Starting phenix.real_space_refine on Tue Jan 21 00:41:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_18891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_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/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_18891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_18891.map" model { file = "/net/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_18891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r54_18891/01_2025/8r54_18891.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10001 2.51 5 N 2705 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 16.21, per 1000 atoms: 1.02 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 4.08 Conformation dependent library (CDL) restraints added in 3.6 seconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 26 sheets defined 7.9% alpha, 38.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 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: 11.48 Time building geometry restraints manager: 4.84 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: 0.00 - 2.14: 21699 2.14 - 4.28: 300 4.28 - 6.42: 35 6.42 - 8.56: 9 8.56 - 10.70: 5 Bond angle restraints: 22048 Sorted by residual: angle pdb=" N GLN A1691 " pdb=" CA GLN A1691 " pdb=" C GLN A1691 " ideal model delta sigma weight residual 113.97 122.28 -8.31 1.28e+00 6.10e-01 4.22e+01 angle pdb=" N GLN A1691 " pdb=" CA GLN A1691 " pdb=" CB GLN A1691 " ideal model delta sigma weight residual 110.67 102.07 8.60 1.39e+00 5.18e-01 3.83e+01 angle pdb=" C CYS A 712 " pdb=" CA CYS A 712 " pdb=" CB CYS A 712 " ideal model delta sigma weight residual 116.54 109.96 6.58 1.15e+00 7.56e-01 3.28e+01 angle pdb=" C ASP A1690 " pdb=" CA ASP A1690 " pdb=" CB ASP A1690 " ideal model delta sigma weight residual 110.42 120.38 -9.96 1.99e+00 2.53e-01 2.50e+01 angle pdb=" C SER A1211 " pdb=" CA SER A1211 " pdb=" CB SER A1211 " ideal model delta sigma weight residual 115.89 109.47 6.42 1.32e+00 5.74e-01 2.37e+01 ... (remaining 22043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8781 21.76 - 43.52: 961 43.52 - 65.27: 173 65.27 - 87.03: 60 87.03 - 108.79: 20 Dihedral angle restraints: 9995 sinusoidal: 4252 harmonic: 5743 Sorted by residual: dihedral pdb=" CB CYS A 712 " pdb=" SG CYS A 712 " pdb=" SG CYS A 722 " pdb=" CB CYS A 722 " ideal model delta sinusoidal sigma weight residual -86.00 -168.76 82.76 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS A 764 " pdb=" SG CYS A 764 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 166.76 -73.76 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -159.46 73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 9992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2175 0.071 - 0.142: 319 0.142 - 0.213: 6 0.213 - 0.284: 4 0.284 - 0.355: 3 Chirality restraints: 2507 Sorted by residual: chirality pdb=" CA ASP A1690 " pdb=" N ASP A1690 " pdb=" C ASP A1690 " pdb=" CB ASP A1690 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A1527 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG A2804 " pdb=" ND2 ASN A1677 " pdb=" C2 NAG A2804 " pdb=" O5 NAG A2804 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2504 not shown) Planarity restraints: 2840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 877 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO A 878 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 985 " 0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 986 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1444 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A1445 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1445 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1445 " -0.026 5.00e-02 4.00e+02 ... (remaining 2837 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 955 2.72 - 3.27: 15194 3.27 - 3.81: 24448 3.81 - 4.36: 28944 4.36 - 4.90: 52551 Nonbonded interactions: 122092 Sorted by model distance: nonbonded pdb=" OG SER A 687 " pdb=" OD2 ASP A1671 " model vdw 2.176 3.040 nonbonded pdb=" O THR A 850 " pdb=" OG1 THR A 895 " model vdw 2.186 3.040 nonbonded pdb=" O LEU A1617 " pdb=" OH TYR A1632 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR A 873 " pdb=" OD1 ASP A 875 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A1824 " pdb=" O GLN A1828 " model vdw 2.234 3.040 ... (remaining 122087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 53.310 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.330 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.678 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.3132 time to fit residues: 48.6657 Evaluate side-chains 100 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2396 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0030 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN A1363 ASN A1697 GLN A1806 HIS ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.080353 restraints weight = 46382.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081525 restraints weight = 30499.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083281 restraints weight = 18596.914| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16241 Z= 0.262 Angle : 0.630 9.280 22048 Z= 0.329 Chirality : 0.047 0.347 2507 Planarity : 0.004 0.055 2827 Dihedral : 10.286 91.536 2693 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 3.13 % Allowed : 29.03 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.19), residues: 1971 helix: 1.80 (0.52), residues: 107 sheet: 0.12 (0.22), residues: 592 loop : -1.29 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.016 0.001 PHE A1524 TYR 0.011 0.001 TYR A2609 ARG 0.005 0.000 ARG A1236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 115 time to evaluate : 1.687 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: A 1671 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7732 (p0) REVERT: A 2409 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.7068 (m100) outliers start: 53 outliers final: 24 residues processed: 160 average time/residue: 0.2849 time to fit residues: 70.3204 Evaluate side-chains 128 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1697 GLN Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 153 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1363 ASN A2023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.109202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.081679 restraints weight = 48658.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083373 restraints weight = 26871.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084447 restraints weight = 17385.085| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1051 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= 0.180 Angle : 0.586 8.253 22048 Z= 0.302 Chirality : 0.046 0.364 2507 Planarity : 0.004 0.060 2827 Dihedral : 8.124 78.846 2691 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.48 % Allowed : 30.27 % 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: -0.74 (0.19), residues: 1971 helix: 1.98 (0.52), residues: 106 sheet: 0.35 (0.22), residues: 597 loop : -1.19 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2444 HIS 0.005 0.001 HIS A1900 PHE 0.011 0.001 PHE A1524 TYR 0.010 0.001 TYR A2609 ARG 0.003 0.000 ARG A1750 *********************** 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 152 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 2.018 Fit side-chains REVERT: A 1671 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7591 (p0) outliers start: 42 outliers final: 25 residues processed: 148 average time/residue: 0.2821 time to fit residues: 64.2849 Evaluate side-chains 126 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 77 optimal weight: 0.0970 chunk 127 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.109783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.080479 restraints weight = 67422.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083817 restraints weight = 25063.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085823 restraints weight = 15181.974| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16241 Z= 0.163 Angle : 0.577 9.915 22048 Z= 0.293 Chirality : 0.045 0.356 2507 Planarity : 0.003 0.051 2827 Dihedral : 7.087 70.699 2691 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.77 % Allowed : 30.32 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1971 helix: 2.12 (0.53), residues: 105 sheet: 0.40 (0.22), residues: 600 loop : -1.15 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2444 HIS 0.005 0.001 HIS A1900 PHE 0.018 0.001 PHE A2025 TYR 0.010 0.001 TYR A2609 ARG 0.002 0.000 ARG A1750 *********************** 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 156 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 1.871 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: A 1848 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7395 (ptt180) outliers start: 47 outliers final: 35 residues processed: 151 average time/residue: 0.2867 time to fit residues: 67.4002 Evaluate side-chains 142 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 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 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 83 optimal weight: 0.0010 chunk 47 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080213 restraints weight = 71860.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082783 restraints weight = 26659.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085042 restraints weight = 17775.667| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16241 Z= 0.204 Angle : 0.576 9.077 22048 Z= 0.294 Chirality : 0.045 0.359 2507 Planarity : 0.003 0.052 2827 Dihedral : 6.577 64.313 2689 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.24 % Allowed : 29.85 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1971 helix: 2.08 (0.53), residues: 106 sheet: 0.42 (0.22), residues: 600 loop : -1.16 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.015 0.001 PHE A2025 TYR 0.012 0.001 TYR A2609 ARG 0.002 0.000 ARG A2656 *********************** 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 162 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 1.780 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: A 1848 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7433 (ptt180) REVERT: A 2294 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9080 (mm) outliers start: 55 outliers final: 39 residues processed: 156 average time/residue: 0.2789 time to fit residues: 67.7660 Evaluate side-chains 146 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 1.787 ------------------------------------------------------------------------------- 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 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 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL 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 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 165 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2339 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.106848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076545 restraints weight = 68240.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.079284 restraints weight = 26031.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081615 restraints weight = 16491.167| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16241 Z= 0.421 Angle : 0.667 8.885 22048 Z= 0.344 Chirality : 0.049 0.384 2507 Planarity : 0.004 0.053 2827 Dihedral : 6.788 60.762 2689 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.83 % Allowed : 29.44 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1971 helix: 1.92 (0.53), residues: 105 sheet: 0.25 (0.22), residues: 609 loop : -1.31 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2444 HIS 0.004 0.001 HIS A1652 PHE 0.029 0.002 PHE A2025 TYR 0.018 0.002 TYR A2609 ARG 0.004 0.000 ARG A1765 *********************** 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 170 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 105 time to evaluate : 1.746 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 1451 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7124 (tptt) REVERT: A 1848 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7556 (ptt180) REVERT: A 2294 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9095 (mm) REVERT: A 2409 TRP cc_start: 0.8569 (OUTLIER) cc_final: 0.7060 (m100) REVERT: A 2495 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7925 (tp) outliers start: 65 outliers final: 54 residues processed: 163 average time/residue: 0.2912 time to fit residues: 72.5462 Evaluate side-chains 159 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 1.817 ------------------------------------------------------------------------------- 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 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 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 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1451 LYS Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2495 LEU Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 76 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.079295 restraints weight = 64861.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082024 restraints weight = 24894.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084130 restraints weight = 15847.052| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16241 Z= 0.187 Angle : 0.583 8.973 22048 Z= 0.298 Chirality : 0.045 0.363 2507 Planarity : 0.003 0.053 2827 Dihedral : 6.257 58.234 2689 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.54 % Allowed : 30.09 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 1971 helix: 2.03 (0.53), residues: 106 sheet: 0.30 (0.21), residues: 612 loop : -1.24 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.012 0.001 PHE A1524 TYR 0.011 0.001 TYR A2609 ARG 0.003 0.000 ARG A1834 *********************** 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 173 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 113 time to evaluate : 1.670 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: A 1848 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7424 (ptt180) REVERT: A 2294 ILE cc_start: 0.9502 (OUTLIER) cc_final: 0.9084 (mm) REVERT: A 2408 SER cc_start: 0.8605 (t) cc_final: 0.8373 (t) outliers start: 60 outliers final: 45 residues processed: 166 average time/residue: 0.2852 time to fit residues: 73.3935 Evaluate side-chains 155 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 107 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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 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 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 142 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 87 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 GLN A2023 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078209 restraints weight = 54300.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.081573 restraints weight = 23051.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084213 restraints weight = 13416.915| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16241 Z= 0.263 Angle : 0.609 9.475 22048 Z= 0.312 Chirality : 0.046 0.367 2507 Planarity : 0.004 0.053 2827 Dihedral : 6.232 59.214 2689 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 3.60 % Allowed : 30.09 % Favored : 66.31 % 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: -0.79 (0.19), residues: 1971 helix: 2.05 (0.53), residues: 106 sheet: 0.28 (0.21), residues: 620 loop : -1.24 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1886 HIS 0.003 0.001 HIS A1900 PHE 0.013 0.001 PHE A1524 TYR 0.013 0.001 TYR A2609 ARG 0.003 0.000 ARG A 769 *********************** 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 169 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 1.541 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: A 1848 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7490 (ptt180) REVERT: A 2294 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9105 (mm) REVERT: A 2408 SER cc_start: 0.8580 (t) cc_final: 0.8370 (t) outliers start: 61 outliers final: 51 residues processed: 163 average time/residue: 0.2718 time to fit residues: 69.4298 Evaluate side-chains 159 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 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 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 1098 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 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 113 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077794 restraints weight = 63673.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080535 restraints weight = 24907.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.082645 restraints weight = 15752.158| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16241 Z= 0.290 Angle : 0.625 9.312 22048 Z= 0.320 Chirality : 0.047 0.373 2507 Planarity : 0.004 0.054 2827 Dihedral : 6.238 56.459 2689 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.60 % Allowed : 30.09 % Favored : 66.31 % 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: -0.83 (0.19), residues: 1971 helix: 2.00 (0.53), residues: 106 sheet: 0.25 (0.21), residues: 621 loop : -1.27 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2444 HIS 0.003 0.001 HIS A1900 PHE 0.016 0.001 PHE A 975 TYR 0.014 0.001 TYR A2609 ARG 0.003 0.000 ARG A2656 *********************** 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 165 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 1.867 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: A 1848 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7502 (ptt180) REVERT: A 2294 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9103 (mm) REVERT: A 2408 SER cc_start: 0.8613 (t) cc_final: 0.8408 (t) REVERT: A 2409 TRP cc_start: 0.8525 (OUTLIER) cc_final: 0.7138 (m100) outliers start: 61 outliers final: 53 residues processed: 160 average time/residue: 0.2755 time to fit residues: 68.3816 Evaluate side-chains 159 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 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 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 1098 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 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE 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 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 1809 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 94 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.078635 restraints weight = 63895.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081397 restraints weight = 24826.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.083568 restraints weight = 15650.183| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16241 Z= 0.232 Angle : 0.601 9.639 22048 Z= 0.306 Chirality : 0.046 0.364 2507 Planarity : 0.004 0.053 2827 Dihedral : 5.984 55.832 2689 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.30 % Allowed : 30.27 % Favored : 66.43 % 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: -0.78 (0.19), residues: 1971 helix: 2.01 (0.53), residues: 106 sheet: 0.29 (0.21), residues: 621 loop : -1.24 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 PHE 0.020 0.001 PHE A 975 TYR 0.012 0.001 TYR A2609 ARG 0.002 0.000 ARG A2592 ********************** 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 161 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 1.923 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: A 1848 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7447 (ptt180) REVERT: A 2294 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9091 (mm) REVERT: A 2408 SER cc_start: 0.8632 (t) cc_final: 0.8375 (t) outliers start: 56 outliers final: 51 residues processed: 156 average time/residue: 0.2888 time to fit residues: 70.8250 Evaluate side-chains 157 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 103 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 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 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 1098 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 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE 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 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1809 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2209 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 10.0000 chunk 151 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 175 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 overall best weight: 0.4928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.110343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080436 restraints weight = 65347.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083186 restraints weight = 24855.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085483 restraints weight = 15698.088| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16241 Z= 0.140 Angle : 0.584 9.856 22048 Z= 0.295 Chirality : 0.045 0.359 2507 Planarity : 0.003 0.053 2827 Dihedral : 5.687 54.838 2689 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.06 % Allowed : 31.45 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1971 helix: 2.13 (0.53), residues: 106 sheet: 0.42 (0.21), residues: 615 loop : -1.16 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1886 HIS 0.005 0.001 HIS A1900 PHE 0.016 0.001 PHE A2025 TYR 0.007 0.001 TYR A2325 ARG 0.002 0.000 ARG A1750 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4965.99 seconds wall clock time: 91 minutes 48.20 seconds (5508.20 seconds total)