Starting phenix.real_space_refine on Sun Nov 17 13:50:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/11_2024/7m1p_23617.cif" } resolution = 3.6 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= 0.984 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 8662 2.51 5 N 2322 2.21 5 O 2476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13511 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13340 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1938, 13331 Classifications: {'peptide': 1938} Incomplete info: {'truncation_to_alanine': 579} Link IDs: {'PTRANS': 100, 'TRANS': 1837} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2175 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1789 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 53, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 27, 'GLU:plan': 71, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 1246 Conformer: "B" Number of residues, atoms: 1938, 13331 Classifications: {'peptide': 1938} Incomplete info: {'truncation_to_alanine': 579} Link IDs: {'PTRANS': 100, 'TRANS': 1837} Chain breaks: 13 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2175 Unresolved non-hydrogen angles: 2757 Unresolved non-hydrogen dihedrals: 1789 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 27, 'ASP:plan': 53, 'TYR:plan': 14, 'ASN:plan1': 25, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 27, 'GLU:plan': 71, 'ARG:plan': 42} Unresolved non-hydrogen planarities: 1246 bond proxies already assigned to first conformer: 13615 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 15.20, per 1000 atoms: 1.13 Number of scatterers: 13511 At special positions: 0 Unit cell: (96.7808, 93.6921, 229.597, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2476 8.00 N 2322 7.00 C 8662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1588 " " NAG B 1 " - " ASN A 415 " " NAG C 1 " - " ASN A1529 " " NAG D 1 " - " ASN A1662 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 4.1 seconds 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3642 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 10 sheets defined 51.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 removed outlier: 3.871A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 46 removed outlier: 3.539A pdb=" N VAL A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Proline residue: A 32 - end of helix removed outlier: 3.531A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.711A pdb=" N TRP A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.226A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.751A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.179A pdb=" N LEU A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 369 through 380 removed outlier: 3.599A pdb=" N ASN A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 404 through 413 Processing helix chain 'A' and resid 415 through 430 removed outlier: 3.555A pdb=" N GLU A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 439 Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.551A pdb=" N ASP A 443 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 444' Processing helix chain 'A' and resid 445 through 454 removed outlier: 3.637A pdb=" N ASN A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 Processing helix chain 'A' and resid 531 through 542 removed outlier: 3.916A pdb=" N THR A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.787A pdb=" N VAL A 578 " --> pdb=" O ILE A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 654 through 680 removed outlier: 4.894A pdb=" N TYR A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 690 removed outlier: 3.759A pdb=" N THR A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 722 removed outlier: 3.903A pdb=" N ILE A 707 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'A' and resid 757 through 772 removed outlier: 3.762A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.779A pdb=" N ILE A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 796 removed outlier: 3.868A pdb=" N LEU A 796 " --> pdb=" O ALA A 793 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 793 through 796' Processing helix chain 'A' and resid 797 through 814 Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.798A pdb=" N ILE A 824 " --> pdb=" O TRP A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.827A pdb=" N GLY A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.571A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 Processing helix chain 'A' and resid 988 through 992 Processing helix chain 'A' and resid 993 through 997 removed outlier: 3.842A pdb=" N THR A 996 " --> pdb=" O ASP A 993 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 997 " --> pdb=" O ILE A 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 993 through 997' Processing helix chain 'A' and resid 1001 through 1005 removed outlier: 3.750A pdb=" N LEU A1005 " --> pdb=" O ARG A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 removed outlier: 4.032A pdb=" N MET A1024 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU A1025 " --> pdb=" O ALA A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1050 removed outlier: 3.600A pdb=" N LEU A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 removed outlier: 3.995A pdb=" N ARG A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1106 Processing helix chain 'A' and resid 1119 through 1127 removed outlier: 3.609A pdb=" N ASP A1124 " --> pdb=" O MET A1120 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A1125 " --> pdb=" O ASP A1121 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY A1127 " --> pdb=" O ALA A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1149 removed outlier: 4.436A pdb=" N ASN A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1216 removed outlier: 3.556A pdb=" N VAL A1211 " --> pdb=" O GLU A1207 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1253 Processing helix chain 'A' and resid 1268 through 1277 removed outlier: 3.613A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A1277 " --> pdb=" O PHE A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1368 removed outlier: 3.556A pdb=" N GLN A1356 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A1357 " --> pdb=" O GLN A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1378 Processing helix chain 'A' and resid 1378 through 1393 Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.890A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1436 Processing helix chain 'A' and resid 1470 through 1475 removed outlier: 3.876A pdb=" N GLN A1475 " --> pdb=" O THR A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1546 removed outlier: 3.968A pdb=" N LYS A1536 " --> pdb=" O ASP A1532 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A1538 " --> pdb=" O LEU A1534 " (cutoff:3.500A) Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1575 through 1586 removed outlier: 3.512A pdb=" N PHE A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A1586 " --> pdb=" O ASP A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1601 removed outlier: 4.529A pdb=" N GLU A1601 " --> pdb=" O GLU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1610 removed outlier: 3.846A pdb=" N PHE A1605 " --> pdb=" O GLU A1601 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A1610 " --> pdb=" O LEU A1606 " (cutoff:3.500A) Processing helix chain 'A' and resid 1626 through 1643 removed outlier: 3.712A pdb=" N LEU A1643 " --> pdb=" O LEU A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1652 Processing helix chain 'A' and resid 1664 through 1691 removed outlier: 3.839A pdb=" N GLU A1670 " --> pdb=" O GLU A1666 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A1671 " --> pdb=" O GLN A1667 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A1678 " --> pdb=" O LEU A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1707 removed outlier: 3.563A pdb=" N ALA A1695 " --> pdb=" O SER A1691 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1709 through 1716 Processing helix chain 'A' and resid 1719 through 1747 removed outlier: 3.682A pdb=" N TYR A1723 " --> pdb=" O SER A1719 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A1737 " --> pdb=" O MET A1733 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A1738 " --> pdb=" O ASN A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1754 Processing helix chain 'A' and resid 1759 through 1779 removed outlier: 3.909A pdb=" N GLY A1771 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1785 removed outlier: 3.791A pdb=" N LEU A1784 " --> pdb=" O PRO A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1789 through 1813 removed outlier: 4.117A pdb=" N VAL A1793 " --> pdb=" O SER A1789 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A1798 " --> pdb=" O ALA A1794 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1813 " --> pdb=" O ILE A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1831 removed outlier: 4.195A pdb=" N ARG A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1832 through 1835 removed outlier: 4.096A pdb=" N VAL A1835 " --> pdb=" O LEU A1832 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1832 through 1835' Processing helix chain 'A' and resid 1836 through 1861 removed outlier: 3.897A pdb=" N ARG A1860 " --> pdb=" O ASP A1856 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A1861 " --> pdb=" O VAL A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1898 removed outlier: 3.565A pdb=" N VAL A1887 " --> pdb=" O VAL A1883 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1986 removed outlier: 3.692A pdb=" N MET A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2009 through 2014 Processing helix chain 'A' and resid 2033 through 2039 Processing helix chain 'A' and resid 2049 through 2056 removed outlier: 3.627A pdb=" N ILE A2055 " --> pdb=" O ALA A2051 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A2056 " --> pdb=" O ASN A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2071 removed outlier: 3.796A pdb=" N TYR A2071 " --> pdb=" O ALA A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2084 removed outlier: 3.627A pdb=" N LYS A2076 " --> pdb=" O SER A2072 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A2077 " --> pdb=" O GLY A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2120 removed outlier: 3.802A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU A2119 " --> pdb=" O SER A2115 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A2120 " --> pdb=" O ILE A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.513A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2161 removed outlier: 3.543A pdb=" N PHE A2161 " --> pdb=" O LEU A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2192 Processing helix chain 'A' and resid 2215 through 2219 Processing helix chain 'A' and resid 2240 through 2249 removed outlier: 3.623A pdb=" N VAL A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.036A pdb=" N ILE A1615 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL A1617 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A1619 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ILE A1560 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A1416 " --> pdb=" O ILE A1560 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A1562 " --> pdb=" O PHE A1416 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER A1418 " --> pdb=" O ILE A1562 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 527 removed outlier: 6.235A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 399 " --> pdb=" O VAL A 551 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 571 Processing sheet with id=AA5, first strand: chain 'A' and resid 932 through 933 Processing sheet with id=AA6, first strand: chain 'A' and resid 961 through 962 removed outlier: 6.414A pdb=" N ALA A1131 " --> pdb=" O LEU A 962 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1007 through 1008 removed outlier: 6.996A pdb=" N CYS A1008 " --> pdb=" O ASP A1086 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1155 through 1158 removed outlier: 7.161A pdb=" N ILE A1230 " --> pdb=" O VAL A1222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2091 through 2094 removed outlier: 6.588A pdb=" N VAL A2092 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE A2142 " --> pdb=" O ARG A2149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2205 through 2209 624 hydrogen bonds defined for protein. 1802 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: 5.89 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4424 1.34 - 1.47: 3330 1.47 - 1.59: 5977 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 13807 Sorted by residual: bond pdb=" C1 NAG A2301 " pdb=" O5 NAG A2301 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG A2303 " pdb=" O5 NAG A2303 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 MAN C 4 " pdb=" C2 MAN C 4 " ideal model delta sigma weight residual 1.526 1.558 -0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 13802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18506 1.79 - 3.58: 353 3.58 - 5.37: 71 5.37 - 7.16: 13 7.16 - 8.95: 3 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N PRO A 458 " pdb=" CA PRO A 458 " pdb=" CB PRO A 458 " ideal model delta sigma weight residual 103.33 110.51 -7.18 9.30e-01 1.16e+00 5.95e+01 angle pdb=" N PRO A 188 " pdb=" CA PRO A 188 " pdb=" CB PRO A 188 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 angle pdb=" C CYS A 930 " pdb=" CA CYS A 930 " pdb=" CB CYS A 930 " ideal model delta sigma weight residual 115.89 110.34 5.55 1.32e+00 5.74e-01 1.77e+01 angle pdb=" CA LYS A2049 " pdb=" CB LYS A2049 " pdb=" CG LYS A2049 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" C ASN A1442 " pdb=" CA ASN A1442 " pdb=" CB ASN A1442 " ideal model delta sigma weight residual 109.80 115.02 -5.22 1.61e+00 3.86e-01 1.05e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 7817 23.07 - 46.15: 364 46.15 - 69.22: 42 69.22 - 92.30: 24 92.30 - 115.37: 25 Dihedral angle restraints: 8272 sinusoidal: 2656 harmonic: 5616 Sorted by residual: dihedral pdb=" CB CYS A1488 " pdb=" SG CYS A1488 " pdb=" SG CYS A1502 " pdb=" CB CYS A1502 " ideal model delta sinusoidal sigma weight residual 93.00 7.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual 93.00 161.90 -68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CA MET A1587 " pdb=" C MET A1587 " pdb=" N ASN A1588 " pdb=" CA ASN A1588 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 8269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1911 0.055 - 0.111: 366 0.111 - 0.166: 30 0.166 - 0.222: 3 0.222 - 0.277: 3 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA PRO A 188 " pdb=" N PRO A 188 " pdb=" C PRO A 188 " pdb=" CB PRO A 188 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2310 not shown) Planarity restraints: 2444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 774 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO A 775 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 775 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 775 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 435 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO A 436 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1588 " 0.026 2.00e-02 2.50e+03 2.36e-02 6.97e+00 pdb=" CG ASN A1588 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A1588 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A1588 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A2303 " 0.027 2.00e-02 2.50e+03 ... (remaining 2441 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2268 2.76 - 3.30: 13644 3.30 - 3.83: 21952 3.83 - 4.37: 23402 4.37 - 4.90: 41608 Nonbonded interactions: 102874 Sorted by model distance: nonbonded pdb=" O ASP A 295 " pdb=" OG1 THR A 300 " model vdw 2.226 3.040 nonbonded pdb=" O VAL A1160 " pdb=" OG SER A1261 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 56 " pdb=" NE2 GLN A 635 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 89 " pdb=" NE2 GLN A 635 " model vdw 2.255 3.120 nonbonded pdb=" O ARG A1241 " pdb=" OG SER A1245 " model vdw 2.261 3.040 ... (remaining 102869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 2.790 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 45.100 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.110 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 0.049 13807 Z= 0.201 Angle : 0.613 8.948 18946 Z= 0.314 Chirality : 0.044 0.277 2313 Planarity : 0.005 0.077 2438 Dihedral : 15.816 115.374 4615 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.37 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -0.96 (0.20), residues: 1911 helix: 1.20 (0.19), residues: 869 sheet: -0.77 (0.49), residues: 139 loop : -2.61 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 663 HIS 0.005 0.001 HIS A 776 PHE 0.031 0.001 PHE A1076 TYR 0.013 0.001 TYR A 633 ARG 0.004 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.563 Fit side-chains REVERT: A 697 TRP cc_start: 0.8520 (m100) cc_final: 0.8018 (m100) REVERT: A 2034 TYR cc_start: 0.6206 (t80) cc_final: 0.5948 (t80) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2139 time to fit residues: 70.0950 Evaluate side-chains 175 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 0.0370 chunk 175 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13807 Z= 0.205 Angle : 0.620 9.595 18946 Z= 0.307 Chirality : 0.045 0.259 2313 Planarity : 0.005 0.066 2438 Dihedral : 10.652 106.600 2287 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.21 % Favored : 90.68 % Rotamer: Outliers : 1.07 % Allowed : 8.10 % Favored : 90.83 % 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: -1.05 (0.20), residues: 1911 helix: 1.08 (0.18), residues: 890 sheet: -0.58 (0.48), residues: 135 loop : -2.73 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 31 HIS 0.012 0.001 HIS A 721 PHE 0.029 0.001 PHE A1533 TYR 0.023 0.001 TYR A1700 ARG 0.011 0.001 ARG A1362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.507 Fit side-chains REVERT: A 697 TRP cc_start: 0.8538 (m100) cc_final: 0.8090 (m100) REVERT: A 1843 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7234 (mmm-85) REVERT: A 2034 TYR cc_start: 0.6474 (t80) cc_final: 0.6017 (t80) outliers start: 12 outliers final: 6 residues processed: 194 average time/residue: 0.2148 time to fit residues: 66.0935 Evaluate side-chains 182 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 ASN A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13807 Z= 0.237 Angle : 0.621 9.412 18946 Z= 0.311 Chirality : 0.045 0.268 2313 Planarity : 0.005 0.063 2438 Dihedral : 8.044 94.547 2287 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.31 % Favored : 89.58 % Rotamer: Outliers : 1.25 % Allowed : 11.40 % Favored : 87.36 % 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: -1.21 (0.20), residues: 1911 helix: 0.92 (0.18), residues: 892 sheet: -1.04 (0.46), residues: 144 loop : -2.74 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 31 HIS 0.009 0.001 HIS A 721 PHE 0.030 0.001 PHE A1076 TYR 0.012 0.001 TYR A2016 ARG 0.004 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 1.758 Fit side-chains REVERT: A 855 TRP cc_start: 0.6747 (t-100) cc_final: 0.6292 (t-100) REVERT: A 1770 TYR cc_start: 0.8469 (t80) cc_final: 0.8227 (t80) REVERT: A 1874 LEU cc_start: 0.7881 (mm) cc_final: 0.7452 (mp) REVERT: A 2034 TYR cc_start: 0.6631 (t80) cc_final: 0.6098 (t80) outliers start: 14 outliers final: 8 residues processed: 191 average time/residue: 0.2235 time to fit residues: 69.2036 Evaluate side-chains 183 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1676 THR Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 83 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13807 Z= 0.173 Angle : 0.581 9.443 18946 Z= 0.289 Chirality : 0.043 0.263 2313 Planarity : 0.004 0.060 2438 Dihedral : 7.468 92.203 2287 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.32 % Favored : 90.58 % Rotamer: Outliers : 1.42 % Allowed : 12.73 % Favored : 85.84 % 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: -1.13 (0.20), residues: 1911 helix: 1.02 (0.18), residues: 894 sheet: -1.05 (0.46), residues: 144 loop : -2.73 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.024 0.001 PHE A1076 TYR 0.014 0.001 TYR A2016 ARG 0.003 0.000 ARG A1514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.470 Fit side-chains REVERT: A 450 MET cc_start: 0.8541 (mmm) cc_final: 0.8319 (mmm) REVERT: A 633 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 855 TRP cc_start: 0.6739 (t-100) cc_final: 0.6314 (t-100) REVERT: A 1874 LEU cc_start: 0.7698 (mm) cc_final: 0.7328 (mp) REVERT: A 2034 TYR cc_start: 0.6551 (t80) cc_final: 0.6002 (t80) outliers start: 16 outliers final: 11 residues processed: 185 average time/residue: 0.2102 time to fit residues: 62.5024 Evaluate side-chains 188 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2067 LEU Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13807 Z= 0.207 Angle : 0.591 9.496 18946 Z= 0.295 Chirality : 0.044 0.264 2313 Planarity : 0.004 0.061 2438 Dihedral : 6.566 90.629 2287 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.26 % Favored : 89.63 % Rotamer: Outliers : 1.51 % Allowed : 14.25 % Favored : 84.24 % 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: -1.15 (0.20), residues: 1911 helix: 1.01 (0.18), residues: 894 sheet: -1.10 (0.46), residues: 142 loop : -2.74 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 31 HIS 0.005 0.001 HIS A 721 PHE 0.025 0.001 PHE A1533 TYR 0.012 0.001 TYR A2016 ARG 0.002 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3822 Ramachandran restraints generated. 1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.705 Fit side-chains REVERT: A 450 MET cc_start: 0.8555 (mmm) cc_final: 0.8327 (mmm) REVERT: A 633 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 842 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6844 (ppp) REVERT: A 855 TRP cc_start: 0.6753 (t-100) cc_final: 0.6453 (t-100) REVERT: A 1690 MET cc_start: 0.8752 (tpp) cc_final: 0.8429 (mmt) REVERT: A 1843 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7510 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7647 (mm) cc_final: 0.7308 (mp) REVERT: A 2034 TYR cc_start: 0.6597 (t80) cc_final: 0.5972 (t80) outliers start: 17 outliers final: 13 residues processed: 189 average time/residue: 0.2207 time to fit residues: 68.8134 Evaluate side-chains 190 residues out of total 1705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2083 ILE Chi-restraints excluded: chain A residue 2109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 721 HIS ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1616 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: