Starting phenix.real_space_refine on Mon Feb 19 07:31:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fet_31563/02_2024/7fet_31563.pdb" } resolution = 3.7 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= 0.061 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 104 5.16 5 C 15318 2.51 5 N 3934 2.21 5 O 4667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24023 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7820 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7798 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 50, 'TRANS': 948} Chain breaks: 9 Chain: "C" Number of atoms: 7831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7831 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 50, 'TRANS': 952} Chain breaks: 7 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: "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: "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: "S" 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: "U" 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: "V" 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" 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 Time building chain proxies: 12.15, per 1000 atoms: 0.51 Number of scatterers: 24023 At special positions: 0 Unit cell: (140.08, 129.2, 201.28, 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 104 16.00 O 4667 8.00 N 3934 7.00 C 15318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG P 1 " - " ASN C 709 " " NAG Q 1 " - " ASN C 717 " " NAG S 1 " - " ASN C1074 " " NAG U 1 " - " ASN C1134 " " NAG V 1 " - " ASN A 709 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.58 Conformation dependent library (CDL) restraints added in 4.2 seconds 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5624 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 52 sheets defined 22.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.637A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.892A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.356A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.744A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.690A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.221A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 939 removed outlier: 6.721A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.514A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.552A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1032 removed outlier: 3.928A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.809A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.816A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.854A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 4.280A pdb=" N THR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 826 removed outlier: 3.642A pdb=" N LYS B 825 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 826 " --> pdb=" O PHE B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 826' Processing helix chain 'B' and resid 866 through 880 removed outlier: 3.512A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 885 Processing helix chain 'B' and resid 886 through 889 removed outlier: 3.980A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 889' Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.604A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.520A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 965 removed outlier: 3.981A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.503A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 3.799A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B1031 " --> pdb=" O THR B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.614A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.542A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.899A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.985A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.140A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.737A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.525A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.547A 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 886 through 891 removed outlier: 3.917A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 940 removed outlier: 4.448A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.613A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.606A 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 982 removed outlier: 4.005A pdb=" N ALA C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.285A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.629A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.917A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.514A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.025A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 removed outlier: 5.638A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.810A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.289A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.953A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.048A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.009A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.990A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722 removed outlier: 6.881A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.707A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.102A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 92 " --> pdb=" O PHE B 192 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.510A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC5, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.894A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.070A pdb=" N VAL B 597 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN B 317 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 595 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.567A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.926A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.901A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AD3, first strand: chain 'B' and resid 609 through 610 removed outlier: 3.818A pdb=" N VAL B 610 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.758A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.577A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.696A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE1, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 3.862A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 6.965A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.235A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.088A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 201 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 103 through 104 removed outlier: 4.352A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.963A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 328 removed outlier: 7.577A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AF1, first strand: chain 'C' and resid 395 through 403 removed outlier: 3.609A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.960A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.924A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.084A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.756A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 4.038A pdb=" N VAL C1133 " --> pdb=" O ALA C1080 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1911 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: 9.60 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7610 1.34 - 1.46: 6015 1.46 - 1.59: 10800 1.59 - 1.71: 0 1.71 - 1.83: 128 Bond restraints: 24553 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CA GLU B 748 " pdb=" C GLU B 748 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.41e-02 5.03e+03 7.91e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.72e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" CB ARG C1107 " pdb=" CG ARG C1107 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.85e+00 ... (remaining 24548 not shown) Histogram of bond angle deviations from ideal: 97.59 - 104.89: 419 104.89 - 112.19: 12279 112.19 - 119.48: 7837 119.48 - 126.78: 12649 126.78 - 134.08: 224 Bond angle restraints: 33408 Sorted by residual: angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" N CYS B 432 " ideal model delta sigma weight residual 114.23 119.55 -5.32 8.80e-01 1.29e+00 3.66e+01 angle pdb=" CA GLY B 431 " pdb=" C GLY B 431 " pdb=" O GLY B 431 " ideal model delta sigma weight residual 122.33 118.61 3.72 8.10e-01 1.52e+00 2.11e+01 angle pdb=" C ARG C 983 " pdb=" CA ARG C 983 " pdb=" CB ARG C 983 " ideal model delta sigma weight residual 109.29 114.70 -5.41 1.51e+00 4.39e-01 1.28e+01 angle pdb=" N GLN A1010 " pdb=" CA GLN A1010 " pdb=" CB GLN A1010 " ideal model delta sigma weight residual 110.28 115.74 -5.46 1.55e+00 4.16e-01 1.24e+01 angle pdb=" N ASP A 985 " pdb=" CA ASP A 985 " pdb=" C ASP A 985 " ideal model delta sigma weight residual 109.81 117.48 -7.67 2.21e+00 2.05e-01 1.21e+01 ... (remaining 33403 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 14276 24.93 - 49.85: 719 49.85 - 74.78: 112 74.78 - 99.70: 38 99.70 - 124.63: 9 Dihedral angle restraints: 15154 sinusoidal: 6422 harmonic: 8732 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 2.37 -88.37 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 1.63 -87.63 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -164.69 78.69 1 1.00e+01 1.00e-02 7.72e+01 ... (remaining 15151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 3796 0.114 - 0.228: 127 0.228 - 0.342: 4 0.342 - 0.456: 0 0.456 - 0.570: 1 Chirality restraints: 3928 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3925 not shown) Planarity restraints: 4302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.030 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP B 64 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 812 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.044 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO C 209 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.036 5.00e-02 4.00e+02 ... (remaining 4299 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 492 2.66 - 3.22: 22807 3.22 - 3.78: 33378 3.78 - 4.34: 44904 4.34 - 4.90: 75776 Nonbonded interactions: 177357 Sorted by model distance: nonbonded pdb=" OD1 ASN A 658 " pdb=" N SER A 659 " model vdw 2.102 2.520 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.149 2.440 nonbonded pdb=" O ALA B 352 " pdb=" NE ARG B 466 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR B 612 " pdb=" O ASN B 616 " model vdw 2.212 2.440 nonbonded pdb=" O SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.225 2.440 ... (remaining 177352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 129 or resid 131 through 591 or resid 593 throu \ gh 827 or resid 855 through 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 27 through 106 or resid 108 through 165 or (resid 166 and \ (name N or name CA or name C or name O or name CB )) or resid 167 through 1147 o \ r resid 1301 through 1306)) selection = (chain 'C' and (resid 27 through 106 or resid 108 through 129 or resid 131 throu \ gh 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 591 or resid 593 through 621 or resid 641 through 827 or resi \ d 855 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.270 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 63.230 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24553 Z= 0.421 Angle : 0.818 10.786 33408 Z= 0.442 Chirality : 0.052 0.570 3928 Planarity : 0.005 0.066 4270 Dihedral : 15.260 124.629 9416 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.94 % Favored : 86.00 % Rotamer: Outliers : 0.08 % Allowed : 0.11 % Favored : 99.81 % 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: -3.35 (0.14), residues: 2949 helix: -0.29 (0.21), residues: 600 sheet: -1.90 (0.23), residues: 509 loop : -3.20 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP B 64 HIS 0.006 0.001 HIS B 66 PHE 0.035 0.002 PHE A 823 TYR 0.025 0.002 TYR A 266 ARG 0.010 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 276 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.6135 (p0) cc_final: 0.5819 (m-30) REVERT: A 697 MET cc_start: 0.8259 (ptp) cc_final: 0.7986 (ptm) REVERT: A 900 MET cc_start: 0.8153 (mtp) cc_final: 0.7830 (mtp) REVERT: A 994 ASP cc_start: 0.7162 (t70) cc_final: 0.6902 (t0) REVERT: B 238 PHE cc_start: 0.8065 (t80) cc_final: 0.7804 (t80) REVERT: B 266 TYR cc_start: 0.8492 (m-80) cc_final: 0.8246 (m-10) REVERT: B 392 PHE cc_start: 0.7037 (m-80) cc_final: 0.6535 (m-80) REVERT: B 396 TYR cc_start: 0.7460 (m-10) cc_final: 0.7209 (m-10) REVERT: B 927 PHE cc_start: 0.9071 (t80) cc_final: 0.8818 (t80) REVERT: C 223 LEU cc_start: 0.7864 (mp) cc_final: 0.7536 (mt) REVERT: C 424 LYS cc_start: 0.8582 (tppp) cc_final: 0.8016 (ttmm) REVERT: C 804 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7476 (tm-30) REVERT: C 870 ILE cc_start: 0.9335 (mm) cc_final: 0.9126 (mt) REVERT: C 1130 ILE cc_start: 0.8691 (pt) cc_final: 0.8429 (mp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.3409 time to fit residues: 150.9415 Evaluate side-chains 152 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 271 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 957 GLN A1011 GLN B 370 ASN B 388 ASN B 607 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN C1135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24553 Z= 0.257 Angle : 0.685 12.511 33408 Z= 0.353 Chirality : 0.049 0.395 3928 Planarity : 0.005 0.064 4270 Dihedral : 10.395 113.736 4065 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.73 % Favored : 88.20 % Rotamer: Outliers : 0.84 % Allowed : 7.93 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.14), residues: 2949 helix: 0.09 (0.21), residues: 617 sheet: -1.76 (0.21), residues: 542 loop : -3.01 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 104 HIS 0.003 0.001 HIS C 655 PHE 0.026 0.002 PHE A 238 TYR 0.016 0.001 TYR C1067 ARG 0.009 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7799 (m-90) cc_final: 0.7559 (m-90) REVERT: A 111 ASP cc_start: 0.6052 (p0) cc_final: 0.5625 (m-30) REVERT: A 900 MET cc_start: 0.8099 (mtp) cc_final: 0.7823 (mtp) REVERT: A 902 MET cc_start: 0.8968 (tpp) cc_final: 0.8705 (tpt) REVERT: A 959 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 994 ASP cc_start: 0.7017 (t70) cc_final: 0.6776 (t0) REVERT: A 1005 GLN cc_start: 0.8238 (tp40) cc_final: 0.7959 (tp40) REVERT: C 424 LYS cc_start: 0.8586 (tppp) cc_final: 0.8071 (ttmm) REVERT: C 515 PHE cc_start: 0.8128 (m-10) cc_final: 0.7884 (m-10) REVERT: C 870 ILE cc_start: 0.9368 (mm) cc_final: 0.9145 (mt) REVERT: C 1130 ILE cc_start: 0.8671 (pt) cc_final: 0.8410 (mp) outliers start: 22 outliers final: 13 residues processed: 193 average time/residue: 0.3324 time to fit residues: 105.1340 Evaluate side-chains 152 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 770 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 225 optimal weight: 0.0870 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 272 optimal weight: 0.5980 chunk 293 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 675 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24553 Z= 0.243 Angle : 0.636 10.669 33408 Z= 0.326 Chirality : 0.047 0.368 3928 Planarity : 0.005 0.061 4270 Dihedral : 9.143 111.608 4065 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.70 % Favored : 88.23 % Rotamer: Outliers : 1.45 % Allowed : 11.14 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.15), residues: 2949 helix: 0.48 (0.21), residues: 607 sheet: -1.49 (0.21), residues: 559 loop : -2.94 (0.13), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 104 HIS 0.007 0.001 HIS A 66 PHE 0.018 0.001 PHE A 238 TYR 0.017 0.001 TYR C 351 ARG 0.005 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8020 (mtp) cc_final: 0.7447 (mtp) REVERT: A 902 MET cc_start: 0.8955 (tpp) cc_final: 0.8739 (tpt) REVERT: A 959 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8541 (tt) REVERT: A 994 ASP cc_start: 0.6910 (t70) cc_final: 0.6633 (t0) REVERT: A 1005 GLN cc_start: 0.8319 (tp40) cc_final: 0.8077 (tp40) REVERT: B 392 PHE cc_start: 0.7343 (m-80) cc_final: 0.6653 (m-80) REVERT: B 480 CYS cc_start: 0.5033 (OUTLIER) cc_final: 0.4390 (p) REVERT: B 483 VAL cc_start: 0.3989 (OUTLIER) cc_final: 0.2918 (p) REVERT: C 347 PHE cc_start: 0.6195 (m-10) cc_final: 0.5773 (m-10) REVERT: C 424 LYS cc_start: 0.8731 (tppp) cc_final: 0.8225 (ttmm) REVERT: C 1130 ILE cc_start: 0.8753 (pt) cc_final: 0.8451 (mt) outliers start: 38 outliers final: 25 residues processed: 183 average time/residue: 0.3425 time to fit residues: 101.6107 Evaluate side-chains 156 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 258 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 784 GLN C 992 GLN C1135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24553 Z= 0.240 Angle : 0.622 9.703 33408 Z= 0.319 Chirality : 0.046 0.388 3928 Planarity : 0.005 0.059 4270 Dihedral : 8.424 111.207 4065 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.02 % Favored : 88.91 % Rotamer: Outliers : 2.25 % Allowed : 13.50 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.15), residues: 2949 helix: 0.72 (0.22), residues: 602 sheet: -1.36 (0.21), residues: 566 loop : -2.84 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 64 HIS 0.003 0.001 HIS B 655 PHE 0.017 0.001 PHE A 238 TYR 0.028 0.001 TYR C 423 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 137 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8064 (mtp) cc_final: 0.7522 (mtp) REVERT: A 902 MET cc_start: 0.8954 (tpp) cc_final: 0.8717 (tpt) REVERT: A 959 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 994 ASP cc_start: 0.6858 (t70) cc_final: 0.6568 (t0) REVERT: A 1005 GLN cc_start: 0.8312 (tp40) cc_final: 0.8019 (tp40) REVERT: B 392 PHE cc_start: 0.7266 (m-80) cc_final: 0.6707 (m-80) REVERT: B 480 CYS cc_start: 0.5151 (OUTLIER) cc_final: 0.4552 (p) REVERT: B 483 VAL cc_start: 0.4401 (OUTLIER) cc_final: 0.3245 (p) REVERT: B 902 MET cc_start: 0.8826 (tpp) cc_final: 0.8589 (tpp) REVERT: C 424 LYS cc_start: 0.8749 (tppp) cc_final: 0.8434 (ttmm) REVERT: C 1130 ILE cc_start: 0.8720 (pt) cc_final: 0.8401 (mp) outliers start: 59 outliers final: 32 residues processed: 188 average time/residue: 0.3220 time to fit residues: 100.4106 Evaluate side-chains 160 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 918 GLU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN C 658 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24553 Z= 0.357 Angle : 0.678 9.243 33408 Z= 0.349 Chirality : 0.047 0.362 3928 Planarity : 0.005 0.062 4270 Dihedral : 8.232 110.038 4065 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.68 % Favored : 87.25 % Rotamer: Outliers : 2.48 % Allowed : 14.99 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.15), residues: 2949 helix: 0.60 (0.22), residues: 601 sheet: -1.43 (0.20), residues: 635 loop : -2.85 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 104 HIS 0.004 0.001 HIS A 66 PHE 0.027 0.002 PHE A1121 TYR 0.021 0.002 TYR B 904 ARG 0.005 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 126 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8586 (ptm) cc_final: 0.8353 (ptm) REVERT: A 900 MET cc_start: 0.8201 (mtp) cc_final: 0.7640 (mtp) REVERT: A 902 MET cc_start: 0.8969 (tpp) cc_final: 0.8723 (tpt) REVERT: A 959 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8630 (tt) REVERT: A 994 ASP cc_start: 0.7074 (t70) cc_final: 0.6768 (t0) REVERT: B 902 MET cc_start: 0.8904 (tpp) cc_final: 0.8668 (tpp) REVERT: B 1050 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7654 (mtm) REVERT: C 515 PHE cc_start: 0.8129 (m-10) cc_final: 0.7857 (m-10) REVERT: C 902 MET cc_start: 0.8832 (tpp) cc_final: 0.8437 (tpt) REVERT: C 1050 MET cc_start: 0.7679 (mtp) cc_final: 0.7460 (mtp) REVERT: C 1130 ILE cc_start: 0.8792 (pt) cc_final: 0.8475 (mp) outliers start: 65 outliers final: 42 residues processed: 185 average time/residue: 0.3208 time to fit residues: 98.7767 Evaluate side-chains 155 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 111 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 chunk 289 optimal weight: 0.9980 chunk 240 optimal weight: 0.0870 chunk 133 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 overall best weight: 0.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 GLN C 87 ASN C 658 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24553 Z= 0.178 Angle : 0.601 8.910 33408 Z= 0.308 Chirality : 0.045 0.360 3928 Planarity : 0.004 0.059 4270 Dihedral : 7.708 109.745 4065 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.87 % Favored : 90.06 % Rotamer: Outliers : 2.36 % Allowed : 16.06 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 2949 helix: 0.89 (0.22), residues: 608 sheet: -1.17 (0.21), residues: 623 loop : -2.78 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 104 HIS 0.004 0.001 HIS A 66 PHE 0.017 0.001 PHE C 220 TYR 0.016 0.001 TYR B 904 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 129 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.8572 (ptm) cc_final: 0.8325 (ptm) REVERT: A 873 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: A 900 MET cc_start: 0.7905 (mtp) cc_final: 0.7352 (mtp) REVERT: A 902 MET cc_start: 0.8932 (tpp) cc_final: 0.8723 (tpt) REVERT: A 959 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 994 ASP cc_start: 0.6787 (t70) cc_final: 0.6458 (t0) REVERT: A 1005 GLN cc_start: 0.8289 (tp40) cc_final: 0.7985 (mm-40) REVERT: B 392 PHE cc_start: 0.7300 (m-80) cc_final: 0.6721 (m-80) REVERT: B 433 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 607 GLN cc_start: 0.7710 (mp10) cc_final: 0.7277 (mp10) REVERT: C 772 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9166 (t) REVERT: C 1130 ILE cc_start: 0.8667 (pt) cc_final: 0.8307 (mt) outliers start: 62 outliers final: 42 residues processed: 183 average time/residue: 0.3159 time to fit residues: 96.7919 Evaluate side-chains 161 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 0.0170 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24553 Z= 0.274 Angle : 0.630 9.132 33408 Z= 0.322 Chirality : 0.046 0.341 3928 Planarity : 0.005 0.059 4270 Dihedral : 7.566 108.017 4065 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.90 % Favored : 88.03 % Rotamer: Outliers : 2.71 % Allowed : 16.25 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.15), residues: 2949 helix: 0.80 (0.22), residues: 612 sheet: -1.30 (0.20), residues: 664 loop : -2.77 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.003 0.001 HIS B 655 PHE 0.020 0.001 PHE A1121 TYR 0.019 0.001 TYR B 904 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 118 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 873 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: A 900 MET cc_start: 0.8103 (mtp) cc_final: 0.7563 (mtp) REVERT: A 902 MET cc_start: 0.8975 (tpp) cc_final: 0.8741 (tpt) REVERT: A 959 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 994 ASP cc_start: 0.6924 (t70) cc_final: 0.6691 (t0) REVERT: A 1005 GLN cc_start: 0.8361 (tp40) cc_final: 0.8119 (tp40) REVERT: A 1029 MET cc_start: 0.8917 (tpp) cc_final: 0.8133 (ttm) REVERT: B 433 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 505 TYR cc_start: 0.7254 (t80) cc_final: 0.6709 (t80) REVERT: B 774 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: B 902 MET cc_start: 0.8844 (tpp) cc_final: 0.8593 (tpp) REVERT: C 902 MET cc_start: 0.8753 (tpp) cc_final: 0.8385 (tpt) REVERT: C 1130 ILE cc_start: 0.8705 (pt) cc_final: 0.8384 (mp) outliers start: 71 outliers final: 51 residues processed: 182 average time/residue: 0.3199 time to fit residues: 97.5235 Evaluate side-chains 171 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 116 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 183 optimal weight: 0.0020 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 226 optimal weight: 1.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 954 GLN B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24553 Z= 0.190 Angle : 0.594 9.599 33408 Z= 0.304 Chirality : 0.045 0.337 3928 Planarity : 0.004 0.060 4270 Dihedral : 7.280 106.994 4065 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.83 % Favored : 90.10 % Rotamer: Outliers : 2.21 % Allowed : 17.20 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2949 helix: 0.97 (0.22), residues: 611 sheet: -1.16 (0.21), residues: 646 loop : -2.72 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.005 0.001 HIS A 66 PHE 0.022 0.001 PHE C 515 TYR 0.016 0.001 TYR C 421 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 125 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7632 (m-90) cc_final: 0.7324 (m-90) REVERT: A 873 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: A 959 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 994 ASP cc_start: 0.6778 (t70) cc_final: 0.6538 (t0) REVERT: A 1005 GLN cc_start: 0.8280 (tp40) cc_final: 0.7982 (mm-40) REVERT: A 1029 MET cc_start: 0.8775 (tpp) cc_final: 0.8305 (ttm) REVERT: B 433 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (p) REVERT: B 505 TYR cc_start: 0.7223 (t80) cc_final: 0.6656 (t80) REVERT: B 774 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7924 (mm-40) REVERT: B 902 MET cc_start: 0.8770 (tpp) cc_final: 0.8523 (tpp) REVERT: C 515 PHE cc_start: 0.7873 (m-10) cc_final: 0.7626 (m-10) REVERT: C 772 VAL cc_start: 0.9390 (OUTLIER) cc_final: 0.9181 (t) REVERT: C 902 MET cc_start: 0.8591 (tpp) cc_final: 0.8344 (tpt) REVERT: C 1130 ILE cc_start: 0.8649 (pt) cc_final: 0.8275 (mp) outliers start: 58 outliers final: 44 residues processed: 178 average time/residue: 0.3339 time to fit residues: 99.1142 Evaluate side-chains 163 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 114 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 0.0060 chunk 242 optimal weight: 0.0070 chunk 253 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 953 ASN C 658 ASN C1135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24553 Z= 0.190 Angle : 0.587 9.171 33408 Z= 0.300 Chirality : 0.045 0.328 3928 Planarity : 0.004 0.059 4270 Dihedral : 7.066 105.499 4065 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.75 % Favored : 89.18 % Rotamer: Outliers : 2.25 % Allowed : 17.39 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2949 helix: 1.04 (0.22), residues: 611 sheet: -1.18 (0.20), residues: 662 loop : -2.65 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 64 HIS 0.005 0.001 HIS A 66 PHE 0.018 0.001 PHE C 515 TYR 0.017 0.001 TYR A 917 ARG 0.007 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 120 time to evaluate : 2.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7619 (m-90) cc_final: 0.7316 (m-90) REVERT: A 873 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: A 900 MET cc_start: 0.8314 (mtt) cc_final: 0.8058 (mtm) REVERT: A 994 ASP cc_start: 0.6968 (t70) cc_final: 0.6670 (t0) REVERT: A 1005 GLN cc_start: 0.8240 (tp40) cc_final: 0.7936 (mm-40) REVERT: A 1029 MET cc_start: 0.8794 (tpp) cc_final: 0.8402 (ttm) REVERT: B 394 ASN cc_start: 0.6031 (t0) cc_final: 0.5828 (t0) REVERT: B 433 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8616 (p) REVERT: B 505 TYR cc_start: 0.7228 (t80) cc_final: 0.6640 (t80) REVERT: B 902 MET cc_start: 0.8780 (tpp) cc_final: 0.8524 (tpp) REVERT: B 927 PHE cc_start: 0.8904 (t80) cc_final: 0.8470 (t80) REVERT: C 515 PHE cc_start: 0.7864 (m-10) cc_final: 0.7596 (m-10) REVERT: C 772 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9132 (t) REVERT: C 902 MET cc_start: 0.8619 (tpp) cc_final: 0.8327 (tpt) REVERT: C 1130 ILE cc_start: 0.8651 (pt) cc_final: 0.8238 (mp) outliers start: 59 outliers final: 47 residues processed: 174 average time/residue: 0.3272 time to fit residues: 95.5829 Evaluate side-chains 164 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 114 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 297 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 658 ASN C1135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24553 Z= 0.224 Angle : 0.602 9.107 33408 Z= 0.308 Chirality : 0.045 0.331 3928 Planarity : 0.004 0.059 4270 Dihedral : 7.012 104.040 4065 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.78 % Favored : 89.15 % Rotamer: Outliers : 2.06 % Allowed : 17.70 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.15), residues: 2949 helix: 1.07 (0.22), residues: 610 sheet: -1.17 (0.20), residues: 672 loop : -2.67 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 64 HIS 0.005 0.001 HIS A 66 PHE 0.024 0.001 PHE C 429 TYR 0.016 0.001 TYR C 421 ARG 0.007 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5898 Ramachandran restraints generated. 2949 Oldfield, 0 Emsley, 2949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 116 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7692 (m-90) cc_final: 0.7392 (m-90) REVERT: A 873 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: A 900 MET cc_start: 0.8296 (mtt) cc_final: 0.8035 (mtm) REVERT: A 994 ASP cc_start: 0.6776 (t70) cc_final: 0.6523 (t0) REVERT: A 1005 GLN cc_start: 0.8259 (tp40) cc_final: 0.7954 (mm-40) REVERT: A 1029 MET cc_start: 0.8786 (tpp) cc_final: 0.8330 (ttm) REVERT: B 433 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8540 (p) REVERT: B 505 TYR cc_start: 0.7291 (t80) cc_final: 0.6699 (t80) REVERT: B 902 MET cc_start: 0.8791 (tpp) cc_final: 0.8558 (tpp) REVERT: C 287 ASP cc_start: 0.7782 (t0) cc_final: 0.7331 (t0) REVERT: C 515 PHE cc_start: 0.7923 (m-10) cc_final: 0.7615 (m-10) REVERT: C 1130 ILE cc_start: 0.8647 (pt) cc_final: 0.8252 (mp) outliers start: 54 outliers final: 48 residues processed: 164 average time/residue: 0.3222 time to fit residues: 88.4859 Evaluate side-chains 164 residues out of total 2623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 114 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 0.3980 chunk 252 optimal weight: 0.0970 chunk 72 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 237 optimal weight: 0.0570 chunk 99 optimal weight: 0.6980 chunk 243 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 658 ASN C1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.123234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088846 restraints weight = 51794.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091622 restraints weight = 27370.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093386 restraints weight = 18301.856| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24553 Z= 0.151 Angle : 0.567 9.491 33408 Z= 0.289 Chirality : 0.044 0.325 3928 Planarity : 0.004 0.059 4270 Dihedral : 6.713 102.533 4065 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.49 % Favored : 90.44 % Rotamer: Outliers : 1.87 % Allowed : 17.89 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2949 helix: 1.30 (0.22), residues: 610 sheet: -0.96 (0.21), residues: 652 loop : -2.59 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 64 HIS 0.004 0.001 HIS A 66 PHE 0.023 0.001 PHE C 429 TYR 0.018 0.001 TYR A 917 ARG 0.007 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.20 seconds wall clock time: 71 minutes 27.03 seconds (4287.03 seconds total)