Starting phenix.real_space_refine on Fri Jun 28 17:28:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/06_2024/8r54_18891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/06_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_18891/06_2024/8r54_18891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/06_2024/8r54_18891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/06_2024/8r54_18891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r54_18891/06_2024/8r54_18891.pdb" } 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 14.28, per 1000 atoms: 0.90 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: 5.96 Conformation dependent library (CDL) restraints added in 5.3 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: 2.73 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: 11.01 Time building geometry restraints manager: 6.54 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 2.440 nonbonded pdb=" O THR A 850 " pdb=" OG1 THR A 895 " model vdw 2.186 2.440 nonbonded pdb=" O LEU A1617 " pdb=" OH TYR A1632 " model vdw 2.225 2.440 nonbonded pdb=" OG1 THR A 873 " pdb=" OD1 ASP A 875 " model vdw 2.228 2.440 nonbonded pdb=" OG SER A1824 " pdb=" O GLN A1828 " model vdw 2.234 2.440 ... (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 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: 0.560 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: 3.440 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 57.230 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.150 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.730 ------------------------------------------------------------------------------- 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 : 1.482 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.2899 time to fit residues: 45.3313 Evaluate side-chains 100 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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: 0.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 0.0050 chunk 51 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1806 HIS ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16241 Z= 0.209 Angle : 0.589 9.329 22048 Z= 0.305 Chirality : 0.046 0.353 2507 Planarity : 0.004 0.050 2827 Dihedral : 10.141 90.622 2693 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.24 % Rotamer: Outliers : 2.71 % Allowed : 30.03 % Favored : 67.26 % 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: -0.93 (0.19), residues: 1971 helix: 1.85 (0.52), residues: 107 sheet: 0.08 (0.22), residues: 609 loop : -1.26 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.013 0.001 PHE A1524 TYR 0.010 0.001 TYR A2609 ARG 0.003 0.000 ARG A1750 *********************** 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 155 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 1.830 Fit side-chains REVERT: A 1671 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7455 (p0) REVERT: A 2048 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8367 (p0) outliers start: 46 outliers final: 25 residues processed: 148 average time/residue: 0.2670 time to fit residues: 61.5713 Evaluate side-chains 130 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1081 VAL 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 1701 ASP 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 2023 ASN Chi-restraints excluded: chain A residue 2048 ASP Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2067 ASN Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2194 ASP Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2297 ASP Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 30.0000 chunk 149 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2339 HIS A2529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 16241 Z= 0.556 Angle : 0.744 8.551 22048 Z= 0.384 Chirality : 0.051 0.412 2507 Planarity : 0.005 0.056 2827 Dihedral : 9.271 85.728 2691 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.32 % Favored : 89.63 % Rotamer: Outliers : 5.31 % Allowed : 28.73 % Favored : 65.96 % 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: -1.27 (0.19), residues: 1971 helix: 1.55 (0.53), residues: 106 sheet: -0.04 (0.22), residues: 612 loop : -1.55 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A2444 HIS 0.007 0.001 HIS A 688 PHE 0.020 0.002 PHE A1524 TYR 0.016 0.002 TYR A1862 ARG 0.005 0.001 ARG A1765 *********************** 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 190 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 100 time to evaluate : 1.771 Fit side-chains REVERT: A 819 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: A 1848 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7678 (ptt180) REVERT: A 2294 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9107 (mm) REVERT: A 2409 TRP cc_start: 0.8577 (OUTLIER) cc_final: 0.7062 (m100) outliers start: 90 outliers final: 57 residues processed: 184 average time/residue: 0.2646 time to fit residues: 74.8501 Evaluate side-chains 160 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 99 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 819 GLN 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 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 1245 THR 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 1408 ILE Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1463 ASP Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1581 ASP Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1701 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 1842 ASP 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 2066 ILE Chi-restraints excluded: chain A residue 2067 ASN Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2194 ASP Chi-restraints excluded: chain A residue 2202 THR 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 Chi-restraints excluded: chain A residue 2611 MET Chi-restraints excluded: chain A residue 2612 THR Chi-restraints excluded: chain A residue 2621 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16241 Z= 0.177 Angle : 0.583 9.798 22048 Z= 0.298 Chirality : 0.045 0.372 2507 Planarity : 0.003 0.054 2827 Dihedral : 7.677 75.313 2691 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.40 % Favored : 93.55 % Rotamer: Outliers : 3.36 % Allowed : 30.97 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1971 helix: 1.83 (0.53), residues: 107 sheet: 0.14 (0.21), residues: 627 loop : -1.33 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2444 HIS 0.005 0.001 HIS A1900 PHE 0.011 0.001 PHE A1524 TYR 0.009 0.001 TYR A2609 ARG 0.004 0.000 ARG A 769 *********************** 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 167 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 110 time to evaluate : 1.738 Fit side-chains REVERT: A 811 TYR cc_start: 0.5957 (t80) cc_final: 0.5656 (t80) REVERT: A 1671 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7385 (p0) REVERT: A 1848 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7448 (ptt180) REVERT: A 2048 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8314 (p0) REVERT: A 2144 ASN cc_start: 0.7290 (p0) cc_final: 0.6967 (m110) outliers start: 57 outliers final: 46 residues processed: 162 average time/residue: 0.2695 time to fit residues: 67.0407 Evaluate side-chains 152 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 103 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 926 TYR 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 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1311 ASN 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 1518 ASP Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1701 ASP 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 1831 SER Chi-restraints excluded: chain A residue 1842 ASP 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 2023 ASN Chi-restraints excluded: chain A residue 2048 ASP Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2067 ASN Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2194 ASP Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16241 Z= 0.418 Angle : 0.657 7.999 22048 Z= 0.337 Chirality : 0.048 0.388 2507 Planarity : 0.004 0.055 2827 Dihedral : 7.470 70.738 2689 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.35 % Favored : 90.60 % Rotamer: Outliers : 4.19 % Allowed : 30.27 % Favored : 65.55 % 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: -1.08 (0.19), residues: 1971 helix: 1.73 (0.53), residues: 107 sheet: 0.07 (0.21), residues: 626 loop : -1.44 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A2444 HIS 0.005 0.001 HIS A2397 PHE 0.016 0.002 PHE A1524 TYR 0.013 0.002 TYR A2609 ARG 0.004 0.000 ARG A1765 *********************** 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 171 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 100 time to evaluate : 1.606 Fit side-chains REVERT: A 1671 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7444 (p0) REVERT: A 1848 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7681 (ptt180) outliers start: 71 outliers final: 61 residues processed: 166 average time/residue: 0.2615 time to fit residues: 67.5144 Evaluate side-chains 164 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 101 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 1100 VAL Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1228 LEU 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 1505 LEU Chi-restraints excluded: chain A residue 1518 ASP 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 1687 MET Chi-restraints excluded: chain A residue 1701 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 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1859 THR 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 2067 ASN Chi-restraints excluded: chain A residue 2076 THR 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 2194 ASP 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 2301 THR Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.0770 chunk 172 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16241 Z= 0.157 Angle : 0.566 10.300 22048 Z= 0.287 Chirality : 0.045 0.369 2507 Planarity : 0.003 0.052 2827 Dihedral : 6.706 61.604 2689 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.05 % Favored : 93.90 % Rotamer: Outliers : 3.54 % Allowed : 30.68 % Favored : 65.78 % 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: -0.89 (0.19), residues: 1971 helix: 2.03 (0.53), residues: 106 sheet: 0.16 (0.21), residues: 644 loop : -1.30 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2409 HIS 0.005 0.001 HIS A1900 PHE 0.011 0.001 PHE A1524 TYR 0.010 0.001 TYR A 894 ARG 0.004 0.000 ARG A 769 *********************** 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 171 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 111 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 811 TYR cc_start: 0.5921 (t80) cc_final: 0.5687 (t80) REVERT: A 1671 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7256 (p0) REVERT: A 2144 ASN cc_start: 0.7297 (p0) cc_final: 0.7002 (m110) REVERT: A 2408 SER cc_start: 0.8648 (t) cc_final: 0.8438 (t) outliers start: 60 outliers final: 54 residues processed: 163 average time/residue: 0.2645 time to fit residues: 67.6325 Evaluate side-chains 163 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 108 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 967 VAL Chi-restraints excluded: chain A residue 1020 ILE 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 1092 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1297 ILE 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 1518 ASP 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 1687 MET Chi-restraints excluded: chain A residue 1701 ASP 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 1831 SER Chi-restraints excluded: chain A residue 1837 THR 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 2067 ASN 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 2194 ASP 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 2257 THR 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 2297 ASP Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16241 Z= 0.205 Angle : 0.573 11.274 22048 Z= 0.289 Chirality : 0.045 0.370 2507 Planarity : 0.003 0.052 2827 Dihedral : 6.372 55.711 2689 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 3.89 % Allowed : 30.44 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 1971 helix: 2.08 (0.53), residues: 106 sheet: 0.21 (0.21), residues: 641 loop : -1.29 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1886 HIS 0.004 0.001 HIS A1900 PHE 0.013 0.001 PHE A1524 TYR 0.010 0.001 TYR A2609 ARG 0.003 0.000 ARG A 769 *********************** 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 174 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 108 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: A 1671 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7260 (p0) REVERT: A 1848 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7591 (ptt180) REVERT: A 2144 ASN cc_start: 0.7383 (p0) cc_final: 0.7069 (m110) REVERT: A 2294 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9056 (mm) REVERT: A 2408 SER cc_start: 0.8682 (t) cc_final: 0.8424 (t) outliers start: 66 outliers final: 58 residues processed: 168 average time/residue: 0.2620 time to fit residues: 68.5538 Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 107 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 852 VAL 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 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 1228 LEU 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 1518 ASP Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1581 ASP 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 1701 ASP 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 1842 ASP Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1859 THR 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 2067 ASN 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 2194 ASP Chi-restraints excluded: chain A residue 2202 THR 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 2294 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 Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1121 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= 0.377 Angle : 0.641 8.432 22048 Z= 0.327 Chirality : 0.047 0.387 2507 Planarity : 0.004 0.054 2827 Dihedral : 6.628 56.959 2689 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.64 % Favored : 91.31 % Rotamer: Outliers : 4.37 % Allowed : 29.97 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1971 helix: 1.90 (0.53), residues: 106 sheet: 0.13 (0.21), residues: 639 loop : -1.39 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2444 HIS 0.004 0.001 HIS A2351 PHE 0.015 0.001 PHE A1524 TYR 0.025 0.001 TYR A 811 ARG 0.006 0.000 ARG A 919 *********************** 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 177 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 103 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: A 1671 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7475 (p0) REVERT: A 1848 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7659 (ptt180) REVERT: A 2144 ASN cc_start: 0.7421 (p0) cc_final: 0.7117 (m110) REVERT: A 2294 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9072 (mm) REVERT: A 2408 SER cc_start: 0.8641 (t) cc_final: 0.8387 (t) outliers start: 74 outliers final: 65 residues processed: 172 average time/residue: 0.2635 time to fit residues: 70.6382 Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 100 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 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 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 1228 LEU 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 1463 ASP Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1581 ASP 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 1701 ASP Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1738 LEU 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 1842 ASP Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1859 THR 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 2067 ASN Chi-restraints excluded: chain A residue 2076 THR 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 2194 ASP Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2257 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 2400 LYS Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2612 THR Chi-restraints excluded: chain A residue 2621 LEU 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: 0.9980 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 0.0670 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1226 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= 0.205 Angle : 0.585 12.356 22048 Z= 0.295 Chirality : 0.045 0.374 2507 Planarity : 0.003 0.052 2827 Dihedral : 6.314 55.974 2689 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.99 % Rotamer: Outliers : 3.95 % Allowed : 30.44 % Favored : 65.60 % 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: -0.90 (0.19), residues: 1971 helix: 1.96 (0.53), residues: 106 sheet: 0.18 (0.21), residues: 641 loop : -1.33 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.012 0.001 PHE A1524 TYR 0.010 0.001 TYR A2609 ARG 0.002 0.000 ARG A 769 *********************** 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 177 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 110 time to evaluate : 1.863 Fit side-chains revert: symmetry clash REVERT: A 1671 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7307 (p0) REVERT: A 1848 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7576 (ptt180) REVERT: A 2048 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (p0) REVERT: A 2144 ASN cc_start: 0.7389 (p0) cc_final: 0.7094 (m110) REVERT: A 2294 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9057 (mm) REVERT: A 2408 SER cc_start: 0.8634 (t) cc_final: 0.8424 (p) outliers start: 67 outliers final: 59 residues processed: 174 average time/residue: 0.2524 time to fit residues: 68.9985 Evaluate side-chains 168 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 105 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 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 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 1228 LEU 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 1505 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1581 ASP 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 1701 ASP 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 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1859 THR 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 2048 ASP Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2067 ASN Chi-restraints excluded: chain A residue 2076 THR 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 2194 ASP 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 2257 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 2612 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 89 optimal weight: 0.2980 chunk 130 optimal weight: 0.0050 chunk 197 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.8249 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16241 Z= 0.142 Angle : 0.573 11.425 22048 Z= 0.286 Chirality : 0.044 0.359 2507 Planarity : 0.003 0.051 2827 Dihedral : 5.900 54.680 2689 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.00 % Favored : 93.95 % Rotamer: Outliers : 2.89 % Allowed : 31.50 % Favored : 65.60 % 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: -0.76 (0.19), residues: 1971 helix: 2.13 (0.52), residues: 106 sheet: 0.29 (0.21), residues: 629 loop : -1.24 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1886 HIS 0.005 0.001 HIS A1900 PHE 0.010 0.001 PHE A 859 TYR 0.008 0.001 TYR A2609 ARG 0.002 0.000 ARG A1750 ********************** 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 158 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 109 time to evaluate : 1.729 Fit side-chains revert: symmetry clash REVERT: A 1421 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 1671 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7245 (p0) REVERT: A 1848 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7512 (ptt180) REVERT: A 2048 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8243 (p0) REVERT: A 2144 ASN cc_start: 0.7301 (p0) cc_final: 0.7041 (m110) REVERT: A 2408 SER cc_start: 0.8689 (t) cc_final: 0.8391 (t) outliers start: 49 outliers final: 41 residues processed: 153 average time/residue: 0.2681 time to fit residues: 63.6552 Evaluate side-chains 149 residues out of total 1720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 104 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 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 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 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1581 ASP Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET 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 1842 ASP Chi-restraints excluded: chain A residue 1848 ARG 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 2048 ASP Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2067 ASN 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 2194 ASP Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2257 THR Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2396 ILE Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2550 ILE Chi-restraints excluded: chain A residue 2612 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 65 optimal weight: 0.1980 chunk 161 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.0070 chunk 138 optimal weight: 7.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2003 GLN ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082574 restraints weight = 69659.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085216 restraints weight = 25961.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087785 restraints weight = 17014.292| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16241 Z= 0.132 Angle : 0.554 12.013 22048 Z= 0.274 Chirality : 0.044 0.354 2507 Planarity : 0.003 0.056 2827 Dihedral : 5.430 54.059 2687 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 2.71 % Allowed : 31.92 % Favored : 65.37 % 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: -0.63 (0.19), residues: 1971 helix: 2.33 (0.53), residues: 106 sheet: 0.43 (0.21), residues: 627 loop : -1.19 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A1886 HIS 0.005 0.000 HIS A1900 PHE 0.008 0.001 PHE A2451 TYR 0.010 0.001 TYR A 811 ARG 0.003 0.000 ARG A 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.17 seconds wall clock time: 51 minutes 57.19 seconds (3117.19 seconds total)