Starting phenix.real_space_refine on Wed Nov 15 16:36:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hyp_0309/11_2023/6hyp_0309_neut_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 10 5.16 5 C 7587 2.51 5 N 2390 2.21 5 O 2401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 1944": "NH1" <-> "NH2" Residue "A TYR 2005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2274": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12392 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2274, 12392 Unusual residues: {'ADP': 2} Classifications: {'peptide': 2272, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1766} Link IDs: {'PTRANS': 83, 'TRANS': 2188, None: 2} Not linked: pdbres="THR A2963 " pdbres="ADP A5001 " Not linked: pdbres="ADP A5001 " pdbres="ADP A5002 " Chain breaks: 22 Unresolved chain link angles: 64 Unresolved non-hydrogen bonds: 5829 Unresolved non-hydrogen angles: 7520 Unresolved non-hydrogen dihedrals: 4650 Unresolved non-hydrogen chiralities: 559 Planarities with less than four sites: {'GLN:plan1': 56, 'ARG:plan': 75, 'TYR:plan': 35, 'UNK:plan-1': 190, 'TRP:plan': 17, 'ASP:plan': 103, 'ASN:plan1': 98, 'PHE:plan': 80, 'GLU:plan': 132, 'HIS:plan': 32} Unresolved non-hydrogen planarities: 2958 Time building chain proxies: 7.94, per 1000 atoms: 0.64 Number of scatterers: 12392 At special positions: 0 Unit cell: (108.9, 170.5, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 4 15.00 O 2401 8.00 N 2390 7.00 C 7587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 2.8 seconds 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 43.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 removed outlier: 3.506A pdb=" N UNK A 23 " --> pdb=" O UNK A 20 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N UNK A 24 " --> pdb=" O UNK A 21 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N UNK A 29 " --> pdb=" O UNK A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.764A pdb=" N UNK A 78 " --> pdb=" O UNK A 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK A 79 " --> pdb=" O UNK A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.068A pdb=" N UNK A 93 " --> pdb=" O UNK A 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK A 94 " --> pdb=" O UNK A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.070A pdb=" N UNK A 119 " --> pdb=" O UNK A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.523A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK A 132 " --> pdb=" O UNK A 128 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK A 138 " --> pdb=" O UNK A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 155 through 161 removed outlier: 4.033A pdb=" N UNK A 160 " --> pdb=" O UNK A 156 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK A 161 " --> pdb=" O UNK A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 209 through 218 Processing helix chain 'A' and resid 237 through 249 Proline residue: A 241 - end of helix removed outlier: 3.671A pdb=" N ILE A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.612A pdb=" N LYS A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.661A pdb=" N ILE A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 removed outlier: 3.702A pdb=" N ALA A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 removed outlier: 4.126A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 401' Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.550A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 removed outlier: 3.600A pdb=" N ILE A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.697A pdb=" N LYS A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 No H-bonds generated for 'chain 'A' and resid 523 through 526' Processing helix chain 'A' and resid 541 through 547 removed outlier: 4.649A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Proline residue: A 568 - end of helix No H-bonds generated for 'chain 'A' and resid 564 through 570' Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.501A pdb=" N CYS A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.623A pdb=" N GLN A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 709 Proline residue: A 703 - end of helix removed outlier: 3.711A pdb=" N GLU A 706 " --> pdb=" O PRO A 703 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN A 707 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 708 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 709 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 730 removed outlier: 3.737A pdb=" N HIS A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 748 removed outlier: 3.912A pdb=" N VAL A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 795 Processing helix chain 'A' and resid 815 through 821 removed outlier: 3.867A pdb=" N THR A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 removed outlier: 3.793A pdb=" N ILE A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 893 removed outlier: 3.921A pdb=" N ARG A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 914 No H-bonds generated for 'chain 'A' and resid 911 through 914' Processing helix chain 'A' and resid 930 through 937 Processing helix chain 'A' and resid 953 through 966 Proline residue: A 957 - end of helix removed outlier: 3.540A pdb=" N LEU A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 978 No H-bonds generated for 'chain 'A' and resid 975 through 978' Processing helix chain 'A' and resid 998 through 1005 removed outlier: 3.708A pdb=" N LYS A1005 " --> pdb=" O GLU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1073 removed outlier: 3.754A pdb=" N LYS A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A1073 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1099 removed outlier: 3.876A pdb=" N ILE A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A1098 " --> pdb=" O LYS A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1225 through 1232 removed outlier: 3.620A pdb=" N ILE A1229 " --> pdb=" O ASP A1225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A1232 " --> pdb=" O GLU A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1239 No H-bonds generated for 'chain 'A' and resid 1236 through 1239' Processing helix chain 'A' and resid 1243 through 1245 No H-bonds generated for 'chain 'A' and resid 1243 through 1245' Processing helix chain 'A' and resid 1261 through 1276 Processing helix chain 'A' and resid 1285 through 1298 removed outlier: 3.686A pdb=" N ALA A1289 " --> pdb=" O TYR A1285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A1298 " --> pdb=" O MET A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1317 removed outlier: 4.174A pdb=" N VAL A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1358 removed outlier: 3.779A pdb=" N ARG A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1352 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1384 removed outlier: 3.623A pdb=" N GLN A1379 " --> pdb=" O THR A1375 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1382 " --> pdb=" O CYS A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1404 No H-bonds generated for 'chain 'A' and resid 1401 through 1404' Processing helix chain 'A' and resid 1478 through 1484 removed outlier: 3.720A pdb=" N ALA A1482 " --> pdb=" O PRO A1478 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1483 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A1484 " --> pdb=" O ILE A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1484' Processing helix chain 'A' and resid 1499 through 1504 Processing helix chain 'A' and resid 1507 through 1510 No H-bonds generated for 'chain 'A' and resid 1507 through 1510' Processing helix chain 'A' and resid 1547 through 1549 No H-bonds generated for 'chain 'A' and resid 1547 through 1549' Processing helix chain 'A' and resid 1572 through 1579 removed outlier: 4.049A pdb=" N VAL A1576 " --> pdb=" O VAL A1572 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A1579 " --> pdb=" O ILE A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1599 Proline residue: A1590 - end of helix removed outlier: 3.661A pdb=" N GLU A1596 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A1599 " --> pdb=" O SER A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1621 removed outlier: 3.586A pdb=" N VAL A1611 " --> pdb=" O ALA A1607 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A1617 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1634 No H-bonds generated for 'chain 'A' and resid 1631 through 1634' Processing helix chain 'A' and resid 1636 through 1640 removed outlier: 3.559A pdb=" N GLN A1640 " --> pdb=" O ALA A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1645 removed outlier: 4.299A pdb=" N VAL A1645 " --> pdb=" O ALA A1642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1645' Processing helix chain 'A' and resid 1653 through 1667 removed outlier: 3.556A pdb=" N LEU A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1737 removed outlier: 3.866A pdb=" N LEU A1730 " --> pdb=" O THR A1726 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A1736 " --> pdb=" O ARG A1732 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A1737 " --> pdb=" O VAL A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1753 through 1763 removed outlier: 3.550A pdb=" N ALA A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1825 through 1830 Processing helix chain 'A' and resid 1873 through 1876 No H-bonds generated for 'chain 'A' and resid 1873 through 1876' Processing helix chain 'A' and resid 1889 through 1895 removed outlier: 3.908A pdb=" N LEU A1893 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1894 " --> pdb=" O ASP A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1907 through 1926 removed outlier: 3.537A pdb=" N MET A1911 " --> pdb=" O ILE A1907 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1912 " --> pdb=" O ILE A1908 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1917 " --> pdb=" O LYS A1913 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1921 " --> pdb=" O THR A1917 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1925 " --> pdb=" O GLN A1921 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A1926 " --> pdb=" O VAL A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1939 through 1949 Processing helix chain 'A' and resid 1962 through 1965 removed outlier: 4.185A pdb=" N ASP A1965 " --> pdb=" O ASP A1962 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1962 through 1965' Processing helix chain 'A' and resid 1976 through 1988 removed outlier: 4.025A pdb=" N LEU A1984 " --> pdb=" O ALA A1981 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A1985 " --> pdb=" O GLN A1982 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A1988 " --> pdb=" O ILE A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2045 removed outlier: 3.704A pdb=" N SER A2039 " --> pdb=" O ALA A2035 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A2041 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A2044 " --> pdb=" O VAL A2040 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A2045 " --> pdb=" O LEU A2041 " (cutoff:3.500A) Processing helix chain 'A' and resid 2062 through 2070 removed outlier: 3.578A pdb=" N LEU A2067 " --> pdb=" O THR A2063 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A2070 " --> pdb=" O PHE A2066 " (cutoff:3.500A) Processing helix chain 'A' and resid 2085 through 2088 No H-bonds generated for 'chain 'A' and resid 2085 through 2088' Processing helix chain 'A' and resid 2099 through 2121 removed outlier: 3.894A pdb=" N TYR A2104 " --> pdb=" O ARG A2100 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A2105 " --> pdb=" O GLN A2101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A2119 " --> pdb=" O GLU A2115 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET A2121 " --> pdb=" O ILE A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2142 removed outlier: 4.336A pdb=" N GLU A2132 " --> pdb=" O THR A2128 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A2136 " --> pdb=" O GLU A2132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A2137 " --> pdb=" O GLY A2133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A2142 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2150 through 2161 removed outlier: 3.534A pdb=" N ARG A2154 " --> pdb=" O PHE A2150 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A2161 " --> pdb=" O PHE A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2183 removed outlier: 3.752A pdb=" N THR A2172 " --> pdb=" O LEU A2169 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A2173 " --> pdb=" O LEU A2170 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A2174 " --> pdb=" O LYS A2171 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A2176 " --> pdb=" O MET A2173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A2177 " --> pdb=" O SER A2174 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A2180 " --> pdb=" O ILE A2177 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A2183 " --> pdb=" O MET A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2198 through 2205 removed outlier: 4.181A pdb=" N GLU A2204 " --> pdb=" O VAL A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2222 through 2226 removed outlier: 3.569A pdb=" N LEU A2225 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A2226 " --> pdb=" O ASP A2223 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2222 through 2226' Processing helix chain 'A' and resid 2271 through 2273 No H-bonds generated for 'chain 'A' and resid 2271 through 2273' Processing helix chain 'A' and resid 2285 through 2288 No H-bonds generated for 'chain 'A' and resid 2285 through 2288' Processing helix chain 'A' and resid 2338 through 2351 removed outlier: 3.975A pdb=" N PHE A2342 " --> pdb=" O ARG A2338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A2344 " --> pdb=" O CYS A2340 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A2345 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A2346 " --> pdb=" O PHE A2342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A2348 " --> pdb=" O GLN A2344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A2349 " --> pdb=" O VAL A2345 " (cutoff:3.500A) Processing helix chain 'A' and resid 2371 through 2382 removed outlier: 3.655A pdb=" N LYS A2375 " --> pdb=" O GLY A2371 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A2378 " --> pdb=" O GLY A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2390 through 2402 removed outlier: 3.734A pdb=" N TYR A2396 " --> pdb=" O ALA A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2408 through 2414 Processing helix chain 'A' and resid 2416 through 2425 removed outlier: 3.770A pdb=" N LEU A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A2421 " --> pdb=" O PRO A2417 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A2424 " --> pdb=" O LEU A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2450 removed outlier: 3.705A pdb=" N THR A2449 " --> pdb=" O TYR A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2487 removed outlier: 3.610A pdb=" N LEU A2463 " --> pdb=" O PRO A2460 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A2464 " --> pdb=" O GLU A2461 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A2465 " --> pdb=" O SER A2462 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A2467 " --> pdb=" O TYR A2464 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER A2468 " --> pdb=" O LEU A2465 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A2469 " --> pdb=" O LEU A2466 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A2472 " --> pdb=" O LEU A2469 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A2475 " --> pdb=" O LEU A2472 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A2476 " --> pdb=" O LEU A2473 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN A2477 " --> pdb=" O ASN A2474 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A2479 " --> pdb=" O LEU A2476 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS A2480 " --> pdb=" O ASN A2477 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A2483 " --> pdb=" O LYS A2480 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A2484 " --> pdb=" O LEU A2481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A2485 " --> pdb=" O ILE A2482 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A2486 " --> pdb=" O ASN A2483 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A2487 " --> pdb=" O GLU A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2496 through 2503 removed outlier: 3.712A pdb=" N SER A2500 " --> pdb=" O TYR A2496 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2531 removed outlier: 3.665A pdb=" N TYR A2522 " --> pdb=" O PHE A2518 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A2526 " --> pdb=" O TYR A2522 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A2528 " --> pdb=" O ILE A2524 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2560 removed outlier: 3.573A pdb=" N LEU A2551 " --> pdb=" O TYR A2547 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A2552 " --> pdb=" O TRP A2548 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A2553 " --> pdb=" O ASP A2549 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A2554 " --> pdb=" O LEU A2550 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A2555 " --> pdb=" O LEU A2551 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2558 " --> pdb=" O VAL A2554 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A2559 " --> pdb=" O ILE A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2578 removed outlier: 3.589A pdb=" N TYR A2572 " --> pdb=" O ARG A2568 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A2577 " --> pdb=" O LYS A2573 " (cutoff:3.500A) Processing helix chain 'A' and resid 2584 through 2586 No H-bonds generated for 'chain 'A' and resid 2584 through 2586' Processing helix chain 'A' and resid 2919 through 2949 removed outlier: 3.714A pdb=" N TYR A2925 " --> pdb=" O ASP A2921 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A2944 " --> pdb=" O LYS A2940 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A2948 " --> pdb=" O ASN A2944 " (cutoff:3.500A) Processing helix chain 'A' and resid 2958 through 2960 No H-bonds generated for 'chain 'A' and resid 2958 through 2960' Processing sheet with id= A, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= B, first strand: chain 'A' and resid 381 through 385 removed outlier: 5.688A pdb=" N GLN A 423 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE A 384 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE A 425 " --> pdb=" O ILE A 384 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 896 through 898 removed outlier: 6.822A pdb=" N VAL A 649 " --> pdb=" O THR A 897 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A 873 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VAL A 652 " --> pdb=" O ILE A 873 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 875 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 876 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1192 through 1195 removed outlier: 3.729A pdb=" N GLN A1194 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A1083 " --> pdb=" O GLN A1194 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1217 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 4.037A pdb=" N VAL A1148 " --> pdb=" O ARG A1106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 3.895A pdb=" N LEU A1173 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1182 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1488 through 1492 removed outlier: 7.592A pdb=" N GLN A1534 " --> pdb=" O PHE A1489 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU A1491 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A1536 " --> pdb=" O LEU A1491 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 1745 through 1747 Processing sheet with id= I, first strand: chain 'A' and resid 1811 through 1814 removed outlier: 6.055A pdb=" N LEU A1854 " --> pdb=" O VAL A1812 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU A1814 " --> pdb=" O LEU A1854 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE A1856 " --> pdb=" O LEU A1814 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 2006 through 2008 removed outlier: 3.536A pdb=" N VAL A2006 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A2008 " --> pdb=" O GLU A2011 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A2011 " --> pdb=" O ILE A2008 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 2050 through 2054 removed outlier: 6.293A pdb=" N VAL A2278 " --> pdb=" O VAL A2051 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL A2053 " --> pdb=" O VAL A2278 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A2280 " --> pdb=" O VAL A2053 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 2075 through 2079 removed outlier: 7.400A pdb=" N TRP A2208 " --> pdb=" O ASP A2076 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE A2078 " --> pdb=" O TRP A2208 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE A2210 " --> pdb=" O PHE A2078 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A2259 " --> pdb=" O LEU A2209 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A2211 " --> pdb=" O PHE A2259 " (cutoff:3.500A) No H-bonds generated for sheet with id= L 362 hydrogen bonds defined for protein. 990 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: 5.56 Time building geometry restraints manager: 5.58 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: 4619 1.34 - 1.46: 1533 1.46 - 1.57: 6283 1.57 - 1.69: 6 1.69 - 1.81: 17 Bond restraints: 12458 Sorted by residual: bond pdb=" C UNK A 30 " pdb=" N UNK A 31 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.33e+00 bond pdb=" C UNK A 23 " pdb=" N UNK A 24 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.29e+00 bond pdb=" C GLU A 863 " pdb=" O GLU A 863 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.22e+00 bond pdb=" C LEU A2447 " pdb=" N PRO A2448 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.50e+00 bond pdb=" N PRO A2219 " pdb=" CA PRO A2219 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.43e+00 ... (remaining 12453 not shown) Histogram of bond angle deviations from ideal: 100.63 - 107.72: 255 107.72 - 114.80: 7227 114.80 - 121.89: 6660 121.89 - 128.98: 3089 128.98 - 136.07: 34 Bond angle restraints: 17265 Sorted by residual: angle pdb=" C UNK A 30 " pdb=" N UNK A 31 " pdb=" CA UNK A 31 " ideal model delta sigma weight residual 121.70 113.00 8.70 1.80e+00 3.09e-01 2.34e+01 angle pdb=" N VAL A2407 " pdb=" CA VAL A2407 " pdb=" C VAL A2407 " ideal model delta sigma weight residual 113.53 109.18 4.35 9.80e-01 1.04e+00 1.97e+01 angle pdb=" C ASP A2212 " pdb=" N ASN A2213 " pdb=" CA ASN A2213 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA TYR A2005 " pdb=" CB TYR A2005 " pdb=" CG TYR A2005 " ideal model delta sigma weight residual 113.90 120.76 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C LYS A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta sigma weight residual 121.19 127.10 -5.91 1.59e+00 3.96e-01 1.38e+01 ... (remaining 17260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 7254 28.96 - 57.92: 31 57.92 - 86.87: 3 86.87 - 115.83: 0 115.83 - 144.79: 4 Dihedral angle restraints: 7292 sinusoidal: 674 harmonic: 6618 Sorted by residual: dihedral pdb=" CA THR A2024 " pdb=" C THR A2024 " pdb=" N GLN A2025 " pdb=" CA GLN A2025 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" C5' ADP A5002 " pdb=" O5' ADP A5002 " pdb=" PA ADP A5002 " pdb=" O2A ADP A5002 " ideal model delta sinusoidal sigma weight residual 300.00 155.22 144.79 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O2A ADP A5001 " pdb=" O3A ADP A5001 " pdb=" PA ADP A5001 " pdb=" PB ADP A5001 " ideal model delta sinusoidal sigma weight residual -60.00 83.49 -143.49 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1985 0.065 - 0.130: 309 0.130 - 0.195: 7 0.195 - 0.260: 1 0.260 - 0.325: 1 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CB ILE A2961 " pdb=" CA ILE A2961 " pdb=" CG1 ILE A2961 " pdb=" CG2 ILE A2961 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ARG A2271 " pdb=" N ARG A2271 " pdb=" C ARG A2271 " pdb=" CB ARG A2271 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR A2005 " pdb=" N TYR A2005 " pdb=" C TYR A2005 " pdb=" CB TYR A2005 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2300 not shown) Planarity restraints: 2381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 460 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO A 461 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2459 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO A2460 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2460 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2054 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A2055 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A2055 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2055 " 0.028 5.00e-02 4.00e+02 ... (remaining 2378 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 20 2.53 - 3.13: 7815 3.13 - 3.72: 18070 3.72 - 4.31: 19725 4.31 - 4.90: 32021 Nonbonded interactions: 77651 Sorted by model distance: nonbonded pdb=" O GLU A 804 " pdb=" N SER A 806 " model vdw 1.943 2.520 nonbonded pdb=" OG1 THR A2061 " pdb=" O3B ADP A5002 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR A 322 " pdb=" O1B ADP A5001 " model vdw 2.204 2.440 nonbonded pdb=" O LYS A 316 " pdb=" NZ LYS A 321 " model vdw 2.238 2.520 nonbonded pdb=" OG1 THR A2002 " pdb=" O ASP A2004 " model vdw 2.345 2.440 ... (remaining 77646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.010 Extract box with map and model: 11.960 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 39.570 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12458 Z= 0.171 Angle : 0.719 8.700 17265 Z= 0.395 Chirality : 0.046 0.325 2303 Planarity : 0.004 0.073 2381 Dihedral : 8.718 144.787 2944 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.31 % Favored : 92.25 % Rotamer: Outliers : 0.34 % Allowed : 6.44 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.99 (0.12), residues: 2038 helix: -5.01 (0.04), residues: 776 sheet: -2.06 (0.35), residues: 181 loop : -3.56 (0.15), residues: 1081 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.412 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.2160 time to fit residues: 40.2914 Evaluate side-chains 80 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.317 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5979 time to fit residues: 2.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.0980 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 132 optimal weight: 0.7980 chunk 206 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2944 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12458 Z= 0.112 Angle : 0.478 8.015 17265 Z= 0.248 Chirality : 0.040 0.173 2303 Planarity : 0.003 0.041 2381 Dihedral : 6.912 149.967 2305 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.51 (0.14), residues: 2038 helix: -3.16 (0.11), residues: 796 sheet: -1.86 (0.36), residues: 185 loop : -3.10 (0.16), residues: 1057 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1612 time to fit residues: 27.1730 Evaluate side-chains 80 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 140 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12458 Z= 0.160 Angle : 0.509 7.597 17265 Z= 0.264 Chirality : 0.041 0.150 2303 Planarity : 0.003 0.035 2381 Dihedral : 6.849 144.060 2305 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.68 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.17), residues: 2038 helix: -1.13 (0.17), residues: 794 sheet: -1.54 (0.39), residues: 169 loop : -2.69 (0.18), residues: 1075 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.414 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1700 time to fit residues: 25.9541 Evaluate side-chains 73 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 chunk 108 optimal weight: 0.0870 chunk 196 optimal weight: 0.0670 chunk 59 optimal weight: 20.0000 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12458 Z= 0.121 Angle : 0.475 7.445 17265 Z= 0.240 Chirality : 0.040 0.138 2303 Planarity : 0.002 0.035 2381 Dihedral : 6.423 138.666 2305 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.41 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.19), residues: 2038 helix: -0.29 (0.19), residues: 805 sheet: -1.33 (0.41), residues: 167 loop : -2.52 (0.18), residues: 1066 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1628 time to fit residues: 24.9422 Evaluate side-chains 76 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 3 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 12458 Z= 0.622 Angle : 1.005 11.444 17265 Z= 0.522 Chirality : 0.053 0.276 2303 Planarity : 0.006 0.066 2381 Dihedral : 9.123 148.210 2305 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.72 % Favored : 84.94 % Rotamer: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.28 (0.17), residues: 2038 helix: -1.36 (0.17), residues: 785 sheet: -2.14 (0.42), residues: 143 loop : -2.89 (0.17), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.382 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1574 time to fit residues: 20.1773 Evaluate side-chains 65 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 0.6980 chunk 197 optimal weight: 0.0470 chunk 43 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 182 optimal weight: 0.1980 chunk 101 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 115 optimal weight: 0.1980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12458 Z= 0.116 Angle : 0.553 7.810 17265 Z= 0.279 Chirality : 0.041 0.215 2303 Planarity : 0.003 0.049 2381 Dihedral : 7.209 148.738 2305 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.19 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 2038 helix: -0.25 (0.19), residues: 818 sheet: -2.03 (0.41), residues: 149 loop : -2.56 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1551 time to fit residues: 24.1770 Evaluate side-chains 77 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 218 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12458 Z= 0.366 Angle : 0.738 9.729 17265 Z= 0.377 Chirality : 0.046 0.215 2303 Planarity : 0.004 0.054 2381 Dihedral : 7.945 143.085 2305 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.52 % Favored : 85.23 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.18), residues: 2038 helix: -0.54 (0.19), residues: 810 sheet: -1.99 (0.45), residues: 132 loop : -2.71 (0.18), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1508 time to fit residues: 21.2149 Evaluate side-chains 72 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 20.0000 chunk 87 optimal weight: 0.0050 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 0.0980 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 171 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12458 Z= 0.110 Angle : 0.530 11.291 17265 Z= 0.264 Chirality : 0.041 0.171 2303 Planarity : 0.003 0.046 2381 Dihedral : 6.791 148.242 2305 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.49 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.82 (0.19), residues: 2038 helix: 0.33 (0.20), residues: 798 sheet: -1.72 (0.45), residues: 137 loop : -2.43 (0.19), residues: 1103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1622 time to fit residues: 25.2728 Evaluate side-chains 76 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 203 optimal weight: 0.4980 chunk 122 optimal weight: 0.0980 chunk 88 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12458 Z= 0.118 Angle : 0.521 11.067 17265 Z= 0.257 Chirality : 0.041 0.171 2303 Planarity : 0.003 0.040 2381 Dihedral : 6.194 136.346 2305 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.67 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.20), residues: 2038 helix: 0.91 (0.21), residues: 773 sheet: -1.45 (0.47), residues: 135 loop : -2.27 (0.19), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1611 time to fit residues: 24.5327 Evaluate side-chains 72 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 0.0270 chunk 102 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 226 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 0.0020 chunk 143 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12458 Z= 0.104 Angle : 0.506 12.021 17265 Z= 0.248 Chirality : 0.041 0.169 2303 Planarity : 0.002 0.037 2381 Dihedral : 5.839 130.770 2305 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.90 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.18 (0.20), residues: 2038 helix: 1.09 (0.21), residues: 767 sheet: -1.34 (0.47), residues: 135 loop : -2.17 (0.19), residues: 1136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.429 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1582 time to fit residues: 23.9740 Evaluate side-chains 73 residues out of total 1871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 22 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.103000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086213 restraints weight = 51386.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085608 restraints weight = 69565.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085761 restraints weight = 72258.261| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12458 Z= 0.274 Angle : 0.660 11.905 17265 Z= 0.330 Chirality : 0.045 0.264 2303 Planarity : 0.003 0.042 2381 Dihedral : 6.702 124.526 2305 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.40 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.62 (0.20), residues: 2038 helix: 0.48 (0.20), residues: 810 sheet: -1.61 (0.49), residues: 127 loop : -2.32 (0.20), residues: 1101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2157.84 seconds wall clock time: 41 minutes 3.79 seconds (2463.79 seconds total)