8431 (t0) outliers start: 274 outliers final: 242 residues processed: 797 average time/residue: 0.4898 time to fit residues: 676.8417 Evaluate side-chains 814 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 557 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1741 ILE Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1753 SER Chi-restraints excluded: chain A residue 1754 ILE Chi-restraints excluded: chain A residue 1775 LEU Chi-restraints excluded: chain A residue 1778 SER Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1904 VAL Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 1932 ASP Chi-restraints excluded: chain A residue 1955 ASN Chi-restraints excluded: chain A residue 1961 THR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 1976 ASN Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2044 VAL Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2055 ILE Chi-restraints excluded: chain A residue 2061 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2114 LEU Chi-restraints excluded: chain A residue 2127 VAL Chi-restraints excluded: chain A residue 2129 GLN Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2157 THR Chi-restraints excluded: chain A residue 2158 THR Chi-restraints excluded: chain A residue 2159 THR Chi-restraints excluded: chain A residue 2170 ASP Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2198 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2211 LEU Chi-restraints excluded: chain A residue 2222 PHE Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2273 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2284 ILE Chi-restraints excluded: chain A residue 2290 LEU Chi-restraints excluded: chain A residue 2298 VAL Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2351 ARG Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2385 ILE Chi-restraints excluded: chain A residue 2455 CYS Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2464 THR Chi-restraints excluded: chain A residue 2503 ILE Chi-restraints excluded: chain A residue 2509 LEU Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2519 THR Chi-restraints excluded: chain A residue 2523 LEU Chi-restraints excluded: chain A residue 2525 SER Chi-restraints excluded: chain A residue 2537 THR Chi-restraints excluded: chain A residue 2552 THR Chi-restraints excluded: chain A residue 2553 VAL Chi-restraints excluded: chain A residue 2573 VAL Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain A residue 2584 THR Chi-restraints excluded: chain A residue 2609 SER Chi-restraints excluded: chain B residue 1724 THR Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1731 GLU Chi-restraints excluded: chain B residue 1735 LYS Chi-restraints excluded: chain B residue 1738 CYS Chi-restraints excluded: chain B residue 1743 SER Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1753 SER Chi-restraints excluded: chain B residue 1760 LEU Chi-restraints excluded: chain B residue 1765 ASN Chi-restraints excluded: chain B residue 1770 LYS Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1869 ILE Chi-restraints excluded: chain B residue 1874 LEU Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1914 MET Chi-restraints excluded: chain B residue 1937 VAL Chi-restraints excluded: chain B residue 1939 GLN Chi-restraints excluded: chain B residue 1952 CYS Chi-restraints excluded: chain B residue 1959 ILE Chi-restraints excluded: chain B residue 1973 LEU Chi-restraints excluded: chain B residue 1975 LEU Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2026 VAL Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2058 LEU Chi-restraints excluded: chain B residue 2121 THR Chi-restraints excluded: chain B residue 2154 ARG Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2173 ASP Chi-restraints excluded: chain B residue 2175 SER Chi-restraints excluded: chain B residue 2207 ILE Chi-restraints excluded: chain B residue 2218 ILE Chi-restraints excluded: chain B residue 2291 THR Chi-restraints excluded: chain B residue 2294 ILE Chi-restraints excluded: chain B residue 2295 VAL Chi-restraints excluded: chain B residue 2298 VAL Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2371 LEU Chi-restraints excluded: chain B residue 2374 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2385 ILE Chi-restraints excluded: chain B residue 2386 VAL Chi-restraints excluded: chain B residue 2463 VAL Chi-restraints excluded: chain B residue 2494 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2498 LEU Chi-restraints excluded: chain B residue 2508 VAL Chi-restraints excluded: chain B residue 2518 ASP Chi-restraints excluded: chain B residue 2519 THR Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain B residue 2525 SER Chi-restraints excluded: chain B residue 2536 THR Chi-restraints excluded: chain B residue 2543 LEU Chi-restraints excluded: chain B residue 2558 HIS Chi-restraints excluded: chain B residue 2573 VAL Chi-restraints excluded: chain B residue 2577 VAL Chi-restraints excluded: chain C residue 1883 ASN Chi-restraints excluded: chain C residue 1894 CYS Chi-restraints excluded: chain C residue 1901 TYR Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1959 ILE Chi-restraints excluded: chain C residue 1962 HIS Chi-restraints excluded: chain C residue 1988 LEU Chi-restraints excluded: chain C residue 1989 VAL Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2055 ILE Chi-restraints excluded: chain C residue 2127 VAL Chi-restraints excluded: chain C residue 2150 GLU Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2158 THR Chi-restraints excluded: chain C residue 2189 ARG Chi-restraints excluded: chain C residue 2202 THR Chi-restraints excluded: chain C residue 2289 ASN Chi-restraints excluded: chain C residue 2290 LEU Chi-restraints excluded: chain C residue 2291 THR Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2329 THR Chi-restraints excluded: chain C residue 2330 SER Chi-restraints excluded: chain C residue 2338 GLU Chi-restraints excluded: chain C residue 2353 GLU Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2371 LEU Chi-restraints excluded: chain C residue 2374 LEU Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2382 LEU Chi-restraints excluded: chain C residue 2385 ILE Chi-restraints excluded: chain C residue 2463 VAL Chi-restraints excluded: chain C residue 2464 THR Chi-restraints excluded: chain C residue 2485 LYS Chi-restraints excluded: chain C residue 2494 VAL Chi-restraints excluded: chain C residue 2499 LEU Chi-restraints excluded: chain C residue 2503 ILE Chi-restraints excluded: chain C residue 2505 ILE Chi-restraints excluded: chain C residue 2506 ILE Chi-restraints excluded: chain C residue 2509 LEU Chi-restraints excluded: chain C residue 2518 ASP Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2525 SER Chi-restraints excluded: chain C residue 2526 GLU Chi-restraints excluded: chain C residue 2532 GLU Chi-restraints excluded: chain C residue 2533 ILE Chi-restraints excluded: chain C residue 2536 THR Chi-restraints excluded: chain C residue 2563 HIS Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2573 VAL Chi-restraints excluded: chain C residue 2581 THR Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2588 SER Chi-restraints excluded: chain C residue 2594 ILE Chi-restraints excluded: chain C residue 2609 SER Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain D residue 1734 THR Chi-restraints excluded: chain D residue 1749 ILE Chi-restraints excluded: chain D residue 1782 SER Chi-restraints excluded: chain D residue 1865 THR Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1889 GLN Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1932 ASP Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 1940 THR Chi-restraints excluded: chain D residue 1964 SER Chi-restraints excluded: chain D residue 2001 LEU Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2020 LEU Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2121 THR Chi-restraints excluded: chain D residue 2127 VAL Chi-restraints excluded: chain D residue 2134 GLU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2155 LEU Chi-restraints excluded: chain D residue 2158 THR Chi-restraints excluded: chain D residue 2159 THR Chi-restraints excluded: chain D residue 2169 SER Chi-restraints excluded: chain D residue 2203 LEU Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2215 ILE Chi-restraints excluded: chain D residue 2219 ILE Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2284 ILE Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2323 HIS Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2329 THR Chi-restraints excluded: chain D residue 2330 SER Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2338 GLU Chi-restraints excluded: chain D residue 2343 ILE Chi-restraints excluded: chain D residue 2353 GLU Chi-restraints excluded: chain D residue 2361 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2374 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2399 VAL Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2476 VAL Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2499 LEU Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2509 LEU Chi-restraints excluded: chain D residue 2518 ASP Chi-restraints excluded: chain D residue 2519 THR Chi-restraints excluded: chain D residue 2525 SER Chi-restraints excluded: chain D residue 2526 GLU Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2553 VAL Chi-restraints excluded: chain D residue 2558 HIS Chi-restraints excluded: chain D residue 2561 LEU Chi-restraints excluded: chain D residue 2573 VAL Chi-restraints excluded: chain D residue 2575 VAL Chi-restraints excluded: chain D residue 2584 THR Chi-restraints excluded: chain D residue 2608 MET Chi-restraints excluded: chain D residue 2609 SER Chi-restraints excluded: chain D residue 2611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 428 optimal weight: 10.0000 chunk 689 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 327 optimal weight: 0.7980 chunk 479 optimal weight: 0.0370 chunk 723 optimal weight: 0.6980 chunk 665 optimal weight: 2.9990 chunk 575 optimal weight: 0.8980 chunk 59 optimal weight: 50.0000 chunk 444 optimal weight: 30.0000 chunk 353 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2216 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1751 GLN ** B2145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1871 GLN C1883 ASN D1884 HIS D1885 ASN D2135 GLN D2472 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 44818 Z= 0.172 Angle : 0.557 15.528 61524 Z= 0.290 Chirality : 0.039 0.315 7949 Planarity : 0.004 0.073 8238 Dihedral : 5.230 66.762 7595 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.37 % Allowed : 36.44 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.10), residues: 7069 helix: 1.64 (0.08), residues: 4708 sheet: -2.34 (0.30), residues: 273 loop : -1.97 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D2204 HIS 0.011 0.001 HIS A1953 PHE 0.032 0.002 PHE C2177 TYR 0.036 0.002 TYR B1947 ARG 0.015 0.001 ARG A2524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14138 Ramachandran restraints generated. 7069 Oldfield, 0 Emsley, 7069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 639 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1898 LYS cc_start: 0.8905 (ptpt) cc_final: 0.8389 (mmtm) REVERT: A 2183 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7284 (tm-30) REVERT: B 1767 GLU cc_start: 0.8592 (tt0) cc_final: 0.8219 (pt0) REVERT: B 2017 LEU cc_start: 0.8820 (tp) cc_final: 0.8588 (tp) REVERT: B 2023 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8716 (tp-100) REVERT: B 2199 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7632 (tpm170) REVERT: B 2275 TYR cc_start: 0.7354 (t80) cc_final: 0.6789 (m-80) REVERT: C 1938 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7252 (pt) REVERT: C 1973 LEU cc_start: 0.6716 (pp) cc_final: 0.5897 (tt) REVERT: C 2071 LEU cc_start: 0.6802 (mp) cc_final: 0.6563 (mt) REVERT: C 2146 PHE cc_start: 0.7258 (m-10) cc_final: 0.6956 (m-10) REVERT: C 2191 MET cc_start: 0.7210 (mpp) cc_final: 0.6890 (mpp) REVERT: D 1785 PHE cc_start: 0.8839 (t80) cc_final: 0.8139 (t80) REVERT: D 1890 ASN cc_start: 0.7146 (m-40) cc_final: 0.6861 (p0) REVERT: D 1901 TYR cc_start: 0.7129 (m-80) cc_final: 0.6651 (m-80) REVERT: D 1902 ASN cc_start: 0.7563 (m-40) cc_final: 0.7260 (p0) REVERT: D 2017 LEU cc_start: 0.7948 (mp) cc_final: 0.7586 (mt) REVERT: D 2033 TYR cc_start: 0.7108 (t80) cc_final: 0.6809 (t80) REVERT: D 2063 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7029 (t-90) REVERT: D 2288 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7681 (mp) outliers start: 104 outliers final: 81 residues processed: 715 average time/residue: 0.5072 time to fit residues: 624.8781 Evaluate side-chains 690 residues out of total 6647 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 606 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1734 THR Chi-restraints excluded: chain A residue 1743 SER Chi-restraints excluded: chain A residue 1868 LEU Chi-restraints excluded: chain A residue 1888 LEU Chi-restraints excluded: chain A residue 1896 ASN Chi-restraints excluded: chain A residue 1899 THR Chi-restraints excluded: chain A residue 1907 THR Chi-restraints excluded: chain A residue 1974 ILE Chi-restraints excluded: chain A residue 2017 LEU Chi-restraints excluded: chain A residue 2018 ILE Chi-restraints excluded: chain A residue 2045 SER Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2148 THR Chi-restraints excluded: chain A residue 2175 SER Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2269 ILE Chi-restraints excluded: chain A residue 2276 LEU Chi-restraints excluded: chain A residue 2301 VAL Chi-restraints excluded: chain A residue 2361 SER Chi-restraints excluded: chain A residue 2362 VAL Chi-restraints excluded: chain A residue 2463 VAL Chi-restraints excluded: chain A residue 2515 VAL Chi-restraints excluded: chain A residue 2575 VAL Chi-restraints excluded: chain B residue 1728 LEU Chi-restraints excluded: chain B residue 1743 SER Chi-restraints excluded: chain B residue 1745 LYS Chi-restraints excluded: chain B residue 1754 ILE Chi-restraints excluded: chain B residue 1765 ASN Chi-restraints excluded: chain B residue 1775 LEU Chi-restraints excluded: chain B residue 1869 ILE Chi-restraints excluded: chain B residue 1904 VAL Chi-restraints excluded: chain B residue 1992 LEU Chi-restraints excluded: chain B residue 2005 GLU Chi-restraints excluded: chain B residue 2299 SER Chi-restraints excluded: chain B residue 2361 SER Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2495 VAL Chi-restraints excluded: chain B residue 2523 LEU Chi-restraints excluded: chain C residue 1910 PHE Chi-restraints excluded: chain C residue 1938 ILE Chi-restraints excluded: chain C residue 1943 THR Chi-restraints excluded: chain C residue 1962 HIS Chi-restraints excluded: chain C residue 2006 SER Chi-restraints excluded: chain C residue 2020 LEU Chi-restraints excluded: chain C residue 2051 HIS Chi-restraints excluded: chain C residue 2155 LEU Chi-restraints excluded: chain C residue 2203 LEU Chi-restraints excluded: chain C residue 2327 ILE Chi-restraints excluded: chain C residue 2361 SER Chi-restraints excluded: chain C residue 2368 SER Chi-restraints excluded: chain C residue 2380 VAL Chi-restraints excluded: chain C residue 2382 LEU Chi-restraints excluded: chain C residue 2523 LEU Chi-restraints excluded: chain C residue 2532 GLU Chi-restraints excluded: chain C residue 2565 MET Chi-restraints excluded: chain C residue 2584 THR Chi-restraints excluded: chain C residue 2609 SER Chi-restraints excluded: chain D residue 1880 LEU Chi-restraints excluded: chain D residue 1904 VAL Chi-restraints excluded: chain D residue 1937 VAL Chi-restraints excluded: chain D residue 2006 SER Chi-restraints excluded: chain D residue 2045 SER Chi-restraints excluded: chain D residue 2063 HIS Chi-restraints excluded: chain D residue 2070 LEU Chi-restraints excluded: chain D residue 2145 GLN Chi-restraints excluded: chain D residue 2148 THR Chi-restraints excluded: chain D residue 2169 SER Chi-restraints excluded: chain D residue 2206 SER Chi-restraints excluded: chain D residue 2208 SER Chi-restraints excluded: chain D residue 2222 PHE Chi-restraints excluded: chain D residue 2261 ILE Chi-restraints excluded: chain D residue 2288 LEU Chi-restraints excluded: chain D residue 2298 VAL Chi-restraints excluded: chain D residue 2327 ILE Chi-restraints excluded: chain D residue 2334 LEU Chi-restraints excluded: chain D residue 2368 SER Chi-restraints excluded: chain D residue 2371 LEU Chi-restraints excluded: chain D residue 2380 VAL Chi-restraints excluded: chain D residue 2385 ILE Chi-restraints excluded: chain D residue 2461 CYS Chi-restraints excluded: chain D residue 2488 SER Chi-restraints excluded: chain D residue 2506 ILE Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2584 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 726 random chunks: chunk 457 optimal weight: 50.0000 chunk 613 optimal weight: 50.0000 chunk 176 optimal weight: 5.9990 chunk 531 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 0.3980 chunk 576 optimal weight: 50.0000 chunk 241 optimal weight: 50.0000 chunk 592 optimal weight: 40.0000 chunk 73 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 overall best weight: 11.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1955 ASN ** A2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1751 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1884 HIS B1949 GLN ** B2292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1751 GLN D1884 HIS ** D1885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2550 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.191985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.160969 restraints weight = 81050.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.157321 restraints weight = 119653.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154725 restraints weight = 104991.428| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.9443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.182 44818 Z= 1.290 Angle : 1.192 20.729 61524 Z= 0.611 Chirality : 0.059 0.331 7949 Planarity : 0.007 0.090 8238 Dihedral : 6.605 66.173 7595 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.11 % Favored : 89.77 % Rotamer: Outliers : 7.60 % Allowed : 33.50 % Favored : 58.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.10), residues: 7069 helix: 0.47 (0.08), residues: 4653 sheet: -2.74 (0.30), residues: 235 loop : -2.44 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A2204 HIS 0.017 0.003 HIS A2153 PHE 0.058 0.004 PHE A2539 TYR 0.035 0.004 TYR A2496 ARG 0.011 0.001 ARG B2007 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11657.64 seconds wall clock time: 210 minutes 42.57 seconds (12642.57 seconds total)