Starting phenix.real_space_refine on Tue Aug 6 09:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/08_2024/8r54_18891.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10001 2.51 5 N 2705 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2325": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15900 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 15570 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1982, 15562 Classifications: {'peptide': 1982} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 76, 'TRANS': 1905} Chain breaks: 6 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Conformer: "B" Number of residues, atoms: 1982, 15562 Classifications: {'peptide': 1982} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 76, 'TRANS': 1905} Chain breaks: 6 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 bond proxies already assigned to first conformer: 15893 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASN A2407 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN A2407 " occ=0.60 Time building chain proxies: 15.35, per 1000 atoms: 0.97 Number of scatterers: 15900 At special positions: 0 Unit cell: (140.876, 122.837, 117.683, 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 80 16.00 O 3114 8.00 N 2705 7.00 C 10001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 681 " - pdb=" SG CYS A 691 " distance=2.03 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 696 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 707 " distance=2.03 Simple disulfide: pdb=" SG CYS A 712 " - pdb=" SG CYS A 722 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 727 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 738 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS A 764 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 795 " - pdb=" SG CYS A 806 " distance=2.03 Simple disulfide: pdb=" SG CYS A 801 " - pdb=" SG CYS A 812 " distance=2.03 Simple disulfide: pdb=" SG CYS A 954 " - pdb=" SG CYS A1088 " distance=2.03 Simple disulfide: pdb=" SG CYS A1160 " - pdb=" SG CYS A1163 " distance=2.03 Simple disulfide: pdb=" SG CYS A1264 " - pdb=" SG CYS A1272 " distance=2.03 Simple disulfide: pdb=" SG CYS A1331 " - pdb=" SG CYS A1384 " distance=2.03 Simple disulfide: pdb=" SG CYS A1448 " - pdb=" SG CYS A1456 " distance=2.03 Simple disulfide: pdb=" SG CYS A1450 " - pdb=" SG CYS A1458 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A2801 " - " ASN A1820 " " NAG A2802 " - " ASN A2576 " " NAG A2803 " - " ASN A1202 " " NAG A2804 " - " ASN A1677 " " NAG B 1 " - " ASN A2264 " " NAG C 1 " - " ASN A1544 " " NAG D 1 " - " ASN A1735 " " NAG E 1 " - " ASN A1640 " " NAG F 1 " - " ASN A1527 " " NAG G 1 " - " ASN A1921 " " NAG H 1 " - " ASN A2124 " " NAG I 1 " - " ASN A2329 " " NAG J 1 " - " ASN A 883 " Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 5.5 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 26 sheets defined 7.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 744 through 750 removed outlier: 3.793A pdb=" N ASN A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 744 through 750' Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.985A pdb=" N ARG A 813 " --> pdb=" O PRO A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.687A pdb=" N ILE A 845 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1142 No H-bonds generated for 'chain 'A' and resid 1140 through 1142' Processing helix chain 'A' and resid 2337 through 2341 Processing helix chain 'A' and resid 2370 through 2378 removed outlier: 4.160A pdb=" N LYS A2377 " --> pdb=" O LYS A2373 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A2378 " --> pdb=" O ARG A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2391 Processing helix chain 'A' and resid 2416 through 2421 removed outlier: 3.954A pdb=" N ALA A2420 " --> pdb=" O HIS A2416 " (cutoff:3.500A) Processing helix chain 'A' and resid 2435 through 2443 removed outlier: 3.613A pdb=" N GLN A2443 " --> pdb=" O VAL A2439 " (cutoff:3.500A) Processing helix chain 'A' and resid 2451 through 2465 removed outlier: 3.663A pdb=" N LEU A2465 " --> pdb=" O ALA A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2529 removed outlier: 3.623A pdb=" N ILE A2522 " --> pdb=" O ASN A2518 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A2523 " --> pdb=" O GLU A2519 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL A2524 " --> pdb=" O ASP A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2555 through 2562 removed outlier: 3.622A pdb=" N LEU A2562 " --> pdb=" O ASP A2558 " (cutoff:3.500A) Processing helix chain 'A' and resid 2612 through 2642 removed outlier: 3.557A pdb=" N GLU A2616 " --> pdb=" O THR A2612 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A2642 " --> pdb=" O GLN A2638 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2662 removed outlier: 3.822A pdb=" N LEU A2659 " --> pdb=" O LYS A2655 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A2660 " --> pdb=" O ARG A2656 " (cutoff:3.500A) Processing helix chain 'A' and resid 2678 through 2682 Processing sheet with id=AA1, first strand: chain 'A' and resid 689 through 692 removed outlier: 3.589A pdb=" N VAL A 690 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET A 692 " --> pdb=" O SER A 695 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 695 " --> pdb=" O MET A 692 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 723 Processing sheet with id=AA3, first strand: chain 'A' and resid 754 through 756 removed outlier: 3.828A pdb=" N THR A 754 " --> pdb=" O HIS A 761 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS A 761 " --> pdb=" O THR A 754 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 902 through 908 removed outlier: 3.777A pdb=" N PHE A 903 " --> pdb=" O GLY A 869 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 902 through 908 removed outlier: 3.777A pdb=" N PHE A 903 " --> pdb=" O GLY A 869 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 894 through 896 removed outlier: 3.792A pdb=" N ASN A 883 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 918 " --> pdb=" O ASN A 883 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 885 " --> pdb=" O VAL A 916 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 965 through 968 Processing sheet with id=AA8, first strand: chain 'A' and resid 984 through 985 Processing sheet with id=AA9, first strand: chain 'A' and resid 1044 through 1050 removed outlier: 4.264A pdb=" N LYS A1033 " --> pdb=" O GLU A1084 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1075 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1121 through 1123 Processing sheet with id=AB2, first strand: chain 'A' and resid 1145 through 1150 removed outlier: 7.029A pdb=" N ILE A1495 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A1494 " --> pdb=" O ASP A1489 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR A1486 " --> pdb=" O LEU A1477 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU A1477 " --> pdb=" O TYR A1486 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA A1488 " --> pdb=" O SER A1475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1177 through 1180 removed outlier: 4.130A pdb=" N ALA A1177 " --> pdb=" O GLY A1189 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A1207 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1218 through 1221 Processing sheet with id=AB5, first strand: chain 'A' and resid 1297 through 1301 removed outlier: 6.750A pdb=" N ILE A1305 " --> pdb=" O LEU A1317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1348 through 1350 removed outlier: 6.524A pdb=" N VAL A1365 " --> pdb=" O ALA A1377 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1405 through 1410 removed outlier: 5.370A pdb=" N ALA A1405 " --> pdb=" O THR A1421 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A1421 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA A1407 " --> pdb=" O THR A1419 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLN A1431 " --> pdb=" O LEU A1440 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU A1440 " --> pdb=" O GLN A1431 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1511 through 1515 removed outlier: 3.618A pdb=" N ILE A1523 " --> pdb=" O TYR A1532 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLN A1531 " --> pdb=" O PHE A1545 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A1543 " --> pdb=" O THR A1533 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A1535 " --> pdb=" O TYR A1541 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR A1541 " --> pdb=" O SER A1535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1565 through 1568 removed outlier: 3.573A pdb=" N ARG A1576 " --> pdb=" O ARG A1567 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A1575 " --> pdb=" O LEU A1587 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A1597 " --> pdb=" O THR A1588 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LYS A1596 " --> pdb=" O PHE A1608 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A1607 " --> pdb=" O LYS A1620 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A1620 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR A1609 " --> pdb=" O ALA A1618 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA A1618 " --> pdb=" O PHE A1630 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A1629 " --> pdb=" O VAL A1641 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL A1641 " --> pdb=" O PHE A1629 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A1631 " --> pdb=" O THR A1639 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR A1639 " --> pdb=" O LEU A1651 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A1651 " --> pdb=" O THR A1639 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1672 " --> pdb=" O ILE A1663 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A1692 " --> pdb=" O GLN A1689 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A1704 " --> pdb=" O TYR A1716 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ASP A1713 " --> pdb=" O MET A1736 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET A1736 " --> pdb=" O ASP A1713 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N HIS A1715 " --> pdb=" O ARG A1734 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG A1734 " --> pdb=" O HIS A1715 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN A1717 " --> pdb=" O ALA A1732 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1745 " --> pdb=" O MET A1736 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A1775 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A1769 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN A1773 " --> pdb=" O VAL A1769 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A1789 " --> pdb=" O SER A1776 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1798 " --> pdb=" O LEU A1811 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1819 " --> pdb=" O TRP A1810 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA A1830 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A1837 " --> pdb=" O ARG A1834 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS A1840 " --> pdb=" O ARG A1852 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A1852 " --> pdb=" O LYS A1840 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP A1842 " --> pdb=" O VAL A1850 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A1850 " --> pdb=" O TYR A1862 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A1891 " --> pdb=" O GLU A1882 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A1926 " --> pdb=" O ASN A1913 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1915 " --> pdb=" O ILE A1924 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A1925 " --> pdb=" O THR A1937 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A1937 " --> pdb=" O ILE A1925 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP A1927 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU A1935 " --> pdb=" O PHE A1948 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER A1957 " --> pdb=" O PHE A1968 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A1965 " --> pdb=" O GLN A1983 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG A2016 " --> pdb=" O GLY A2032 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A2032 " --> pdb=" O ARG A2016 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A2018 " --> pdb=" O MET A2030 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A2030 " --> pdb=" O ASP A2018 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A2020 " --> pdb=" O THR A2028 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A2034 " --> pdb=" O THR A2037 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1751 through 1756 removed outlier: 7.052A pdb=" N ARG A1752 " --> pdb=" O PHE A1763 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE A1763 " --> pdb=" O ARG A1752 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A1754 " --> pdb=" O ASN A1761 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A1775 " --> pdb=" O LEU A1767 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL A1769 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN A1773 " --> pdb=" O VAL A1769 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A1789 " --> pdb=" O SER A1776 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1798 " --> pdb=" O LEU A1811 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1819 " --> pdb=" O TRP A1810 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ALA A1830 " --> pdb=" O VAL A1841 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A1837 " --> pdb=" O ARG A1834 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS A1840 " --> pdb=" O ARG A1852 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG A1852 " --> pdb=" O LYS A1840 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP A1842 " --> pdb=" O VAL A1850 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL A1850 " --> pdb=" O TYR A1862 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A1891 " --> pdb=" O GLU A1882 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A1926 " --> pdb=" O ASN A1913 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A1915 " --> pdb=" O ILE A1924 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE A1925 " --> pdb=" O THR A1937 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR A1937 " --> pdb=" O ILE A1925 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP A1927 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU A1935 " --> pdb=" O PHE A1948 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER A1957 " --> pdb=" O PHE A1968 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A1965 " --> pdb=" O GLN A1983 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG A2016 " --> pdb=" O GLY A2032 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A2032 " --> pdb=" O ARG A2016 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A2018 " --> pdb=" O MET A2030 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A2030 " --> pdb=" O ASP A2018 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER A2020 " --> pdb=" O THR A2028 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR A2028 " --> pdb=" O TYR A2044 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU A2054 " --> pdb=" O VAL A2061 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A2056 " --> pdb=" O PHE A2059 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A2076 " --> pdb=" O TYR A2092 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR A2092 " --> pdb=" O THR A2076 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A2078 " --> pdb=" O ILE A2090 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A2090 " --> pdb=" O THR A2078 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS A2080 " --> pdb=" O LYS A2088 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS A2088 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR A2103 " --> pdb=" O LYS A2088 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A2090 " --> pdb=" O TRP A2101 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP A2101 " --> pdb=" O ILE A2090 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A2092 " --> pdb=" O MET A2099 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A2114 " --> pdb=" O GLN A2105 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR A2113 " --> pdb=" O TYR A2130 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A2130 " --> pdb=" O THR A2113 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLN A2139 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG A2150 " --> pdb=" O GLN A2139 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A2141 " --> pdb=" O MET A2148 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ARG A2150 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A2162 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN A2152 " --> pdb=" O HIS A2160 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N HIS A2160 " --> pdb=" O LEU A2173 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU A2184 " --> pdb=" O PRO A2172 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A2174 " --> pdb=" O THR A2182 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR A2182 " --> pdb=" O TYR A2189 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG A2198 " --> pdb=" O PHE A2205 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A2215 " --> pdb=" O GLU A2206 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR A2214 " --> pdb=" O TYR A2227 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1995 through 1996 Processing sheet with id=AC3, first strand: chain 'A' and resid 2248 through 2249 removed outlier: 3.892A pdb=" N HIS A2261 " --> pdb=" O PHE A2249 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2271 through 2275 removed outlier: 3.727A pdb=" N ALA A2283 " --> pdb=" O TYR A2274 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE A2282 " --> pdb=" O ILE A2294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A2290 " --> pdb=" O ILE A2286 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A2304 " --> pdb=" O ALA A2295 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU A2303 " --> pdb=" O GLN A2315 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN A2315 " --> pdb=" O LEU A2303 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A2305 " --> pdb=" O LEU A2313 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN A2315 " --> pdb=" O ASP A2327 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP A2327 " --> pdb=" O GLN A2315 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN A2317 " --> pdb=" O TYR A2325 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2342 through 2344 removed outlier: 3.765A pdb=" N ASP A2344 " --> pdb=" O LEU A2349 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A2349 " --> pdb=" O ASP A2344 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A2363 " --> pdb=" O ASP A2358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 2500 through 2505 removed outlier: 3.778A pdb=" N ASN A2512 " --> pdb=" O MET A2501 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 2532 through 2541 removed outlier: 10.457A pdb=" N GLU A2535 " --> pdb=" O ILE A2550 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N ILE A2550 " --> pdb=" O GLU A2535 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A2537 " --> pdb=" O TYR A2548 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR A2548 " --> pdb=" O LEU A2537 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A2539 " --> pdb=" O THR A2546 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A2594 " --> pdb=" O TYR A2609 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A2582 " --> pdb=" O PHE A2593 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A2577 " --> pdb=" O LYS A2569 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 2667 through 2671 removed outlier: 3.834A pdb=" N ASP A2668 " --> pdb=" O LEU A2691 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1476 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: 11.08 Time building geometry restraints manager: 7.18 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: 5213 1.34 - 1.47: 4022 1.47 - 1.59: 6885 1.59 - 1.71: 0 1.71 - 1.83: 121 Bond restraints: 16241 Sorted by residual: bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.31e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 16236 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.36: 252 105.36 - 112.57: 8491 112.57 - 119.77: 5389 119.77 - 126.98: 7739 126.98 - 134.19: 177 Bond angle restraints: 22048 Sorted by residual: angle pdb=" N GLN A1691 " pdb=" CA GLN A1691 " pdb=" C GLN A1691 " ideal model delta sigma weight residual 113.97 122.28 -8.31 1.28e+00 6.10e-01 4.22e+01 angle pdb=" N GLN A1691 " pdb=" CA GLN A1691 " pdb=" CB GLN A1691 " ideal model delta sigma weight residual 110.67 102.07 8.60 1.39e+00 5.18e-01 3.83e+01 angle pdb=" C CYS A 712 " pdb=" CA CYS A 712 " pdb=" CB CYS A 712 " ideal model delta sigma weight residual 116.54 109.96 6.58 1.15e+00 7.56e-01 3.28e+01 angle pdb=" C ASP A1690 " pdb=" CA ASP A1690 " pdb=" CB ASP A1690 " ideal model delta sigma weight residual 110.42 120.38 -9.96 1.99e+00 2.53e-01 2.50e+01 angle pdb=" C SER A1211 " pdb=" CA SER A1211 " pdb=" CB SER A1211 " ideal model delta sigma weight residual 115.89 109.47 6.42 1.32e+00 5.74e-01 2.37e+01 ... (remaining 22043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8781 21.76 - 43.52: 961 43.52 - 65.27: 173 65.27 - 87.03: 60 87.03 - 108.79: 20 Dihedral angle restraints: 9995 sinusoidal: 4252 harmonic: 5743 Sorted by residual: dihedral pdb=" CB CYS A 712 " pdb=" SG CYS A 712 " pdb=" SG CYS A 722 " pdb=" CB CYS A 722 " ideal model delta sinusoidal sigma weight residual -86.00 -168.76 82.76 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS A 764 " pdb=" SG CYS A 764 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -159.46 73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 9992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2175 0.071 - 0.142: 319 0.142 - 0.213: 6 0.213 - 0.284: 4 0.284 - 0.355: 3 Chirality restraints: 2507 Sorted by residual: chirality pdb=" CA ASP A1690 " pdb=" N ASP A1690 " pdb=" C ASP A1690 " pdb=" CB ASP A1690 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A1527 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG A2804 " pdb=" ND2 ASN A1677 " pdb=" C2 NAG A2804 " pdb=" O5 NAG A2804 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2504 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 877 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO A 878 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 985 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 986 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1444 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A1445 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1445 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1445 " -0.026 5.00e-02 4.00e+02 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 955 2.72 - 3.27: 15194 3.27 - 3.81: 24448 3.81 - 4.36: 28944 4.36 - 4.90: 52551 Nonbonded interactions: 122092 Sorted by model distance: nonbonded pdb=" OG SER A 687 " pdb=" OD2 ASP A1671 " model vdw 2.176 3.040 nonbonded pdb=" O THR A 850 " pdb=" OG1 THR A 895 " model vdw 2.186 3.040 nonbonded pdb=" O LEU A1617 " pdb=" OH TYR A1632 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 873 " pdb=" OD1 ASP A 875 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A1824 " pdb=" O GLN A1828 " model vdw 2.234 3.040 ... (remaining 122087 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.40 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: 0.720 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 60.980 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.006 0.042 16241 Z= 0.368 Angle : 0.649 10.696 22048 Z= 0.330 Chirality : 0.049 0.355 2507 Planarity : 0.004 0.058 2827 Dihedral : 18.747 108.791 6278 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.79 % Favored : 91.16 % Rotamer: Outliers : 0.35 % Allowed : 31.27 % Favored : 68.38 % Cbeta Deviations : 0.05 % 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: -1.09 (0.19), residues: 1971 helix: 1.93 (0.53), residues: 106 sheet: -0.11 (0.22), residues: 603 loop : -1.33 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1886 HIS 0.005 0.001 HIS A1806 PHE 0.011 0.001 PHE A1524 TYR 0.013 0.001 TYR A2609 ARG 0.004 0.000 ARG A1765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.811 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.2912 time to fit residues: 45.7948 Evaluate side-chains 100 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2396 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0030 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN A1363 ASN A1697 GLN A1806 HIS ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16241 Z= 0.262 Angle : 0.630 9.280 22048 Z= 0.329 Chirality : 0.047 0.347 2507 Planarity : 0.004 0.055 2827 Dihedral : 10.286 91.536 2693 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 3.13 % Allowed : 29.03 % Favored : 67.85 % 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 (0.19), residues: 1971 helix: 1.80 (0.52), residues: 107 sheet: 0.12 (0.22), residues: 592 loop : -1.29 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.016 0.001 PHE A1524 TYR 0.011 0.001 TYR A2609 ARG 0.005 0.000 ARG A1236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 115 time to evaluate : 1.766 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: A 1671 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7743 (p0) REVERT: A 2409 TRP cc_start: 0.8570 (OUTLIER) cc_final: 0.7093 (m100) outliers start: 53 outliers final: 24 residues processed: 160 average time/residue: 0.2805 time to fit residues: 68.5222 Evaluate side-chains 128 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1697 GLN Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 149 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1363 ASN A2023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16241 Z= 0.365 Angle : 0.656 7.985 22048 Z= 0.340 Chirality : 0.048 0.381 2507 Planarity : 0.004 0.062 2827 Dihedral : 8.841 83.291 2691 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.33 % Favored : 91.62 % Rotamer: Outliers : 3.78 % Allowed : 29.32 % Favored : 66.90 % 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: -1.01 (0.19), residues: 1971 helix: 1.76 (0.53), residues: 106 sheet: 0.13 (0.22), residues: 592 loop : -1.35 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2444 HIS 0.003 0.001 HIS A 927 PHE 0.015 0.001 PHE A1524 TYR 0.015 0.001 TYR A2609 ARG 0.004 0.000 ARG A2592 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 104 time to evaluate : 1.651 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 1671 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7735 (p0) REVERT: A 1848 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7553 (ptt180) REVERT: A 2294 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9094 (mm) REVERT: A 2409 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7082 (m100) outliers start: 64 outliers final: 40 residues processed: 163 average time/residue: 0.2741 time to fit residues: 67.8900 Evaluate side-chains 144 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 99 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16241 Z= 0.346 Angle : 0.653 9.914 22048 Z= 0.336 Chirality : 0.048 0.378 2507 Planarity : 0.004 0.059 2827 Dihedral : 7.878 76.200 2691 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.31 % Allowed : 28.97 % Favored : 66.73 % 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: -1.02 (0.19), residues: 1971 helix: 1.81 (0.53), residues: 105 sheet: 0.08 (0.22), residues: 606 loop : -1.36 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2444 HIS 0.005 0.001 HIS A2397 PHE 0.015 0.001 PHE A2025 TYR 0.014 0.001 TYR A2609 ARG 0.003 0.000 ARG A2592 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 105 time to evaluate : 1.668 Fit side-chains REVERT: A 1671 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7730 (p0) REVERT: A 1848 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7530 (ptt180) REVERT: A 2294 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9097 (mm) REVERT: A 2409 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.7166 (m100) outliers start: 73 outliers final: 55 residues processed: 172 average time/residue: 0.2593 time to fit residues: 69.4433 Evaluate side-chains 160 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 101 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 97 optimal weight: 0.9990 chunk 171 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16241 Z= 0.154 Angle : 0.576 8.606 22048 Z= 0.295 Chirality : 0.045 0.357 2507 Planarity : 0.004 0.057 2827 Dihedral : 6.579 63.604 2689 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.60 % Allowed : 30.91 % Favored : 66.49 % 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: -0.80 (0.19), residues: 1971 helix: 2.02 (0.53), residues: 106 sheet: 0.29 (0.21), residues: 609 loop : -1.24 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2486 HIS 0.005 0.001 HIS A1900 PHE 0.029 0.001 PHE A2025 TYR 0.008 0.001 TYR A1083 ARG 0.003 0.000 ARG A1834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.804 Fit side-chains REVERT: A 811 TYR cc_start: 0.5923 (t80) cc_final: 0.5681 (t80) REVERT: A 1367 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: A 1421 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8204 (p) outliers start: 44 outliers final: 37 residues processed: 158 average time/residue: 0.2694 time to fit residues: 65.9321 Evaluate side-chains 145 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 106 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN A2512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16241 Z= 0.175 Angle : 0.579 9.360 22048 Z= 0.293 Chirality : 0.045 0.361 2507 Planarity : 0.003 0.052 2827 Dihedral : 6.161 55.201 2689 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.19 % Allowed : 30.56 % Favored : 66.25 % 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: -0.70 (0.19), residues: 1971 helix: 2.22 (0.53), residues: 105 sheet: 0.36 (0.21), residues: 618 loop : -1.20 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1886 HIS 0.004 0.001 HIS A1900 PHE 0.011 0.001 PHE A1524 TYR 0.013 0.001 TYR A2402 ARG 0.002 0.000 ARG A2656 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 114 time to evaluate : 1.759 Fit side-chains REVERT: A 796 MET cc_start: 0.7398 (mmm) cc_final: 0.7105 (mmm) REVERT: A 1367 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: A 1848 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (ptt180) outliers start: 54 outliers final: 41 residues processed: 161 average time/residue: 0.2703 time to fit residues: 67.0128 Evaluate side-chains 150 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16241 Z= 0.147 Angle : 0.575 9.634 22048 Z= 0.291 Chirality : 0.045 0.356 2507 Planarity : 0.003 0.051 2827 Dihedral : 5.899 54.861 2689 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.83 % Allowed : 30.80 % Favored : 66.37 % 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: -0.65 (0.19), residues: 1971 helix: 2.23 (0.53), residues: 105 sheet: 0.41 (0.21), residues: 613 loop : -1.16 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1886 HIS 0.005 0.001 HIS A1900 PHE 0.019 0.001 PHE A2025 TYR 0.009 0.001 TYR A2402 ARG 0.004 0.000 ARG A2592 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.941 Fit side-chains REVERT: A 796 MET cc_start: 0.7482 (mmm) cc_final: 0.7260 (mmm) REVERT: A 1111 MET cc_start: 0.8594 (mmp) cc_final: 0.8356 (mmp) REVERT: A 1367 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: A 1848 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7499 (ptt180) REVERT: A 2294 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9057 (mm) outliers start: 48 outliers final: 34 residues processed: 157 average time/residue: 0.2767 time to fit residues: 66.1073 Evaluate side-chains 146 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN A2339 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16241 Z= 0.354 Angle : 0.653 9.114 22048 Z= 0.334 Chirality : 0.048 0.380 2507 Planarity : 0.004 0.053 2827 Dihedral : 6.209 56.907 2687 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.24 % Allowed : 30.38 % Favored : 66.37 % 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: -0.81 (0.19), residues: 1971 helix: 1.97 (0.53), residues: 106 sheet: 0.33 (0.21), residues: 618 loop : -1.28 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1886 HIS 0.003 0.001 HIS A 927 PHE 0.017 0.001 PHE A1524 TYR 0.015 0.001 TYR A2609 ARG 0.003 0.000 ARG A1765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 106 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7353 (mmm) cc_final: 0.7090 (mmm) REVERT: A 1848 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7635 (ptt180) REVERT: A 2294 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9073 (mm) outliers start: 55 outliers final: 48 residues processed: 156 average time/residue: 0.2607 time to fit residues: 63.6730 Evaluate side-chains 152 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 102 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16241 Z= 0.217 Angle : 0.610 9.788 22048 Z= 0.309 Chirality : 0.046 0.369 2507 Planarity : 0.003 0.053 2827 Dihedral : 6.020 56.173 2687 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.07 % Allowed : 30.56 % Favored : 66.37 % 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: -0.77 (0.19), residues: 1971 helix: 2.07 (0.53), residues: 105 sheet: 0.34 (0.21), residues: 615 loop : -1.25 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1886 HIS 0.004 0.001 HIS A1900 PHE 0.013 0.001 PHE A1524 TYR 0.013 0.001 TYR A2402 ARG 0.002 0.000 ARG A2592 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 1.890 Fit side-chains REVERT: A 796 MET cc_start: 0.7408 (mmm) cc_final: 0.7135 (mmm) REVERT: A 1598 MET cc_start: 0.7895 (ttp) cc_final: 0.7659 (ttp) REVERT: A 1848 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7565 (ptt180) REVERT: A 2294 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9075 (mm) outliers start: 52 outliers final: 44 residues processed: 154 average time/residue: 0.2689 time to fit residues: 64.6301 Evaluate side-chains 148 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 102 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 157 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16241 Z= 0.290 Angle : 0.793 59.182 22048 Z= 0.439 Chirality : 0.047 0.370 2507 Planarity : 0.004 0.085 2827 Dihedral : 6.029 56.189 2687 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.89 % Allowed : 30.56 % Favored : 66.55 % Cbeta Deviations : 0.05 % 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: -0.78 (0.19), residues: 1971 helix: 2.05 (0.53), residues: 105 sheet: 0.33 (0.21), residues: 616 loop : -1.25 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1886 HIS 0.004 0.001 HIS A2397 PHE 0.013 0.001 PHE A1524 TYR 0.012 0.001 TYR A2402 ARG 0.008 0.000 ARG A2656 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 102 time to evaluate : 2.295 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7449 (mmm) cc_final: 0.7178 (mmm) REVERT: A 1598 MET cc_start: 0.7906 (ttp) cc_final: 0.7675 (ttp) REVERT: A 1848 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7567 (ptt180) REVERT: A 2294 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9101 (mm) outliers start: 49 outliers final: 45 residues processed: 147 average time/residue: 0.2551 time to fit residues: 59.6699 Evaluate side-chains 149 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 102 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078288 restraints weight = 69755.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080862 restraints weight = 26071.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.083329 restraints weight = 16761.734| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16241 Z= 0.290 Angle : 0.793 59.182 22048 Z= 0.439 Chirality : 0.047 0.370 2507 Planarity : 0.004 0.085 2827 Dihedral : 6.029 56.189 2687 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.77 % Allowed : 30.68 % Favored : 66.55 % Cbeta Deviations : 0.05 % 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: -0.78 (0.19), residues: 1971 helix: 2.05 (0.53), residues: 105 sheet: 0.33 (0.21), residues: 616 loop : -1.25 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1886 HIS 0.004 0.001 HIS A2397 PHE 0.013 0.001 PHE A1524 TYR 0.012 0.001 TYR A2402 ARG 0.008 0.000 ARG A2656 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.20 seconds wall clock time: 53 minutes 20.86 seconds (3200.86 seconds total)