Starting phenix.real_space_refine on Sat Oct 11 16:35:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r54_18891/10_2025/8r54_18891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r54_18891/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r54_18891/10_2025/8r54_18891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r54_18891/10_2025/8r54_18891.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r54_18891/10_2025/8r54_18891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r54_18891/10_2025/8r54_18891.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 3} 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: {'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 3} 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: 6.88, per 1000 atoms: 0.43 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: 1.44 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.09 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: 5.57 Time building geometry restraints manager: 1.95 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 23.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- 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 16282 Z= 0.244 Angle : 0.664 10.696 22154 Z= 0.333 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 : 9.06 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A1765 TYR 0.013 0.001 TYR A2609 PHE 0.011 0.001 PHE A1524 TRP 0.019 0.002 TRP A1886 HIS 0.005 0.001 HIS A1806 Details of bonding type rmsd covalent geometry : bond 0.00566 (16241) covalent geometry : angle 0.64873 (22048) SS BOND : bond 0.00234 ( 17) SS BOND : angle 0.66457 ( 34) hydrogen bonds : bond 0.25744 ( 466) hydrogen bonds : angle 9.63724 ( 1476) link_BETA1-4 : bond 0.00538 ( 11) link_BETA1-4 : angle 2.19602 ( 33) link_NAG-ASN : bond 0.00607 ( 13) link_NAG-ASN : angle 2.80828 ( 39) *********************** 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 : 0.625 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 102 average time/residue: 0.1378 time to fit residues: 21.4982 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 : 0.620 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.9680 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079253 restraints weight = 65186.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082753 restraints weight = 25092.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084442 restraints weight = 14546.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084992 restraints weight = 11659.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087094 restraints weight = 9994.936| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16282 Z= 0.138 Angle : 0.628 9.387 22154 Z= 0.322 Chirality : 0.047 0.346 2507 Planarity : 0.004 0.056 2827 Dihedral : 10.024 89.781 2693 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 2.65 % Allowed : 29.26 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.19), residues: 1971 helix: 1.84 (0.52), residues: 107 sheet: 0.16 (0.22), residues: 593 loop : -1.24 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1306 TYR 0.010 0.001 TYR A2325 PHE 0.015 0.001 PHE A1524 TRP 0.010 0.001 TRP A2444 HIS 0.005 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00309 (16241) covalent geometry : angle 0.61310 (22048) SS BOND : bond 0.00190 ( 17) SS BOND : angle 0.74361 ( 34) hydrogen bonds : bond 0.04753 ( 466) hydrogen bonds : angle 6.11462 ( 1476) link_BETA1-4 : bond 0.00460 ( 11) link_BETA1-4 : angle 2.17468 ( 33) link_NAG-ASN : bond 0.00421 ( 13) link_NAG-ASN : angle 2.65202 ( 39) *********************** 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 159 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.666 Fit side-chains REVERT: A 1367 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: A 1671 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7681 (p0) outliers start: 45 outliers final: 21 residues processed: 152 average time/residue: 0.1246 time to fit residues: 29.1576 Evaluate side-chains 123 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 1081 VAL 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 1597 SER 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 2284 MET Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2501 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 83 optimal weight: 0.0030 overall best weight: 4.3796 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.107556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078521 restraints weight = 65710.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080882 restraints weight = 25469.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083470 restraints weight = 16838.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083766 restraints weight = 12881.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083844 restraints weight = 10813.742| |-----------------------------------------------------------------------------| 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 = 0.38 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: 0.8339 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16282 Z= 0.228 Angle : 0.664 9.831 22154 Z= 0.338 Chirality : 0.048 0.379 2507 Planarity : 0.004 0.061 2827 Dihedral : 8.622 81.933 2691 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.08 % Favored : 91.87 % Rotamer: Outliers : 3.60 % Allowed : 29.38 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 1971 helix: 1.85 (0.53), residues: 106 sheet: 0.27 (0.22), residues: 600 loop : -1.31 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2592 TYR 0.015 0.001 TYR A2609 PHE 0.015 0.001 PHE A1524 TRP 0.017 0.001 TRP A2444 HIS 0.003 0.001 HIS A 927 Details of bonding type rmsd covalent geometry : bond 0.00539 (16241) covalent geometry : angle 0.64708 (22048) SS BOND : bond 0.00240 ( 17) SS BOND : angle 1.19500 ( 34) hydrogen bonds : bond 0.04983 ( 466) hydrogen bonds : angle 5.73762 ( 1476) link_BETA1-4 : bond 0.00512 ( 11) link_BETA1-4 : angle 2.14663 ( 33) link_NAG-ASN : bond 0.00567 ( 13) link_NAG-ASN : angle 2.94250 ( 39) *********************** 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 165 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 0.654 Fit side-chains REVERT: A 796 MET cc_start: 0.7577 (mmm) cc_final: 0.7320 (mmm) REVERT: A 1367 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: A 1671 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7724 (p0) REVERT: A 2294 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9069 (mm) REVERT: A 2409 TRP cc_start: 0.8587 (OUTLIER) cc_final: 0.7090 (m100) outliers start: 61 outliers final: 39 residues processed: 160 average time/residue: 0.1236 time to fit residues: 30.0009 Evaluate side-chains 143 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2208 SER Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2294 ILE Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2426 VAL Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 30.0000 chunk 162 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.105865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.075724 restraints weight = 56641.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079101 restraints weight = 24034.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081735 restraints weight = 13780.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081870 restraints weight = 10381.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082323 restraints weight = 9109.575| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16282 Z= 0.280 Angle : 0.704 10.164 22154 Z= 0.357 Chirality : 0.049 0.382 2507 Planarity : 0.004 0.060 2827 Dihedral : 7.923 75.948 2691 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.13 % Allowed : 29.03 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1971 helix: 1.77 (0.53), residues: 105 sheet: 0.16 (0.22), residues: 599 loop : -1.44 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1765 TYR 0.016 0.002 TYR A2609 PHE 0.021 0.002 PHE A2025 TRP 0.021 0.001 TRP A2444 HIS 0.005 0.001 HIS A2397 Details of bonding type rmsd covalent geometry : bond 0.00661 (16241) covalent geometry : angle 0.68725 (22048) SS BOND : bond 0.00266 ( 17) SS BOND : angle 1.03259 ( 34) hydrogen bonds : bond 0.04953 ( 466) hydrogen bonds : angle 5.60901 ( 1476) link_BETA1-4 : bond 0.00550 ( 11) link_BETA1-4 : angle 2.09642 ( 33) link_NAG-ASN : bond 0.00606 ( 13) link_NAG-ASN : angle 3.15920 ( 39) *********************** 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 174 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 104 time to evaluate : 0.660 Fit side-chains REVERT: A 796 MET cc_start: 0.7554 (mmm) cc_final: 0.7290 (mmm) REVERT: A 1671 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 1697 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7516 (mm-40) REVERT: A 1848 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7572 (ptt180) REVERT: A 2294 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9086 (mm) REVERT: A 2409 TRP cc_start: 0.8554 (OUTLIER) cc_final: 0.7174 (m100) outliers start: 70 outliers final: 51 residues processed: 169 average time/residue: 0.1245 time to fit residues: 32.6658 Evaluate side-chains 156 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1361 ASP Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1697 GLN Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 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 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP Chi-restraints excluded: chain A residue 2500 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 171 optimal weight: 0.0980 chunk 72 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.107684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.077533 restraints weight = 55229.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080932 restraints weight = 23282.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083557 restraints weight = 13405.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083738 restraints weight = 10056.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.084182 restraints weight = 8810.645| |-----------------------------------------------------------------------------| 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 = 0.49 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16282 Z= 0.172 Angle : 0.632 9.720 22154 Z= 0.321 Chirality : 0.047 0.374 2507 Planarity : 0.004 0.060 2827 Dihedral : 7.237 68.965 2691 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.89 % Allowed : 29.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.19), residues: 1971 helix: 1.84 (0.53), residues: 106 sheet: 0.21 (0.22), residues: 596 loop : -1.37 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2592 TYR 0.012 0.001 TYR A2609 PHE 0.013 0.001 PHE A2025 TRP 0.015 0.001 TRP A2444 HIS 0.004 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00402 (16241) covalent geometry : angle 0.61548 (22048) SS BOND : bond 0.00208 ( 17) SS BOND : angle 0.80821 ( 34) hydrogen bonds : bond 0.04237 ( 466) hydrogen bonds : angle 5.35518 ( 1476) link_BETA1-4 : bond 0.00462 ( 11) link_BETA1-4 : angle 2.07410 ( 33) link_NAG-ASN : bond 0.00458 ( 13) link_NAG-ASN : angle 2.90580 ( 39) *********************** 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 176 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 110 time to evaluate : 0.644 Fit side-chains REVERT: A 796 MET cc_start: 0.7613 (mmm) cc_final: 0.7348 (mmm) REVERT: A 1671 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 1848 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7527 (ptt180) REVERT: A 2409 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7120 (m100) outliers start: 66 outliers final: 54 residues processed: 168 average time/residue: 0.1282 time to fit residues: 33.7125 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 : 0.681 ------------------------------------------------------------------------------- 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 982 SER Chi-restraints excluded: chain A residue 1020 ILE Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1048 TRP Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1098 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 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 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1714 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1738 LEU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 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 1900 HIS Chi-restraints excluded: chain A residue 1942 THR 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 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 2270 ILE Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain A residue 2301 THR Chi-restraints excluded: chain A residue 2400 LYS Chi-restraints excluded: chain A residue 2409 TRP 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 112 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 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 = 0.3637 r_free = 0.3637 target = 0.108940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078908 restraints weight = 58827.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081410 restraints weight = 23449.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.084077 restraints weight = 15263.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084441 restraints weight = 11796.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084441 restraints weight = 9993.628| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16282 Z= 0.127 Angle : 0.610 9.587 22154 Z= 0.307 Chirality : 0.045 0.366 2507 Planarity : 0.003 0.057 2827 Dihedral : 6.555 60.656 2689 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.48 % Allowed : 30.44 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.19), residues: 1971 helix: 2.02 (0.53), residues: 105 sheet: 0.25 (0.21), residues: 611 loop : -1.32 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2592 TYR 0.013 0.001 TYR A2402 PHE 0.022 0.001 PHE A2025 TRP 0.012 0.001 TRP A2409 HIS 0.005 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00293 (16241) covalent geometry : angle 0.59373 (22048) SS BOND : bond 0.00297 ( 17) SS BOND : angle 1.05972 ( 34) hydrogen bonds : bond 0.03771 ( 466) hydrogen bonds : angle 5.13070 ( 1476) link_BETA1-4 : bond 0.00466 ( 11) link_BETA1-4 : angle 2.05329 ( 33) link_NAG-ASN : bond 0.00424 ( 13) link_NAG-ASN : angle 2.71237 ( 39) *********************** 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 175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.721 Fit side-chains REVERT: A 796 MET cc_start: 0.7411 (mmm) cc_final: 0.7120 (mmm) REVERT: A 1367 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: A 1671 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7648 (p0) REVERT: A 1848 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7470 (ptt180) REVERT: A 2294 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9062 (mm) outliers start: 59 outliers final: 47 residues processed: 169 average time/residue: 0.1250 time to fit residues: 32.7582 Evaluate side-chains 157 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 982 SER 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 1245 THR Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1367 GLN Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2027 VAL Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain A residue 2550 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 183 optimal weight: 0.0170 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2023 ASN A2512 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.109121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079022 restraints weight = 59719.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081828 restraints weight = 23724.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.084031 restraints weight = 15094.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084486 restraints weight = 12040.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.084503 restraints weight = 10185.490| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16282 Z= 0.129 Angle : 0.612 9.903 22154 Z= 0.307 Chirality : 0.046 0.365 2507 Planarity : 0.003 0.056 2827 Dihedral : 6.260 55.691 2689 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.07 % Allowed : 29.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 1971 helix: 2.09 (0.53), residues: 105 sheet: 0.28 (0.21), residues: 618 loop : -1.26 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 769 TYR 0.010 0.001 TYR A2609 PHE 0.012 0.001 PHE A1524 TRP 0.018 0.001 TRP A1886 HIS 0.004 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00298 (16241) covalent geometry : angle 0.59700 (22048) SS BOND : bond 0.00391 ( 17) SS BOND : angle 0.73601 ( 34) hydrogen bonds : bond 0.03682 ( 466) hydrogen bonds : angle 4.98654 ( 1476) link_BETA1-4 : bond 0.00460 ( 11) link_BETA1-4 : angle 2.04140 ( 33) link_NAG-ASN : bond 0.00424 ( 13) link_NAG-ASN : angle 2.67351 ( 39) *********************** 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 176 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 107 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7481 (mmm) cc_final: 0.7252 (mmm) REVERT: A 1367 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: A 1671 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7631 (p0) REVERT: A 1848 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7506 (ptt180) REVERT: A 2294 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9066 (mm) outliers start: 69 outliers final: 55 residues processed: 170 average time/residue: 0.1187 time to fit residues: 31.3502 Evaluate side-chains 164 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 105 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 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 1245 THR 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 1437 GLU Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1741 GLU Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain A residue 2550 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 83 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 11 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1697 GLN A2023 ASN A2339 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076470 restraints weight = 78876.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078963 restraints weight = 28497.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081109 restraints weight = 18196.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.081397 restraints weight = 13601.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081974 restraints weight = 11458.630| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16282 Z= 0.283 Angle : 0.703 10.048 22154 Z= 0.355 Chirality : 0.049 0.382 2507 Planarity : 0.004 0.057 2827 Dihedral : 6.614 57.236 2689 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.25 % Allowed : 29.20 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.19), residues: 1971 helix: 1.87 (0.53), residues: 105 sheet: 0.15 (0.21), residues: 618 loop : -1.40 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2656 TYR 0.017 0.002 TYR A2609 PHE 0.018 0.002 PHE A1524 TRP 0.019 0.002 TRP A2444 HIS 0.006 0.001 HIS A2397 Details of bonding type rmsd covalent geometry : bond 0.00669 (16241) covalent geometry : angle 0.68660 (22048) SS BOND : bond 0.00280 ( 17) SS BOND : angle 0.96372 ( 34) hydrogen bonds : bond 0.04616 ( 466) hydrogen bonds : angle 5.21787 ( 1476) link_BETA1-4 : bond 0.00536 ( 11) link_BETA1-4 : angle 2.11408 ( 33) link_NAG-ASN : bond 0.00635 ( 13) link_NAG-ASN : angle 3.05724 ( 39) *********************** 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 175 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 103 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7341 (mmm) cc_final: 0.7083 (mmm) REVERT: A 1671 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7739 (p0) REVERT: A 1848 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7622 (ptt180) REVERT: A 2294 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9089 (mm) outliers start: 72 outliers final: 62 residues processed: 169 average time/residue: 0.1290 time to fit residues: 33.2884 Evaluate side-chains 163 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 98 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1434 THR Chi-restraints excluded: chain A residue 1467 LYS Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1697 GLN 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 1741 GLU Chi-restraints excluded: chain A residue 1765 ARG Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1837 THR Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1853 VAL Chi-restraints excluded: chain A residue 1859 THR Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 2023 ASN Chi-restraints excluded: chain A residue 2049 ILE Chi-restraints excluded: chain A residue 2076 THR Chi-restraints excluded: chain A residue 2078 THR Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ILE Chi-restraints excluded: chain A residue 2134 VAL Chi-restraints excluded: chain A residue 2137 GLN Chi-restraints excluded: chain A residue 2202 THR Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain A residue 2550 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 chunk 167 optimal weight: 0.2980 chunk 105 optimal weight: 8.9990 chunk 68 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.109677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.079903 restraints weight = 62704.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082679 restraints weight = 24319.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084789 restraints weight = 15559.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085207 restraints weight = 12224.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085495 restraints weight = 10280.134| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16282 Z= 0.105 Angle : 0.617 10.174 22154 Z= 0.307 Chirality : 0.046 0.360 2507 Planarity : 0.004 0.057 2827 Dihedral : 6.061 55.517 2689 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.83 % Allowed : 30.62 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.19), residues: 1971 helix: 2.08 (0.53), residues: 105 sheet: 0.29 (0.21), residues: 614 loop : -1.25 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1834 TYR 0.013 0.001 TYR A1696 PHE 0.010 0.001 PHE A1524 TRP 0.013 0.001 TRP A2409 HIS 0.006 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00230 (16241) covalent geometry : angle 0.60309 (22048) SS BOND : bond 0.00249 ( 17) SS BOND : angle 0.65995 ( 34) hydrogen bonds : bond 0.03446 ( 466) hydrogen bonds : angle 4.93324 ( 1476) link_BETA1-4 : bond 0.00470 ( 11) link_BETA1-4 : angle 2.00564 ( 33) link_NAG-ASN : bond 0.00450 ( 13) link_NAG-ASN : angle 2.60803 ( 39) *********************** 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 157 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7417 (mmm) cc_final: 0.7125 (mmm) REVERT: A 1848 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7418 (ptt180) outliers start: 48 outliers final: 43 residues processed: 150 average time/residue: 0.1284 time to fit residues: 29.4936 Evaluate side-chains 149 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1519 GLN Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1584 VAL Chi-restraints excluded: chain A residue 1687 MET Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1719 GLU Chi-restraints excluded: chain A residue 1765 ARG Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 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 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 175 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.108222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078061 restraints weight = 64219.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.080966 restraints weight = 24908.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.083430 restraints weight = 15586.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083798 restraints weight = 11871.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083912 restraints weight = 10024.751| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16282 Z= 0.188 Angle : 0.641 9.691 22154 Z= 0.321 Chirality : 0.046 0.370 2507 Planarity : 0.004 0.052 2827 Dihedral : 6.106 56.090 2689 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.07 % Allowed : 30.27 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.19), residues: 1971 helix: 2.07 (0.53), residues: 105 sheet: 0.26 (0.21), residues: 620 loop : -1.29 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1834 TYR 0.013 0.001 TYR A2609 PHE 0.014 0.001 PHE A1524 TRP 0.019 0.001 TRP A1886 HIS 0.004 0.001 HIS A2397 Details of bonding type rmsd covalent geometry : bond 0.00443 (16241) covalent geometry : angle 0.62580 (22048) SS BOND : bond 0.00235 ( 17) SS BOND : angle 0.72511 ( 34) hydrogen bonds : bond 0.03973 ( 466) hydrogen bonds : angle 4.95752 ( 1476) link_BETA1-4 : bond 0.00478 ( 11) link_BETA1-4 : angle 2.05138 ( 33) link_NAG-ASN : bond 0.00486 ( 13) link_NAG-ASN : angle 2.78991 ( 39) ********************** 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 156 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 104 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 796 MET cc_start: 0.7397 (mmm) cc_final: 0.7088 (mmm) REVERT: A 1367 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: A 1848 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7548 (ptt180) outliers start: 52 outliers final: 48 residues processed: 151 average time/residue: 0.1270 time to fit residues: 29.6273 Evaluate side-chains 154 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 104 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 788 GLU Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 926 TYR Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 THR 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 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 1765 ARG Chi-restraints excluded: chain A residue 1816 LEU Chi-restraints excluded: chain A residue 1822 THR Chi-restraints excluded: chain A residue 1826 THR Chi-restraints excluded: chain A residue 1831 SER Chi-restraints excluded: chain A residue 1848 ARG Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1900 HIS Chi-restraints excluded: chain A residue 1942 THR Chi-restraints excluded: chain A residue 1989 CYS Chi-restraints excluded: chain A residue 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 2262 VAL Chi-restraints excluded: chain A residue 2270 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 45 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 169 optimal weight: 0.0370 chunk 196 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2512 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.109214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079298 restraints weight = 62454.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.082244 restraints weight = 24310.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084754 restraints weight = 15259.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085148 restraints weight = 11709.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085206 restraints weight = 9845.668| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16282 Z= 0.116 Angle : 0.610 9.789 22154 Z= 0.304 Chirality : 0.045 0.361 2507 Planarity : 0.003 0.053 2827 Dihedral : 5.881 55.449 2689 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.07 % Allowed : 30.38 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 1971 helix: 2.15 (0.53), residues: 105 sheet: 0.33 (0.21), residues: 617 loop : -1.22 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2592 TYR 0.010 0.001 TYR A2609 PHE 0.019 0.001 PHE A2025 TRP 0.018 0.001 TRP A1886 HIS 0.005 0.001 HIS A1900 Details of bonding type rmsd covalent geometry : bond 0.00264 (16241) covalent geometry : angle 0.59599 (22048) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.61061 ( 34) hydrogen bonds : bond 0.03542 ( 466) hydrogen bonds : angle 4.83919 ( 1476) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 2.00757 ( 33) link_NAG-ASN : bond 0.00422 ( 13) link_NAG-ASN : angle 2.60713 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.52 seconds wall clock time: 48 minutes 38.89 seconds (2918.89 seconds total)