Starting phenix.real_space_refine on Mon Apr 8 12:38:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/04_2024/7m1p_23617.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/04_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_23617/04_2024/7m1p_23617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/04_2024/7m1p_23617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/04_2024/7m1p_23617.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m1p_23617/04_2024/7m1p_23617.pdb" } 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 Residue "A ASP 613": "OD1" <-> "OD2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A PHE 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1889": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.07, per 1000 atoms: 1.04 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 - 3.50 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 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: 6.04 Conformation dependent library (CDL) restraints added in 5.4 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: 1.95 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: 5.72 Time building geometry restraints manager: 6.11 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: 99.96 - 106.79: 474 106.79 - 113.61: 7719 113.61 - 120.43: 5050 120.43 - 127.25: 5532 127.25 - 134.07: 171 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 2.440 nonbonded pdb=" O VAL A1160 " pdb=" OG SER A1261 " model vdw 2.249 2.440 nonbonded pdb=" O PHE A 56 " pdb=" NE2 GLN A 635 " model vdw 2.254 2.520 nonbonded pdb=" OE2 GLU A 89 " pdb=" NE2 GLN A 635 " model vdw 2.255 2.520 nonbonded pdb=" O ARG A1241 " pdb=" OG SER A1245 " model vdw 2.261 2.440 ... (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 ========== 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: 4.780 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: 10.500 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 50.340 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.515 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: 0.2138 time to fit residues: 69.9570 Evaluate side-chains 175 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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: 0.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.0030 chunk 112 optimal weight: 0.0030 chunk 175 optimal weight: 2.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 721 HIS 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: 0.7360 moved from start: 0.0801 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 : 0.609 9.607 18946 Z= 0.300 Chirality : 0.045 0.270 2313 Planarity : 0.005 0.066 2438 Dihedral : 10.858 107.520 2287 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.79 % Favored : 90.10 % Rotamer: Outliers : 1.07 % Allowed : 8.01 % Favored : 90.92 % 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: -1.03 (0.20), residues: 1911 helix: 1.09 (0.18), residues: 897 sheet: -0.66 (0.47), residues: 137 loop : -2.75 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 31 HIS 0.015 0.001 HIS A1871 PHE 0.030 0.001 PHE A1533 TYR 0.026 0.001 TYR A1700 ARG 0.005 0.000 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 199 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.393 Fit side-chains REVERT: A 697 TRP cc_start: 0.8542 (m100) cc_final: 0.8145 (m100) REVERT: A 2034 TYR cc_start: 0.6354 (t80) cc_final: 0.5992 (t80) outliers start: 12 outliers final: 8 residues processed: 193 average time/residue: 0.2083 time to fit residues: 63.4651 Evaluate side-chains 183 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 175 optimal weight: 0.0770 chunk 189 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13807 Z= 0.168 Angle : 0.577 9.429 18946 Z= 0.283 Chirality : 0.043 0.268 2313 Planarity : 0.004 0.061 2438 Dihedral : 8.280 97.567 2287 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.79 % Favored : 90.10 % Rotamer: Outliers : 0.89 % Allowed : 10.60 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1911 helix: 1.18 (0.18), residues: 895 sheet: -0.27 (0.52), residues: 115 loop : -2.69 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 431 HIS 0.008 0.001 HIS A 721 PHE 0.028 0.001 PHE A1533 TYR 0.021 0.001 TYR A1700 ARG 0.003 0.000 ARG A1514 *********************** 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 202 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.343 Fit side-chains REVERT: A 697 TRP cc_start: 0.8436 (m100) cc_final: 0.8158 (m100) REVERT: A 855 TRP cc_start: 0.6711 (t-100) cc_final: 0.6250 (t-100) REVERT: A 1843 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7350 (mmm160) REVERT: A 2034 TYR cc_start: 0.6379 (t80) cc_final: 0.5982 (t80) outliers start: 10 outliers final: 6 residues processed: 197 average time/residue: 0.1977 time to fit residues: 62.2708 Evaluate side-chains 190 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1712 LEU 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: 0.7980 chunk 132 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13807 Z= 0.286 Angle : 0.634 9.669 18946 Z= 0.317 Chirality : 0.045 0.280 2313 Planarity : 0.005 0.060 2438 Dihedral : 7.569 92.475 2287 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.84 % Favored : 89.01 % Rotamer: Outliers : 1.87 % Allowed : 12.38 % Favored : 85.75 % 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: -1.19 (0.20), residues: 1911 helix: 0.93 (0.18), residues: 898 sheet: -1.14 (0.46), residues: 146 loop : -2.72 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 431 HIS 0.006 0.001 HIS A 776 PHE 0.028 0.002 PHE A1076 TYR 0.014 0.001 TYR A1700 ARG 0.004 0.000 ARG A 452 *********************** 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 203 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.428 Fit side-chains REVERT: A 450 MET cc_start: 0.8569 (mmm) cc_final: 0.8353 (mmm) REVERT: A 633 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: A 855 TRP cc_start: 0.6793 (t-100) cc_final: 0.6341 (t-100) REVERT: A 1843 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7564 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7816 (mm) cc_final: 0.7368 (mp) REVERT: A 2034 TYR cc_start: 0.6580 (t80) cc_final: 0.6070 (t80) outliers start: 21 outliers final: 14 residues processed: 191 average time/residue: 0.2099 time to fit residues: 63.5708 Evaluate side-chains 188 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 726 HIS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 974 SER Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 159 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 167 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13807 Z= 0.191 Angle : 0.588 9.487 18946 Z= 0.292 Chirality : 0.043 0.273 2313 Planarity : 0.004 0.059 2438 Dihedral : 6.863 91.272 2287 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.95 % Favored : 89.95 % Rotamer: Outliers : 1.60 % Allowed : 14.43 % Favored : 83.97 % 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: 1.00 (0.18), residues: 899 sheet: -0.74 (0.50), residues: 122 loop : -2.76 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.022 0.001 PHE A1076 TYR 0.014 0.001 TYR A1700 ARG 0.010 0.000 ARG A1514 *********************** 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 202 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.574 Fit side-chains REVERT: A 450 MET cc_start: 0.8564 (mmm) cc_final: 0.8332 (mmm) REVERT: A 633 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: A 855 TRP cc_start: 0.6732 (t-100) cc_final: 0.6309 (t-100) REVERT: A 1843 ARG cc_start: 0.7996 (mmm160) cc_final: 0.7442 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7643 (mm) cc_final: 0.7239 (mp) REVERT: A 2034 TYR cc_start: 0.6486 (t80) cc_final: 0.5944 (t80) outliers start: 18 outliers final: 12 residues processed: 191 average time/residue: 0.2119 time to fit residues: 65.0430 Evaluate side-chains 193 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 506 THR 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 974 SER 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 2109 LEU Chi-restraints excluded: chain A residue 2126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.0370 chunk 168 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1561 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= 0.198 Angle : 0.584 9.537 18946 Z= 0.290 Chirality : 0.043 0.272 2313 Planarity : 0.004 0.059 2438 Dihedral : 6.513 90.555 2287 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.90 % Favored : 90.00 % Rotamer: Outliers : 2.05 % Allowed : 14.96 % Favored : 82.99 % 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: -1.11 (0.20), residues: 1911 helix: 1.03 (0.18), residues: 899 sheet: -0.90 (0.50), residues: 127 loop : -2.74 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.022 0.001 PHE A1533 TYR 0.014 0.001 TYR A1700 ARG 0.005 0.000 ARG A1514 *********************** REFINEMENT MACRO_CYCLE 6 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 202 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.599 Fit side-chains REVERT: A 450 MET cc_start: 0.8571 (mmm) cc_final: 0.8335 (mmm) REVERT: A 633 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: A 855 TRP cc_start: 0.6756 (t-100) cc_final: 0.6476 (t-100) REVERT: A 1843 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7563 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7565 (mm) cc_final: 0.7173 (mp) REVERT: A 2034 TYR cc_start: 0.6511 (t80) cc_final: 0.5908 (t80) outliers start: 23 outliers final: 18 residues processed: 188 average time/residue: 0.2047 time to fit residues: 61.9842 Evaluate side-chains 196 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 TYR Chi-restraints excluded: chain A residue 704 SER 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 974 SER Chi-restraints excluded: chain A residue 1119 HIS 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 Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13807 Z= 0.259 Angle : 0.627 9.628 18946 Z= 0.314 Chirality : 0.044 0.277 2313 Planarity : 0.005 0.059 2438 Dihedral : 6.699 90.172 2287 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.20 % Favored : 88.69 % Rotamer: Outliers : 2.05 % Allowed : 15.14 % Favored : 82.81 % 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: -1.26 (0.20), residues: 1911 helix: 0.93 (0.18), residues: 898 sheet: -1.31 (0.46), residues: 141 loop : -2.79 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.026 0.001 PHE A1076 TYR 0.014 0.001 TYR A1700 ARG 0.004 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 7 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 198 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.558 Fit side-chains REVERT: A 450 MET cc_start: 0.8597 (mmm) cc_final: 0.8339 (mmm) REVERT: A 633 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: A 648 MET cc_start: 0.8511 (mmp) cc_final: 0.7946 (mmp) REVERT: A 855 TRP cc_start: 0.6835 (t-100) cc_final: 0.6422 (t-100) REVERT: A 1843 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7709 (mmm-85) REVERT: A 1874 LEU cc_start: 0.7652 (mm) cc_final: 0.7259 (mp) outliers start: 23 outliers final: 16 residues processed: 188 average time/residue: 0.2140 time to fit residues: 64.6920 Evaluate side-chains 189 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 506 THR 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 704 SER 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 974 SER Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 2058 LEU Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2150 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 17 optimal weight: 0.0060 chunk 146 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7402 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13807 Z= 0.162 Angle : 0.577 9.363 18946 Z= 0.285 Chirality : 0.042 0.255 2313 Planarity : 0.004 0.060 2438 Dihedral : 6.336 88.052 2287 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 1.25 % Allowed : 15.94 % Favored : 82.81 % 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: 1.11 (0.18), residues: 899 sheet: -0.65 (0.52), residues: 120 loop : -2.77 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.019 0.001 PHE A1533 TYR 0.013 0.001 TYR A2016 ARG 0.005 0.000 ARG A1514 *********************** REFINEMENT MACRO_CYCLE 8 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 202 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 188 time to evaluate : 1.477 Fit side-chains REVERT: A 450 MET cc_start: 0.8627 (mmm) cc_final: 0.8389 (mmm) REVERT: A 633 TYR cc_start: 0.8121 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: A 648 MET cc_start: 0.8362 (mmp) cc_final: 0.7865 (mmp) REVERT: A 855 TRP cc_start: 0.6795 (t-100) cc_final: 0.6497 (t-100) REVERT: A 1843 ARG cc_start: 0.7983 (mmm160) cc_final: 0.7474 (mmm160) REVERT: A 1874 LEU cc_start: 0.7407 (mm) cc_final: 0.7141 (mp) REVERT: A 2034 TYR cc_start: 0.6445 (t80) cc_final: 0.5794 (t80) REVERT: A 2049 LYS cc_start: 0.7304 (tppt) cc_final: 0.6978 (tppt) outliers start: 14 outliers final: 11 residues processed: 192 average time/residue: 0.2093 time to fit residues: 65.6427 Evaluate side-chains 192 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE 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 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 2058 LEU Chi-restraints excluded: chain A residue 2083 ILE Chi-restraints excluded: chain A residue 2109 LEU Chi-restraints excluded: chain A residue 2126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.0980 chunk 162 optimal weight: 8.9990 chunk 173 optimal weight: 0.2980 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 0.0050 chunk 136 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13807 Z= 0.160 Angle : 0.569 9.509 18946 Z= 0.282 Chirality : 0.042 0.257 2313 Planarity : 0.004 0.058 2438 Dihedral : 6.132 87.299 2287 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.58 % Favored : 90.31 % Rotamer: Outliers : 1.34 % Allowed : 16.38 % Favored : 82.28 % 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: -0.95 (0.20), residues: 1911 helix: 1.19 (0.18), residues: 900 sheet: -0.33 (0.52), residues: 117 loop : -2.76 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.018 0.001 PHE A1533 TYR 0.013 0.001 TYR A1700 ARG 0.004 0.000 ARG A1514 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 1.469 Fit side-chains REVERT: A 450 MET cc_start: 0.8635 (mmm) cc_final: 0.8406 (mmm) REVERT: A 633 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: A 648 MET cc_start: 0.8345 (mmp) cc_final: 0.7970 (mmp) REVERT: A 855 TRP cc_start: 0.6862 (t-100) cc_final: 0.6597 (t-100) REVERT: A 1843 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7334 (mmm160) REVERT: A 1874 LEU cc_start: 0.7323 (mm) cc_final: 0.7082 (mp) REVERT: A 2034 TYR cc_start: 0.6468 (t80) cc_final: 0.5831 (t80) REVERT: A 2049 LYS cc_start: 0.7299 (tppt) cc_final: 0.6994 (tppt) outliers start: 15 outliers final: 12 residues processed: 191 average time/residue: 0.2032 time to fit residues: 62.6583 Evaluate side-chains 195 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE Chi-restraints excluded: chain A residue 311 THR 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 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 1882 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 176 optimal weight: 0.0980 chunk 153 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13807 Z= 0.158 Angle : 0.567 9.495 18946 Z= 0.279 Chirality : 0.042 0.257 2313 Planarity : 0.004 0.058 2438 Dihedral : 5.981 86.146 2287 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.32 % Favored : 90.58 % Rotamer: Outliers : 1.16 % Allowed : 17.10 % Favored : 81.75 % 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: -0.85 (0.20), residues: 1911 helix: 1.23 (0.18), residues: 900 sheet: -0.30 (0.53), residues: 117 loop : -2.66 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 431 HIS 0.005 0.001 HIS A 776 PHE 0.018 0.001 PHE A 734 TYR 0.013 0.001 TYR A1700 ARG 0.003 0.000 ARG A1514 ********************** REFINEMENT MACRO_CYCLE 10 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 197 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.435 Fit side-chains REVERT: A 450 MET cc_start: 0.8657 (mmm) cc_final: 0.8439 (mmm) REVERT: A 633 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: A 855 TRP cc_start: 0.6843 (t-100) cc_final: 0.6589 (t-100) REVERT: A 1874 LEU cc_start: 0.7257 (mm) cc_final: 0.7036 (mp) REVERT: A 2034 TYR cc_start: 0.6445 (t80) cc_final: 0.5808 (t80) REVERT: A 2049 LYS cc_start: 0.7353 (tppt) cc_final: 0.7115 (tppt) outliers start: 13 outliers final: 10 residues processed: 188 average time/residue: 0.2019 time to fit residues: 61.0999 Evaluate side-chains 194 residues out of total 1705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 PHE 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 774 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1882 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.0170 chunk 46 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 134 optimal weight: 0.3980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 721 HIS A1442 ASN ** A1513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.163747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.144799 restraints weight = 30386.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144625 restraints weight = 20632.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.145962 restraints weight = 18179.580| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13807 Z= 0.168 Angle : 0.571 9.484 18946 Z= 0.282 Chirality : 0.042 0.256 2313 Planarity : 0.004 0.059 2438 Dihedral : 5.958 86.284 2287 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.90 % Favored : 90.00 % Rotamer: Outliers : 1.25 % Allowed : 17.10 % Favored : 81.66 % 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: -0.85 (0.20), residues: 1911 helix: 1.24 (0.18), residues: 900 sheet: -0.30 (0.53), residues: 117 loop : -2.66 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 499 HIS 0.005 0.001 HIS A 776 PHE 0.016 0.001 PHE A1076 TYR 0.013 0.001 TYR A1700 ARG 0.013 0.000 ARG A1514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.19 seconds wall clock time: 51 minutes 10.49 seconds (3070.49 seconds total)