Starting phenix.real_space_refine on Sat Feb 17 13:53:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtd_23983/02_2024/7mtd_23983.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 79 5.16 5 C 12006 2.51 5 N 3058 2.21 5 O 3690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18833 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6271 Classifications: {'peptide': 806} Link IDs: {'PTRANS': 39, 'TRANS': 766} Chain breaks: 16 Chain: "B" Number of atoms: 5900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5900 Classifications: {'peptide': 759} Link IDs: {'PTRANS': 38, 'TRANS': 720} Chain breaks: 9 Chain: "C" Number of atoms: 6088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6088 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 41, 'TRANS': 741} Chain breaks: 14 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" 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 Time building chain proxies: 9.99, per 1000 atoms: 0.53 Number of scatterers: 18833 At special positions: 0 Unit cell: (132.525, 134.235, 152.19, 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 79 16.00 O 3690 8.00 N 3058 7.00 C 12006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.4 seconds 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4402 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 44 sheets defined 26.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.125A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.936A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.727A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.994A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 940 removed outlier: 6.991A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.040A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 4.067A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1032 removed outlier: 3.970A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.505A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.883A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.654A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 754 removed outlier: 3.762A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.093A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.550A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.114A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.921A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.595A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 955 removed outlier: 3.527A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.556A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 968 removed outlier: 3.709A pdb=" N SER B 968 " --> pdb=" O GLN B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.617A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1023 removed outlier: 3.579A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B1014 " --> pdb=" O GLN B1010 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.644A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.059A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.139A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 761 through 783 removed outlier: 3.926A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.744A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.678A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 910 " --> pdb=" O PHE C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.752A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.959A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.054A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 989 through 1032 removed outlier: 4.216A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.956A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.715A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.564A pdb=" N PHE A 43 " --> pdb=" O PHE C 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.595A pdb=" N THR A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.192A pdb=" N LEU A 118 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.588A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.676A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.679A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.148A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.785A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 719 removed outlier: 6.538A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 removed outlier: 3.726A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 3.502A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 3.819A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 8.392A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.799A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.257A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.265A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.609A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 318 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.240A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.721A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.698A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.715A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.558A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.525A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD5, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.508A pdb=" N VAL B1104 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.617A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.851A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.989A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.996A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 719 removed outlier: 6.786A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.511A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.561A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.580A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1692 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: 7.21 Time building geometry restraints manager: 7.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5942 1.35 - 1.48: 5011 1.48 - 1.61: 8152 1.61 - 1.74: 0 1.74 - 1.87: 103 Bond restraints: 19208 Sorted by residual: bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.04e+00 ... (remaining 19203 not shown) Histogram of bond angle deviations from ideal: 99.30 - 107.08: 669 107.08 - 114.86: 11560 114.86 - 122.63: 11552 122.63 - 130.41: 2274 130.41 - 138.19: 59 Bond angle restraints: 26114 Sorted by residual: angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 121.54 132.66 -11.12 1.91e+00 2.74e-01 3.39e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C GLY A 744 " pdb=" N ASP A 745 " pdb=" CA ASP A 745 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.21 -5.51 1.22e+00 6.72e-01 2.04e+01 ... (remaining 26109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 11303 14.88 - 29.77: 480 29.77 - 44.65: 142 44.65 - 59.53: 39 59.53 - 74.42: 15 Dihedral angle restraints: 11979 sinusoidal: 5181 harmonic: 6798 Sorted by residual: dihedral pdb=" CA VAL C 524 " pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta harmonic sigma weight residual 180.00 122.24 57.76 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -149.45 63.45 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA TYR B 904 " pdb=" C TYR B 904 " pdb=" N ARG B 905 " pdb=" CA ARG B 905 " ideal model delta harmonic sigma weight residual 180.00 145.25 34.75 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2654 0.081 - 0.162: 467 0.162 - 0.242: 33 0.242 - 0.323: 2 0.323 - 0.404: 3 Chirality restraints: 3159 Sorted by residual: chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.09 -0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" C2 NAG C1301 " pdb=" C1 NAG C1301 " pdb=" C3 NAG C1301 " pdb=" N2 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CB THR C 33 " pdb=" CA THR C 33 " pdb=" OG1 THR C 33 " pdb=" CG2 THR C 33 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 3156 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO A 987 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 727 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO B 728 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 728 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 728 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 560 " -0.038 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO A 561 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.031 5.00e-02 4.00e+02 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5614 2.83 - 3.34: 15435 3.34 - 3.86: 28814 3.86 - 4.38: 31223 4.38 - 4.90: 56465 Nonbonded interactions: 137551 Sorted by model distance: nonbonded pdb=" OE2 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.308 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.309 2.440 nonbonded pdb=" OD2 ASP A 578 " pdb=" OG1 THR A 581 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR B 741 " pdb=" O LEU B 962 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.329 2.440 ... (remaining 137546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 65 or resid 81 through 95 or resid 102 through \ 108 or resid 126 through 130 or resid 189 through 208 or resid 216 through 241 o \ r resid 265 or resid 270 through 329 or resid 384 or resid 529 through 620 or re \ sid 641 through 826 or resid 855 through 940 or resid 944 through 1143 or resid \ 1301 through 1304)) selection = (chain 'B' and (resid 27 through 95 or resid 102 through 241 or resid 266 or res \ id 270 through 330 or resid 529 through 620 or resid 641 through 940 or resid 94 \ 4 through 1143 or resid 1301 through 1304)) selection = (chain 'C' and (resid 27 through 108 or resid 126 through 130 or resid 189 throu \ gh 208 or resid 216 through 241 or resid 265 or resid 270 through 329 or resid 3 \ 84 or resid 529 through 620 or resid 641 through 826 or resid 855 through 1143 o \ r resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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=1.00 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: 5.420 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: 17.780 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 50.920 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.007 0.065 19208 Z= 0.427 Angle : 0.894 16.776 26114 Z= 0.468 Chirality : 0.059 0.404 3159 Planarity : 0.007 0.089 3295 Dihedral : 9.992 74.419 7499 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.49 % Favored : 93.46 % Rotamer: Outliers : 0.15 % Allowed : 1.36 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.14), residues: 2264 helix: -2.39 (0.16), residues: 584 sheet: -2.28 (0.21), residues: 486 loop : -3.08 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 64 HIS 0.011 0.002 HIS A1048 PHE 0.037 0.003 PHE B 823 TYR 0.036 0.003 TYR C 873 ARG 0.008 0.001 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6201 (m-90) cc_final: 0.5932 (m-90) REVERT: A 202 LYS cc_start: 0.7608 (mttm) cc_final: 0.7261 (mtmt) REVERT: A 206 LYS cc_start: 0.7701 (tppt) cc_final: 0.7211 (tptm) REVERT: A 237 ARG cc_start: 0.4928 (ptm160) cc_final: 0.4592 (ptp90) REVERT: A 529 LYS cc_start: 0.6434 (tppt) cc_final: 0.6145 (tttm) REVERT: A 651 ILE cc_start: 0.8931 (mt) cc_final: 0.8630 (mp) REVERT: A 859 THR cc_start: 0.8759 (t) cc_final: 0.8538 (p) REVERT: B 92 PHE cc_start: 0.7080 (t80) cc_final: 0.6782 (t80) REVERT: B 192 PHE cc_start: 0.6875 (m-80) cc_final: 0.6667 (m-10) REVERT: B 200 TYR cc_start: 0.5947 (m-10) cc_final: 0.5513 (m-80) REVERT: B 296 LEU cc_start: 0.8113 (tp) cc_final: 0.7859 (tp) REVERT: B 673 SER cc_start: 0.8138 (t) cc_final: 0.7752 (p) REVERT: B 855 PHE cc_start: 0.6091 (m-10) cc_final: 0.5728 (m-80) REVERT: B 902 MET cc_start: 0.8813 (tpt) cc_final: 0.8468 (tpt) REVERT: B 1125 ASN cc_start: 0.7224 (m-40) cc_final: 0.7009 (t0) REVERT: C 192 PHE cc_start: 0.7220 (m-80) cc_final: 0.6820 (m-80) REVERT: C 281 GLU cc_start: 0.7221 (pt0) cc_final: 0.6674 (mp0) REVERT: C 544 ASN cc_start: 0.7015 (m-40) cc_final: 0.6623 (m-40) REVERT: C 558 LYS cc_start: 0.6982 (mppt) cc_final: 0.6781 (mtmt) REVERT: C 756 TYR cc_start: 0.8218 (m-10) cc_final: 0.7937 (m-80) REVERT: C 776 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8410 (ttmt) outliers start: 3 outliers final: 1 residues processed: 408 average time/residue: 0.3490 time to fit residues: 205.8783 Evaluate side-chains 182 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 196 optimal weight: 0.9990 chunk 176 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 70 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 606 ASN A 824 ASN A 901 GLN A 913 GLN A 953 ASN A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 540 ASN B 751 ASN B 804 GLN B 901 GLN B 913 GLN B 953 ASN B 960 ASN B1010 GLN B1135 ASN C 207 HIS C 234 ASN C 655 HIS C 658 ASN C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1119 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19208 Z= 0.199 Angle : 0.622 12.219 26114 Z= 0.316 Chirality : 0.046 0.264 3159 Planarity : 0.005 0.066 3295 Dihedral : 7.287 56.879 3326 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.99 % Allowed : 6.52 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 2264 helix: -0.33 (0.21), residues: 580 sheet: -1.55 (0.22), residues: 508 loop : -2.72 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.007 0.001 HIS C 207 PHE 0.034 0.002 PHE A 592 TYR 0.022 0.001 TYR B 904 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 213 time to evaluate : 2.035 Fit side-chains REVERT: A 44 ARG cc_start: 0.7463 (mtt90) cc_final: 0.6845 (mtt180) REVERT: A 202 LYS cc_start: 0.7683 (mttm) cc_final: 0.7293 (mtmt) REVERT: A 298 GLU cc_start: 0.7708 (tt0) cc_final: 0.7424 (mt-10) REVERT: A 651 ILE cc_start: 0.8621 (mt) cc_final: 0.8315 (mp) REVERT: B 200 TYR cc_start: 0.6129 (m-10) cc_final: 0.5678 (m-80) REVERT: B 282 ASN cc_start: 0.6358 (m-40) cc_final: 0.5941 (t0) REVERT: B 296 LEU cc_start: 0.8125 (tp) cc_final: 0.7919 (tp) REVERT: B 634 ARG cc_start: 0.6886 (ptp-110) cc_final: 0.6495 (ttp-110) REVERT: B 673 SER cc_start: 0.7959 (t) cc_final: 0.7697 (p) REVERT: B 1050 MET cc_start: 0.8827 (ptm) cc_final: 0.8454 (ptp) REVERT: C 53 ASP cc_start: 0.7595 (t0) cc_final: 0.7325 (t0) REVERT: C 558 LYS cc_start: 0.7026 (mppt) cc_final: 0.6617 (mtmm) REVERT: C 776 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8385 (ttmt) REVERT: C 886 TRP cc_start: 0.8589 (p90) cc_final: 0.8054 (p90) REVERT: C 1138 TYR cc_start: 0.6973 (t80) cc_final: 0.6771 (t80) outliers start: 41 outliers final: 29 residues processed: 245 average time/residue: 0.2968 time to fit residues: 111.3888 Evaluate side-chains 198 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 978 ASN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 960 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 824 ASN A1002 GLN A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 207 HIS ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1005 GLN B1088 HIS ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19208 Z= 0.220 Angle : 0.603 11.815 26114 Z= 0.304 Chirality : 0.046 0.242 3159 Planarity : 0.004 0.062 3295 Dihedral : 6.588 57.613 3325 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 2.82 % Allowed : 8.46 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2264 helix: 0.68 (0.22), residues: 571 sheet: -1.12 (0.22), residues: 484 loop : -2.51 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.005 0.001 HIS A1058 PHE 0.034 0.002 PHE A 592 TYR 0.022 0.002 TYR B 904 ARG 0.004 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 186 time to evaluate : 2.195 Fit side-chains REVERT: A 44 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7208 (mtt90) REVERT: A 64 TRP cc_start: 0.7356 (t60) cc_final: 0.6889 (t60) REVERT: A 92 PHE cc_start: 0.6186 (t80) cc_final: 0.5950 (t80) REVERT: A 202 LYS cc_start: 0.7660 (mttm) cc_final: 0.7271 (mtpt) REVERT: A 421 TYR cc_start: 0.6239 (m-10) cc_final: 0.5618 (t80) REVERT: A 529 LYS cc_start: 0.6353 (tppt) cc_final: 0.5932 (tttm) REVERT: A 651 ILE cc_start: 0.8615 (mt) cc_final: 0.8346 (mp) REVERT: A 988 GLU cc_start: 0.7552 (pp20) cc_final: 0.7328 (pp20) REVERT: B 200 TYR cc_start: 0.6270 (m-10) cc_final: 0.5778 (m-80) REVERT: B 282 ASN cc_start: 0.6326 (m-40) cc_final: 0.5888 (t0) REVERT: B 634 ARG cc_start: 0.6904 (ptp-110) cc_final: 0.6595 (ttp-110) REVERT: B 673 SER cc_start: 0.8029 (t) cc_final: 0.7746 (p) REVERT: B 902 MET cc_start: 0.9129 (tpt) cc_final: 0.8576 (tpt) REVERT: C 53 ASP cc_start: 0.7581 (t0) cc_final: 0.7261 (t0) REVERT: C 558 LYS cc_start: 0.7106 (mppt) cc_final: 0.6663 (mtmm) REVERT: C 886 TRP cc_start: 0.8520 (p90) cc_final: 0.8062 (p90) REVERT: C 1138 TYR cc_start: 0.7019 (t80) cc_final: 0.6767 (t80) outliers start: 58 outliers final: 38 residues processed: 232 average time/residue: 0.2999 time to fit residues: 108.5064 Evaluate side-chains 197 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 209 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 201 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 188 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19208 Z= 0.286 Angle : 0.639 10.254 26114 Z= 0.323 Chirality : 0.048 0.261 3159 Planarity : 0.005 0.059 3295 Dihedral : 6.638 59.899 3325 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 3.26 % Allowed : 10.31 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2264 helix: 0.93 (0.22), residues: 572 sheet: -0.99 (0.23), residues: 490 loop : -2.50 (0.16), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 64 HIS 0.006 0.001 HIS A1058 PHE 0.030 0.002 PHE A 592 TYR 0.026 0.002 TYR B 904 ARG 0.005 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 179 time to evaluate : 2.114 Fit side-chains REVERT: A 44 ARG cc_start: 0.7457 (mtt90) cc_final: 0.7110 (mtt90) REVERT: A 64 TRP cc_start: 0.7298 (t60) cc_final: 0.6695 (t60) REVERT: A 104 TRP cc_start: 0.6130 (m-90) cc_final: 0.5409 (m-90) REVERT: A 202 LYS cc_start: 0.7660 (mttm) cc_final: 0.7267 (mtpt) REVERT: A 421 TYR cc_start: 0.6503 (m-10) cc_final: 0.5800 (t80) REVERT: A 529 LYS cc_start: 0.6595 (tppt) cc_final: 0.6146 (tttm) REVERT: A 651 ILE cc_start: 0.8618 (mt) cc_final: 0.8393 (mm) REVERT: A 984 LEU cc_start: 0.7367 (mt) cc_final: 0.7100 (mt) REVERT: B 200 TYR cc_start: 0.6303 (m-10) cc_final: 0.5876 (m-80) REVERT: B 282 ASN cc_start: 0.6327 (m-40) cc_final: 0.5976 (t0) REVERT: B 633 TRP cc_start: 0.5922 (t-100) cc_final: 0.5071 (t-100) REVERT: B 673 SER cc_start: 0.8045 (t) cc_final: 0.7823 (p) REVERT: B 902 MET cc_start: 0.9113 (tpt) cc_final: 0.8451 (tpt) REVERT: B 1050 MET cc_start: 0.8588 (ptm) cc_final: 0.8384 (ptp) REVERT: B 1107 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7793 (ttm110) REVERT: C 53 ASP cc_start: 0.7804 (t0) cc_final: 0.7502 (t0) REVERT: C 558 LYS cc_start: 0.7030 (mppt) cc_final: 0.6711 (mtpp) REVERT: C 886 TRP cc_start: 0.8477 (p90) cc_final: 0.7906 (p90) REVERT: C 1138 TYR cc_start: 0.7059 (t80) cc_final: 0.6818 (t80) outliers start: 67 outliers final: 55 residues processed: 232 average time/residue: 0.2997 time to fit residues: 108.1430 Evaluate side-chains 215 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 160 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 187 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 155 optimal weight: 10.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 317 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19208 Z= 0.191 Angle : 0.562 10.908 26114 Z= 0.284 Chirality : 0.045 0.243 3159 Planarity : 0.004 0.061 3295 Dihedral : 6.180 58.922 3325 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 3.60 % Allowed : 10.75 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2264 helix: 1.33 (0.23), residues: 565 sheet: -0.73 (0.23), residues: 488 loop : -2.37 (0.16), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.003 0.001 HIS A1058 PHE 0.047 0.001 PHE A 592 TYR 0.020 0.001 TYR B 904 ARG 0.004 0.000 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 169 time to evaluate : 2.240 Fit side-chains REVERT: A 44 ARG cc_start: 0.7469 (mtt90) cc_final: 0.7142 (mtt90) REVERT: A 64 TRP cc_start: 0.7217 (t60) cc_final: 0.6742 (t60) REVERT: A 104 TRP cc_start: 0.6102 (m-90) cc_final: 0.5416 (m-90) REVERT: A 202 LYS cc_start: 0.7640 (mttm) cc_final: 0.7273 (mtpt) REVERT: A 421 TYR cc_start: 0.6428 (m-10) cc_final: 0.5786 (t80) REVERT: B 200 TYR cc_start: 0.6391 (m-10) cc_final: 0.5906 (m-80) REVERT: B 201 PHE cc_start: 0.6791 (t80) cc_final: 0.6147 (t80) REVERT: B 206 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6369 (tttt) REVERT: B 282 ASN cc_start: 0.6327 (m-40) cc_final: 0.5875 (t0) REVERT: B 673 SER cc_start: 0.8062 (t) cc_final: 0.7830 (p) REVERT: B 1050 MET cc_start: 0.8607 (ptm) cc_final: 0.8295 (ptp) REVERT: B 1107 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7736 (ttm110) REVERT: C 53 ASP cc_start: 0.7785 (t0) cc_final: 0.7402 (t0) REVERT: C 102 ARG cc_start: 0.4161 (mmp-170) cc_final: 0.1802 (mmp80) REVERT: C 398 ASP cc_start: 0.6154 (m-30) cc_final: 0.5903 (t0) REVERT: C 558 LYS cc_start: 0.6974 (mppt) cc_final: 0.6640 (mtpp) REVERT: C 886 TRP cc_start: 0.8444 (p90) cc_final: 0.7850 (p90) REVERT: C 1138 TYR cc_start: 0.7060 (t80) cc_final: 0.6816 (t80) outliers start: 74 outliers final: 48 residues processed: 230 average time/residue: 0.2969 time to fit residues: 106.9083 Evaluate side-chains 201 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 152 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 75 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19208 Z= 0.188 Angle : 0.556 11.993 26114 Z= 0.279 Chirality : 0.045 0.243 3159 Planarity : 0.004 0.061 3295 Dihedral : 5.938 59.449 3325 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 3.26 % Allowed : 11.62 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2264 helix: 1.51 (0.23), residues: 565 sheet: -0.62 (0.23), residues: 491 loop : -2.22 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 633 HIS 0.003 0.001 HIS A1058 PHE 0.045 0.001 PHE A 592 TYR 0.020 0.001 TYR B 904 ARG 0.006 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 167 time to evaluate : 1.954 Fit side-chains REVERT: A 44 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7157 (mtt90) REVERT: A 64 TRP cc_start: 0.7245 (t60) cc_final: 0.6744 (t60) REVERT: A 104 TRP cc_start: 0.6138 (m-90) cc_final: 0.5484 (m-90) REVERT: A 202 LYS cc_start: 0.7645 (mttm) cc_final: 0.7293 (mtpt) REVERT: A 421 TYR cc_start: 0.6517 (m-10) cc_final: 0.5756 (t80) REVERT: B 200 TYR cc_start: 0.6408 (m-10) cc_final: 0.5976 (m-80) REVERT: B 201 PHE cc_start: 0.6751 (t80) cc_final: 0.6158 (t80) REVERT: B 206 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6381 (tttt) REVERT: B 282 ASN cc_start: 0.6252 (m-40) cc_final: 0.5745 (t0) REVERT: B 673 SER cc_start: 0.8062 (t) cc_final: 0.7832 (p) REVERT: C 53 ASP cc_start: 0.7841 (t0) cc_final: 0.7464 (t0) REVERT: C 102 ARG cc_start: 0.4195 (mmp-170) cc_final: 0.1831 (mmp80) REVERT: C 398 ASP cc_start: 0.6136 (m-30) cc_final: 0.5857 (t0) REVERT: C 558 LYS cc_start: 0.7023 (mppt) cc_final: 0.6731 (mtpp) REVERT: C 886 TRP cc_start: 0.8416 (p90) cc_final: 0.7786 (p90) REVERT: C 1138 TYR cc_start: 0.7030 (t80) cc_final: 0.6785 (t80) outliers start: 67 outliers final: 54 residues processed: 222 average time/residue: 0.2986 time to fit residues: 103.0824 Evaluate side-chains 209 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 154 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 217 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19208 Z= 0.196 Angle : 0.561 11.530 26114 Z= 0.281 Chirality : 0.045 0.240 3159 Planarity : 0.004 0.063 3295 Dihedral : 5.860 58.834 3325 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.61 % Favored : 94.30 % Rotamer: Outliers : 3.79 % Allowed : 11.33 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2264 helix: 1.54 (0.23), residues: 571 sheet: -0.48 (0.23), residues: 490 loop : -2.23 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.004 0.001 HIS A1058 PHE 0.048 0.001 PHE A 592 TYR 0.019 0.001 TYR B 904 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 156 time to evaluate : 2.151 Fit side-chains REVERT: A 44 ARG cc_start: 0.7467 (mtt90) cc_final: 0.7132 (mtt90) REVERT: A 64 TRP cc_start: 0.7234 (t60) cc_final: 0.6747 (t60) REVERT: A 104 TRP cc_start: 0.6143 (m-90) cc_final: 0.5500 (m-90) REVERT: A 202 LYS cc_start: 0.7697 (mttm) cc_final: 0.7307 (mtpt) REVERT: A 203 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7520 (tt) REVERT: A 421 TYR cc_start: 0.6438 (m-10) cc_final: 0.5665 (t80) REVERT: B 200 TYR cc_start: 0.6481 (m-10) cc_final: 0.5936 (m-80) REVERT: B 206 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6343 (tttt) REVERT: B 282 ASN cc_start: 0.6228 (m-40) cc_final: 0.5683 (t0) REVERT: B 633 TRP cc_start: 0.5957 (t-100) cc_final: 0.5246 (t-100) REVERT: B 673 SER cc_start: 0.8042 (t) cc_final: 0.7808 (p) REVERT: C 102 ARG cc_start: 0.4177 (mmp-170) cc_final: 0.1775 (mmp80) REVERT: C 398 ASP cc_start: 0.6146 (m-30) cc_final: 0.5871 (t0) REVERT: C 558 LYS cc_start: 0.6995 (mppt) cc_final: 0.6694 (mtpp) REVERT: C 886 TRP cc_start: 0.8366 (p90) cc_final: 0.7777 (p90) REVERT: C 1138 TYR cc_start: 0.7003 (t80) cc_final: 0.6771 (t80) outliers start: 78 outliers final: 60 residues processed: 222 average time/residue: 0.2903 time to fit residues: 101.3018 Evaluate side-chains 212 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 150 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19208 Z= 0.227 Angle : 0.582 9.964 26114 Z= 0.292 Chirality : 0.046 0.239 3159 Planarity : 0.004 0.050 3295 Dihedral : 5.968 59.967 3325 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 3.55 % Allowed : 11.72 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2264 helix: 1.55 (0.23), residues: 572 sheet: -0.52 (0.23), residues: 502 loop : -2.22 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.004 0.001 HIS A1058 PHE 0.046 0.001 PHE A 592 TYR 0.032 0.002 TYR C 904 ARG 0.011 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 159 time to evaluate : 1.953 Fit side-chains REVERT: A 44 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7108 (mtt90) REVERT: A 104 TRP cc_start: 0.6147 (m-90) cc_final: 0.5500 (m-90) REVERT: A 202 LYS cc_start: 0.7631 (mttm) cc_final: 0.7282 (mtpt) REVERT: A 203 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7521 (tt) REVERT: A 421 TYR cc_start: 0.6471 (m-10) cc_final: 0.5627 (t80) REVERT: A 881 THR cc_start: 0.8169 (m) cc_final: 0.7957 (m) REVERT: B 200 TYR cc_start: 0.6509 (m-10) cc_final: 0.5946 (m-80) REVERT: B 633 TRP cc_start: 0.5990 (t-100) cc_final: 0.5312 (t-100) REVERT: B 790 LYS cc_start: 0.7528 (mtpp) cc_final: 0.7228 (mmtp) REVERT: B 902 MET cc_start: 0.9101 (tpt) cc_final: 0.8595 (tpt) REVERT: C 102 ARG cc_start: 0.4151 (mmp-170) cc_final: 0.1767 (mmp80) REVERT: C 398 ASP cc_start: 0.6215 (m-30) cc_final: 0.5846 (t0) REVERT: C 558 LYS cc_start: 0.7136 (mppt) cc_final: 0.6834 (mtpp) REVERT: C 886 TRP cc_start: 0.8362 (p90) cc_final: 0.7700 (p90) REVERT: C 1138 TYR cc_start: 0.6998 (t80) cc_final: 0.6770 (t80) outliers start: 73 outliers final: 62 residues processed: 220 average time/residue: 0.2925 time to fit residues: 99.5601 Evaluate side-chains 215 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 152 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 209 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 19208 Z= 0.208 Angle : 0.574 9.904 26114 Z= 0.288 Chirality : 0.046 0.240 3159 Planarity : 0.004 0.048 3295 Dihedral : 6.026 84.886 3325 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 3.40 % Allowed : 12.21 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2264 helix: 1.67 (0.23), residues: 572 sheet: -0.44 (0.23), residues: 502 loop : -2.19 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.004 0.001 HIS A1058 PHE 0.051 0.001 PHE A 592 TYR 0.027 0.001 TYR C 904 ARG 0.007 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 152 time to evaluate : 2.143 Fit side-chains REVERT: A 44 ARG cc_start: 0.7453 (mtt90) cc_final: 0.7093 (mtt90) REVERT: A 104 TRP cc_start: 0.6146 (m-90) cc_final: 0.5505 (m-90) REVERT: A 202 LYS cc_start: 0.7610 (mttm) cc_final: 0.7288 (mtpt) REVERT: A 203 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 421 TYR cc_start: 0.6492 (m-10) cc_final: 0.5671 (t80) REVERT: A 881 THR cc_start: 0.8170 (m) cc_final: 0.7954 (m) REVERT: B 189 LEU cc_start: 0.5689 (mt) cc_final: 0.5328 (tt) REVERT: B 633 TRP cc_start: 0.6035 (t-100) cc_final: 0.5445 (t-100) REVERT: B 790 LYS cc_start: 0.7531 (mtpp) cc_final: 0.7241 (mmtp) REVERT: B 902 MET cc_start: 0.9105 (tpt) cc_final: 0.8647 (tpt) REVERT: C 102 ARG cc_start: 0.4143 (mmp-170) cc_final: 0.1747 (mmp80) REVERT: C 398 ASP cc_start: 0.6195 (m-30) cc_final: 0.5845 (t0) REVERT: C 558 LYS cc_start: 0.7086 (mppt) cc_final: 0.6882 (mtpp) REVERT: C 823 PHE cc_start: 0.7630 (m-80) cc_final: 0.7343 (m-80) REVERT: C 886 TRP cc_start: 0.8344 (p90) cc_final: 0.7666 (p90) REVERT: C 1138 TYR cc_start: 0.6933 (t80) cc_final: 0.6722 (t80) outliers start: 70 outliers final: 64 residues processed: 211 average time/residue: 0.2860 time to fit residues: 94.8405 Evaluate side-chains 210 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 145 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 137 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 232 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 19208 Z= 0.257 Angle : 0.607 10.017 26114 Z= 0.306 Chirality : 0.047 0.244 3159 Planarity : 0.004 0.051 3295 Dihedral : 6.269 77.924 3325 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.60 % Rotamer: Outliers : 3.40 % Allowed : 12.21 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2264 helix: 1.59 (0.22), residues: 572 sheet: -0.52 (0.23), residues: 502 loop : -2.22 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.005 0.001 HIS B1058 PHE 0.050 0.002 PHE A 592 TYR 0.029 0.002 TYR C 904 ARG 0.009 0.001 ARG B1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4528 Ramachandran restraints generated. 2264 Oldfield, 0 Emsley, 2264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 146 time to evaluate : 2.241 Fit side-chains REVERT: A 44 ARG cc_start: 0.7466 (mtt90) cc_final: 0.7097 (mtt90) REVERT: A 104 TRP cc_start: 0.6148 (m-90) cc_final: 0.5494 (m-90) REVERT: A 203 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 421 TYR cc_start: 0.6660 (m-10) cc_final: 0.5760 (t80) REVERT: B 633 TRP cc_start: 0.6083 (t-100) cc_final: 0.5398 (t-100) REVERT: B 902 MET cc_start: 0.9132 (tpt) cc_final: 0.8660 (tpt) REVERT: B 977 LEU cc_start: 0.8052 (tp) cc_final: 0.7813 (pt) REVERT: C 398 ASP cc_start: 0.6200 (m-30) cc_final: 0.5863 (t0) REVERT: C 558 LYS cc_start: 0.7170 (mppt) cc_final: 0.6967 (mtpp) REVERT: C 886 TRP cc_start: 0.8459 (p90) cc_final: 0.7655 (p90) REVERT: C 1138 TYR cc_start: 0.6935 (t80) cc_final: 0.6719 (t80) outliers start: 70 outliers final: 64 residues processed: 206 average time/residue: 0.2969 time to fit residues: 96.9887 Evaluate side-chains 205 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 140 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 557 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 635 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 233 random chunks: chunk 146 optimal weight: 0.9980 chunk 196 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.0000 chunk 77 optimal weight: 0.0980 chunk 190 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN C 317 ASN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.135576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101088 restraints weight = 34492.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103855 restraints weight = 20183.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104421 restraints weight = 13828.028| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 19208 Z= 0.145 Angle : 0.537 9.787 26114 Z= 0.270 Chirality : 0.045 0.239 3159 Planarity : 0.004 0.044 3295 Dihedral : 5.638 75.199 3325 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 1.95 % Allowed : 13.72 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2264 helix: 1.96 (0.23), residues: 571 sheet: -0.24 (0.23), residues: 492 loop : -2.03 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.001 0.000 HIS C1048 PHE 0.050 0.001 PHE A 592 TYR 0.024 0.001 TYR B1138 ARG 0.004 0.000 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3676.40 seconds wall clock time: 68 minutes 43.13 seconds (4123.13 seconds total)