Starting phenix.real_space_refine on Wed Nov 20 13:46:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mtc_23982/11_2024/7mtc_23982.cif" } resolution = 2.6 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= 0.002 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 91 5.16 5 C 13511 2.51 5 N 3448 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21178 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 7139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7139 Classifications: {'peptide': 914} Link IDs: {'PTRANS': 45, 'TRANS': 868} Chain breaks: 15 Chain: "B" Number of atoms: 6435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6435 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 43, 'TRANS': 786} Chain breaks: 13 Chain: "C" Number of atoms: 7016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7016 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 46, 'TRANS': 851} Chain breaks: 16 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 13.79, per 1000 atoms: 0.65 Number of scatterers: 21178 At special positions: 0 Unit cell: (131.67, 132.525, 164.16, 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 91 16.00 O 4128 8.00 N 3448 7.00 C 13511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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=2.02 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=2.04 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.03 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=2.04 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " 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: 6.12 Conformation dependent library (CDL) restraints added in 2.8 seconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4966 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 41 sheets defined 26.2% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.901A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.396A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.603A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.546A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.577A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.591A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.638A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 940 removed outlier: 4.180A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.948A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.775A 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 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.102A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.667A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.783A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.606A 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: 3.834A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.212A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.959A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.567A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.645A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.841A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.544A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 4.021A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.516A 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: 3.916A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.713A 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 909 removed outlier: 3.666A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.514A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.713A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.164A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.001A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.866A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.612A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 279 removed outlier: 6.707A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.134A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.520A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.196A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.820A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.424A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.819A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.670A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.585A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 8.440A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.176A 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 55 removed outlier: 7.570A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.071A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.887A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.664A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.463A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.721A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.699A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.988A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.569A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.773A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR C 266 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.569A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.584A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 538 through 543 removed outlier: 3.545A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.669A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.776A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.801A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 842 hydrogen bonds defined for protein. 2337 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: 8.40 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4904 1.33 - 1.45: 5552 1.45 - 1.58: 11037 1.58 - 1.71: 0 1.71 - 1.83: 115 Bond restraints: 21608 Sorted by residual: bond pdb=" CG LEU B 916 " pdb=" CD1 LEU B 916 " ideal model delta sigma weight residual 1.521 1.407 0.114 3.30e-02 9.18e+02 1.19e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" CA SER B 758 " pdb=" CB SER B 758 " ideal model delta sigma weight residual 1.531 1.426 0.105 3.12e-02 1.03e+03 1.12e+01 bond pdb=" CG1 ILE B 896 " pdb=" CD1 ILE B 896 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.68e+00 bond pdb=" CB VAL B1094 " pdb=" CG1 VAL B1094 " ideal model delta sigma weight residual 1.521 1.421 0.100 3.30e-02 9.18e+02 9.17e+00 ... (remaining 21603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 28965 3.55 - 7.09: 369 7.09 - 10.64: 36 10.64 - 14.19: 5 14.19 - 17.73: 1 Bond angle restraints: 29376 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 121.54 134.30 -12.76 1.91e+00 2.74e-01 4.46e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.72 106.41 7.31 1.30e+00 5.92e-01 3.16e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 117.25 -6.55 1.22e+00 6.72e-01 2.89e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.71e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.03 -6.33 1.22e+00 6.72e-01 2.69e+01 ... (remaining 29371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 12667 16.01 - 32.02: 541 32.02 - 48.03: 154 48.03 - 64.05: 46 64.05 - 80.06: 17 Dihedral angle restraints: 13425 sinusoidal: 5759 harmonic: 7666 Sorted by residual: 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 -149.73 63.73 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CA ASN B 616 " pdb=" C ASN B 616 " pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta harmonic sigma weight residual 180.00 149.83 30.17 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 150.39 29.61 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 13422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 3364 0.143 - 0.287: 161 0.287 - 0.430: 4 0.430 - 0.573: 0 0.573 - 0.717: 2 Chirality restraints: 3531 Sorted by residual: chirality pdb=" CG LEU C 916 " pdb=" CB LEU C 916 " pdb=" CD1 LEU C 916 " pdb=" CD2 LEU C 916 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.39e+00 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 -2.07 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 3528 not shown) Planarity restraints: 3736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 823 " -0.027 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE C 823 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE C 823 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE C 823 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 823 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 823 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 823 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 823 " -0.022 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A 823 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 823 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 823 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 823 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 823 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 823 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 800 " -0.026 2.00e-02 2.50e+03 2.69e-02 1.27e+01 pdb=" CG PHE A 800 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 800 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 800 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 800 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 800 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 800 " -0.007 2.00e-02 2.50e+03 ... (remaining 3733 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3284 2.76 - 3.29: 17642 3.29 - 3.83: 32646 3.83 - 4.36: 37650 4.36 - 4.90: 67458 Nonbonded interactions: 158680 Sorted by model distance: nonbonded pdb=" OE2 GLU A 298 " pdb=" OG SER A 316 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.254 3.040 nonbonded pdb=" O TRP C 353 " pdb=" NH1 ARG C 466 " model vdw 2.305 3.120 nonbonded pdb=" OD2 ASP B 808 " pdb=" OG SER B 810 " model vdw 2.338 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.354 3.040 ... (remaining 158675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 65 or resid 81 through 95 or resid 100 through \ 121 or resid 126 through 131 or resid 169 through 241 or resid 265 through 343 o \ r resid 358 through 368 or resid 383 through 395 or resid 399 through 400 or res \ id 492 or resid 521 through 620 or resid 641 through 675 or resid 690 through 82 \ 6 or resid 855 through 940 or resid 943 through 1143 or resid 1301 through 1304) \ ) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 109 or resid 115 throug \ h 172 or resid 189 through 209 or resid 216 through 241 or resid 265 through 395 \ or resid 514 through 515 or resid 518 or resid 521 through 620 or resid 641 thr \ ough 675 or resid 690 through 940 or resid 943 through 1143 or resid 1302 throug \ h 1305)) selection = (chain 'C' and (resid 27 through 65 or resid 81 through 130 or resid 166 or resi \ d 169 through 172 or resid 189 through 241 or resid 265 through 343 or resid 358 \ through 368 or resid 383 through 395 or resid 399 through 400 or resid 492 or r \ esid 521 through 620 or resid 641 through 826 or resid 855 through 1143 or 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 individual isotropic 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: 6.100 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: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 51.870 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.013 0.121 21608 Z= 0.865 Angle : 1.135 17.735 29376 Z= 0.619 Chirality : 0.076 0.717 3531 Planarity : 0.009 0.077 3708 Dihedral : 10.878 80.057 8372 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.56 % Allowed : 2.33 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.84 (0.14), residues: 2548 helix: -1.38 (0.17), residues: 628 sheet: -0.67 (0.21), residues: 566 loop : -2.76 (0.13), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP A 886 HIS 0.019 0.005 HIS B1048 PHE 0.065 0.006 PHE C 823 TYR 0.043 0.005 TYR B 279 ARG 0.019 0.002 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 279 time to evaluate : 2.564 Fit side-chains revert: symmetry clash REVERT: B 619 GLU cc_start: 0.7585 (mp0) cc_final: 0.7310 (mt-10) REVERT: B 809 PRO cc_start: 0.7746 (Cg_endo) cc_final: 0.7177 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8192 (mp0) cc_final: 0.7944 (mp0) REVERT: C 239 GLN cc_start: 0.8064 (pt0) cc_final: 0.7584 (pt0) outliers start: 13 outliers final: 3 residues processed: 292 average time/residue: 1.3548 time to fit residues: 451.1148 Evaluate side-chains 153 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 738 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 238 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 370 ASN A 414 GLN A 901 GLN A 957 GLN A1010 GLN B 207 HIS B 540 ASN B 606 ASN B 762 GLN B 804 GLN B 901 GLN B 935 GLN B 957 GLN B1002 GLN C 354 ASN C 370 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21608 Z= 0.191 Angle : 0.648 15.413 29376 Z= 0.334 Chirality : 0.052 1.315 3531 Planarity : 0.005 0.061 3708 Dihedral : 6.974 59.796 3670 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.94 % Allowed : 6.51 % Favored : 91.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.42 (0.15), residues: 2548 helix: 0.47 (0.21), residues: 630 sheet: 0.14 (0.20), residues: 595 loop : -2.28 (0.14), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 886 HIS 0.006 0.001 HIS B 207 PHE 0.022 0.002 PHE C 168 TYR 0.024 0.002 TYR B 904 ARG 0.009 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 2.382 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7167 (mmp-170) cc_final: 0.6770 (mmt90) REVERT: A 127 VAL cc_start: 0.7345 (p) cc_final: 0.7075 (p) REVERT: A 200 TYR cc_start: 0.7217 (m-80) cc_final: 0.6800 (m-80) REVERT: A 347 PHE cc_start: 0.5330 (OUTLIER) cc_final: 0.4512 (m-80) REVERT: A 529 LYS cc_start: 0.8266 (mppt) cc_final: 0.7963 (mmmt) REVERT: A 556 ASN cc_start: 0.7682 (t0) cc_final: 0.7458 (t0) REVERT: A 654 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: A 740 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7204 (ttp) REVERT: B 102 ARG cc_start: 0.7667 (mmm160) cc_final: 0.6928 (mmm-85) REVERT: B 271 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8171 (mt0) REVERT: B 314 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8046 (tm-30) REVERT: B 529 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7954 (mtpp) REVERT: B 809 PRO cc_start: 0.7699 (Cg_endo) cc_final: 0.7111 (Cg_exo) REVERT: B 904 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.5761 (p90) REVERT: B 988 GLU cc_start: 0.8140 (mp0) cc_final: 0.7866 (mp0) REVERT: C 33 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7551 (p) REVERT: C 239 GLN cc_start: 0.7899 (pt0) cc_final: 0.7499 (pt0) REVERT: C 560 LEU cc_start: 0.8049 (mt) cc_final: 0.7651 (mp) REVERT: C 1092 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6979 (pm20) outliers start: 45 outliers final: 7 residues processed: 219 average time/residue: 1.3432 time to fit residues: 337.6300 Evaluate side-chains 166 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 132 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 239 optimal weight: 0.1980 chunk 258 optimal weight: 1.9990 chunk 213 optimal weight: 0.2980 chunk 237 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN A1005 GLN B 207 HIS B 957 GLN B1002 GLN C 87 ASN C1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21608 Z= 0.222 Angle : 0.624 14.052 29376 Z= 0.320 Chirality : 0.049 0.855 3531 Planarity : 0.005 0.065 3708 Dihedral : 6.466 59.290 3669 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.07 % Allowed : 8.19 % Favored : 89.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2548 helix: 1.05 (0.21), residues: 636 sheet: 0.35 (0.20), residues: 605 loop : -2.06 (0.15), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.006 0.001 HIS A1064 PHE 0.023 0.002 PHE C 168 TYR 0.023 0.001 TYR B1067 ARG 0.009 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7291 (m-80) cc_final: 0.6804 (m-80) REVERT: A 347 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4692 (m-80) REVERT: A 529 LYS cc_start: 0.8264 (mppt) cc_final: 0.8023 (mmmt) REVERT: A 556 ASN cc_start: 0.7734 (t0) cc_final: 0.7437 (t0) REVERT: A 654 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: A 740 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7239 (ttp) REVERT: B 271 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: B 314 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: B 529 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7838 (mtpp) REVERT: B 581 THR cc_start: 0.7959 (OUTLIER) cc_final: 0.7746 (p) REVERT: B 809 PRO cc_start: 0.7751 (Cg_endo) cc_final: 0.7230 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8184 (mp0) cc_final: 0.7885 (mp0) REVERT: C 33 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7561 (p) REVERT: C 239 GLN cc_start: 0.7899 (pt0) cc_final: 0.7565 (pt0) REVERT: C 515 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7791 (p90) REVERT: C 560 LEU cc_start: 0.8039 (mt) cc_final: 0.7622 (mp) REVERT: C 855 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: C 1092 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6959 (pm20) outliers start: 48 outliers final: 16 residues processed: 190 average time/residue: 1.1962 time to fit residues: 264.8928 Evaluate side-chains 160 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 236 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 124 optimal weight: 0.0370 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 207 HIS B 957 GLN B1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21608 Z= 0.285 Angle : 0.651 14.758 29376 Z= 0.334 Chirality : 0.050 0.666 3531 Planarity : 0.005 0.043 3708 Dihedral : 6.255 58.337 3669 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.72 % Allowed : 7.98 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.71 (0.16), residues: 2548 helix: 1.26 (0.22), residues: 630 sheet: 0.51 (0.21), residues: 595 loop : -1.90 (0.15), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 886 HIS 0.007 0.002 HIS A1064 PHE 0.021 0.002 PHE A 823 TYR 0.024 0.002 TYR B 904 ARG 0.010 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 157 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7286 (mmp-170) cc_final: 0.6700 (mmt90) REVERT: A 200 TYR cc_start: 0.7343 (m-80) cc_final: 0.6779 (m-80) REVERT: A 304 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8202 (mttm) REVERT: A 529 LYS cc_start: 0.8295 (mppt) cc_final: 0.8074 (mmmt) REVERT: A 556 ASN cc_start: 0.7697 (t0) cc_final: 0.7379 (t0) REVERT: A 654 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: A 740 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7441 (ttt) REVERT: B 314 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: B 581 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7705 (p) REVERT: B 809 PRO cc_start: 0.7523 (Cg_endo) cc_final: 0.7035 (Cg_exo) REVERT: B 988 GLU cc_start: 0.8213 (mp0) cc_final: 0.7903 (mp0) REVERT: C 33 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7591 (p) REVERT: C 239 GLN cc_start: 0.7943 (pt0) cc_final: 0.7616 (pt0) REVERT: C 560 LEU cc_start: 0.7988 (mt) cc_final: 0.7554 (mp) REVERT: C 855 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6828 (m-80) outliers start: 63 outliers final: 24 residues processed: 203 average time/residue: 1.1970 time to fit residues: 282.9119 Evaluate side-chains 175 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 211 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 228 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 121 ASN B 207 HIS B 957 GLN B1002 GLN C 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 21608 Z= 0.313 Angle : 0.661 15.419 29376 Z= 0.340 Chirality : 0.050 0.601 3531 Planarity : 0.005 0.043 3708 Dihedral : 6.071 59.995 3669 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.67 % Allowed : 8.75 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.61 (0.16), residues: 2548 helix: 1.30 (0.22), residues: 629 sheet: 0.61 (0.21), residues: 593 loop : -1.83 (0.15), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 886 HIS 0.007 0.002 HIS A1064 PHE 0.021 0.002 PHE C 32 TYR 0.027 0.002 TYR B 904 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 154 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7317 (m-80) cc_final: 0.6738 (m-80) REVERT: A 207 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.6741 (p-80) REVERT: A 304 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8218 (mttm) REVERT: A 462 LYS cc_start: 0.8851 (mppt) cc_final: 0.8490 (mtpm) REVERT: A 529 LYS cc_start: 0.8324 (mppt) cc_final: 0.8078 (mmmt) REVERT: A 556 ASN cc_start: 0.7635 (t0) cc_final: 0.7321 (t0) REVERT: A 654 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: A 740 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7440 (ttt) REVERT: B 314 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: B 529 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7828 (mttm) REVERT: B 809 PRO cc_start: 0.7501 (Cg_endo) cc_final: 0.7032 (Cg_exo) REVERT: B 904 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5671 (p90) REVERT: C 33 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7686 (p) REVERT: C 239 GLN cc_start: 0.7909 (pt0) cc_final: 0.7629 (pt0) REVERT: C 560 LEU cc_start: 0.8012 (mt) cc_final: 0.7574 (mp) outliers start: 62 outliers final: 27 residues processed: 199 average time/residue: 1.1053 time to fit residues: 259.2318 Evaluate side-chains 176 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 85 optimal weight: 0.9980 chunk 228 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 211 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 0.0040 chunk 133 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN B 207 HIS B 804 GLN B 935 GLN B 957 GLN B1002 GLN C 354 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 21608 Z= 0.153 Angle : 0.573 15.701 29376 Z= 0.291 Chirality : 0.046 0.610 3531 Planarity : 0.004 0.041 3708 Dihedral : 5.473 57.605 3669 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.64 % Allowed : 9.87 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.22 (0.16), residues: 2548 helix: 1.63 (0.22), residues: 635 sheet: 0.81 (0.21), residues: 613 loop : -1.63 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.005 0.001 HIS A 207 PHE 0.017 0.001 PHE C 32 TYR 0.023 0.001 TYR A 170 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 2.469 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7290 (mmp-170) cc_final: 0.6672 (mmt90) REVERT: A 200 TYR cc_start: 0.7241 (m-80) cc_final: 0.6718 (m-80) REVERT: A 304 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8143 (mttm) REVERT: A 347 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4842 (m-80) REVERT: A 529 LYS cc_start: 0.8249 (mppt) cc_final: 0.8017 (mmmt) REVERT: A 556 ASN cc_start: 0.7588 (t0) cc_final: 0.7241 (t0) REVERT: A 654 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: A 740 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7141 (ttp) REVERT: B 314 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: B 529 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7688 (mttm) REVERT: B 809 PRO cc_start: 0.7313 (Cg_endo) cc_final: 0.6904 (Cg_exo) REVERT: C 33 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 560 LEU cc_start: 0.7867 (mt) cc_final: 0.7430 (mp) REVERT: C 794 ILE cc_start: 0.7840 (mm) cc_final: 0.7564 (pp) REVERT: C 855 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6776 (m-80) outliers start: 38 outliers final: 11 residues processed: 187 average time/residue: 1.1691 time to fit residues: 256.5512 Evaluate side-chains 153 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 chunk 253 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 414 GLN A 957 GLN B 121 ASN B 207 HIS C 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21608 Z= 0.243 Angle : 0.608 13.624 29376 Z= 0.312 Chirality : 0.048 0.543 3531 Planarity : 0.004 0.041 3708 Dihedral : 5.462 57.301 3669 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.85 % Allowed : 10.13 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.26 (0.16), residues: 2548 helix: 1.58 (0.22), residues: 636 sheet: 0.75 (0.21), residues: 609 loop : -1.61 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.007 0.001 HIS B 207 PHE 0.020 0.002 PHE C 32 TYR 0.027 0.001 TYR B 904 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 2.563 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7351 (m-80) cc_final: 0.6771 (m-80) REVERT: A 304 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8212 (mttm) REVERT: A 347 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.5053 (m-80) REVERT: A 529 LYS cc_start: 0.8272 (mppt) cc_final: 0.8029 (mmmt) REVERT: A 556 ASN cc_start: 0.7625 (t0) cc_final: 0.7273 (t0) REVERT: A 654 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: A 740 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: B 314 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: B 528 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7791 (mtpt) REVERT: B 529 LYS cc_start: 0.8026 (mmtm) cc_final: 0.7704 (mttm) REVERT: B 809 PRO cc_start: 0.7302 (Cg_endo) cc_final: 0.6916 (Cg_exo) REVERT: C 33 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7558 (p) REVERT: C 515 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7840 (p90) REVERT: C 560 LEU cc_start: 0.7910 (mt) cc_final: 0.7475 (mp) REVERT: C 794 ILE cc_start: 0.7981 (mm) cc_final: 0.7632 (pp) REVERT: C 855 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6788 (m-80) outliers start: 43 outliers final: 20 residues processed: 180 average time/residue: 1.0537 time to fit residues: 225.4460 Evaluate side-chains 165 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 414 GLN A 532 ASN A 957 GLN B 207 HIS C 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21608 Z= 0.215 Angle : 0.597 13.728 29376 Z= 0.306 Chirality : 0.047 0.489 3531 Planarity : 0.004 0.041 3708 Dihedral : 5.323 56.935 3669 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 10.65 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.18 (0.16), residues: 2548 helix: 1.61 (0.21), residues: 637 sheet: 0.81 (0.21), residues: 604 loop : -1.55 (0.16), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.008 0.001 HIS B 207 PHE 0.023 0.001 PHE C 168 TYR 0.026 0.001 TYR A 170 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 2.580 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7349 (m-80) cc_final: 0.6779 (m-80) REVERT: A 304 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8184 (mttm) REVERT: A 347 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.5062 (m-80) REVERT: A 529 LYS cc_start: 0.8269 (mppt) cc_final: 0.8020 (mmmt) REVERT: A 556 ASN cc_start: 0.7629 (t0) cc_final: 0.7279 (t0) REVERT: A 654 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: A 740 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7208 (ttp) REVERT: B 102 ARG cc_start: 0.7604 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: B 314 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: B 528 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7775 (mtpt) REVERT: B 529 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7691 (mttm) REVERT: B 809 PRO cc_start: 0.7251 (Cg_endo) cc_final: 0.6881 (Cg_exo) REVERT: C 33 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7555 (p) REVERT: C 560 LEU cc_start: 0.7884 (mt) cc_final: 0.7449 (mp) REVERT: C 794 ILE cc_start: 0.7955 (mm) cc_final: 0.7634 (pp) REVERT: C 855 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6772 (m-80) outliers start: 46 outliers final: 23 residues processed: 175 average time/residue: 1.1052 time to fit residues: 228.6166 Evaluate side-chains 170 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 242 optimal weight: 0.6980 chunk 221 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 414 GLN B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21608 Z= 0.196 Angle : 0.578 13.061 29376 Z= 0.297 Chirality : 0.047 0.564 3531 Planarity : 0.004 0.040 3708 Dihedral : 5.199 56.709 3669 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.68 % Allowed : 11.08 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.12 (0.16), residues: 2548 helix: 1.70 (0.21), residues: 636 sheet: 0.84 (0.21), residues: 611 loop : -1.53 (0.16), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.008 0.001 HIS B 207 PHE 0.022 0.001 PHE C 168 TYR 0.025 0.001 TYR A 453 ARG 0.005 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 2.377 Fit side-chains revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7344 (mmp-170) cc_final: 0.7027 (mmp-170) REVERT: A 200 TYR cc_start: 0.7351 (m-80) cc_final: 0.6771 (m-80) REVERT: A 304 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8193 (mttm) REVERT: A 347 PHE cc_start: 0.5430 (OUTLIER) cc_final: 0.5151 (m-80) REVERT: A 529 LYS cc_start: 0.8263 (mppt) cc_final: 0.8017 (mmmt) REVERT: A 556 ASN cc_start: 0.7629 (t0) cc_final: 0.7283 (t0) REVERT: A 654 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 740 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7189 (ttp) REVERT: A 1142 GLN cc_start: 0.6626 (tp40) cc_final: 0.6388 (tp40) REVERT: B 102 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.7285 (mmm-85) REVERT: B 314 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: B 528 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7782 (mtpt) REVERT: B 529 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7661 (mttm) REVERT: B 809 PRO cc_start: 0.7187 (Cg_endo) cc_final: 0.6773 (Cg_exo) REVERT: C 33 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7527 (p) REVERT: C 239 GLN cc_start: 0.7638 (tt0) cc_final: 0.7301 (tt0) REVERT: C 560 LEU cc_start: 0.7892 (mt) cc_final: 0.7464 (mp) REVERT: C 794 ILE cc_start: 0.7941 (mm) cc_final: 0.7623 (pp) REVERT: C 855 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6766 (m-80) outliers start: 39 outliers final: 25 residues processed: 175 average time/residue: 1.1347 time to fit residues: 235.2819 Evaluate side-chains 170 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 208 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 957 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 21608 Z= 0.312 Angle : 0.646 14.109 29376 Z= 0.335 Chirality : 0.050 0.527 3531 Planarity : 0.004 0.041 3708 Dihedral : 5.438 57.777 3669 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.85 % Allowed : 11.04 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.32 (0.16), residues: 2548 helix: 1.49 (0.21), residues: 635 sheet: 0.82 (0.21), residues: 591 loop : -1.65 (0.15), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 886 HIS 0.007 0.001 HIS A1064 PHE 0.028 0.002 PHE C 168 TYR 0.029 0.002 TYR B 904 ARG 0.004 0.001 ARG A 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 2.654 Fit side-chains revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7403 (m-80) cc_final: 0.6793 (m-80) REVERT: A 304 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8212 (mttm) REVERT: A 529 LYS cc_start: 0.8290 (mppt) cc_final: 0.8024 (mmmt) REVERT: A 556 ASN cc_start: 0.7637 (t0) cc_final: 0.7297 (t0) REVERT: A 654 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: A 740 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7411 (ttt) REVERT: B 314 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: B 528 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7771 (mtpt) REVERT: B 529 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7676 (mttm) REVERT: B 809 PRO cc_start: 0.7238 (Cg_endo) cc_final: 0.6837 (Cg_exo) REVERT: C 239 GLN cc_start: 0.7718 (tt0) cc_final: 0.7373 (tt0) REVERT: C 560 LEU cc_start: 0.7910 (mt) cc_final: 0.7456 (mp) REVERT: C 794 ILE cc_start: 0.8028 (mm) cc_final: 0.7687 (pp) REVERT: C 855 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6781 (m-80) outliers start: 43 outliers final: 28 residues processed: 176 average time/residue: 1.1554 time to fit residues: 239.5305 Evaluate side-chains 171 residues out of total 2319 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 183 optimal weight: 5.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.083180 restraints weight = 29953.040| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.23 r_work: 0.2854 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2644 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: