Starting phenix.real_space_refine on Fri Dec 15 06:40:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r40_14250/12_2023/7r40_14250.pdb" } resolution = 2.9 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= 0.001 sd= 0.027 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 132 5.16 5 C 19449 2.51 5 N 5052 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30615 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "B" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "C" Number of atoms: 8230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8230 Classifications: {'peptide': 1053} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 996} Chain breaks: 7 Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 905 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" 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: "T" 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: "A" 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: "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: 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 Time building chain proxies: 15.42, per 1000 atoms: 0.50 Number of scatterers: 30615 At special positions: 0 Unit cell: (152.52, 158.72, 230.64, 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 132 16.00 O 5982 8.00 N 5052 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 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 L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " 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=2.03 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=2.03 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 F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 331 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 17 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 17 " " NAG C1308 " - " ASN C 331 " " NAG C1309 " - " ASN C 343 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C1134 " " NAG U 1 " - " ASN C 801 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.82 Conformation dependent library (CDL) restraints added in 5.3 seconds 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7122 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.2% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.797A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.846A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.560A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.667A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.527A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.608A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.598A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.898A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.015A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.534A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.845A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.798A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.711A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 897 through 908 removed outlier: 4.770A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.588A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.677A 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 977 through 984 removed outlier: 3.667A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.528A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.609A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 8.036A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 157 removed outlier: 4.020A pdb=" N SER A 155 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 145 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.462A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.538A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.734A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.711A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG L 45 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 20 through 21 removed outlier: 3.846A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 98 " --> pdb=" O PHE H 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 109 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.021A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.487A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 141 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.537A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 448 through 454 removed outlier: 6.311A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.398A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE2, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.732A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.205A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.649A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS D 98 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE D 109 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.898A pdb=" N GLU D 46 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.022A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.718A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 49 removed outlier: 8.037A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 151 through 157 removed outlier: 4.019A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C 141 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.463A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.539A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.733A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.309A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.397A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 removed outlier: 4.219A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.309A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'G' and resid 5 through 6 removed outlier: 4.206A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.650A pdb=" N ARG G 45 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 20 through 21 removed outlier: 3.847A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS E 98 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE E 109 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.899A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 92 " --> pdb=" O VAL E 116 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2505 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: 12.59 Time building geometry restraints manager: 11.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9759 1.35 - 1.47: 8051 1.47 - 1.60: 13339 1.60 - 1.72: 0 1.72 - 1.84: 168 Bond restraints: 31317 Sorted by residual: bond pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.66e+01 bond pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 ... (remaining 31312 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.38: 869 106.38 - 113.47: 16820 113.47 - 120.55: 12028 120.55 - 127.64: 12655 127.64 - 134.73: 219 Bond angle restraints: 42591 Sorted by residual: angle pdb=" CA PRO B 899 " pdb=" N PRO B 899 " pdb=" CD PRO B 899 " ideal model delta sigma weight residual 112.00 99.29 12.71 1.40e+00 5.10e-01 8.24e+01 angle pdb=" CA PRO A 899 " pdb=" N PRO A 899 " pdb=" CD PRO A 899 " ideal model delta sigma weight residual 112.00 99.31 12.69 1.40e+00 5.10e-01 8.22e+01 angle pdb=" CA PRO C 899 " pdb=" N PRO C 899 " pdb=" CD PRO C 899 " ideal model delta sigma weight residual 112.00 99.33 12.67 1.40e+00 5.10e-01 8.19e+01 angle pdb=" C LYS A 529 " pdb=" CA LYS A 529 " pdb=" CB LYS A 529 " ideal model delta sigma weight residual 115.89 109.77 6.12 1.32e+00 5.74e-01 2.15e+01 angle pdb=" C LYS C 529 " pdb=" CA LYS C 529 " pdb=" CB LYS C 529 " ideal model delta sigma weight residual 115.89 109.80 6.09 1.32e+00 5.74e-01 2.13e+01 ... (remaining 42586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 17418 17.63 - 35.26: 1421 35.26 - 52.89: 313 52.89 - 70.52: 52 70.52 - 88.15: 53 Dihedral angle restraints: 19257 sinusoidal: 8148 harmonic: 11109 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.11 -61.89 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.14 -61.86 1 1.00e+01 1.00e-02 5.07e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -24.15 -61.85 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 19254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4299 0.083 - 0.167: 596 0.167 - 0.250: 19 0.250 - 0.333: 0 0.333 - 0.416: 6 Chirality restraints: 4920 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 4917 not shown) Planarity restraints: 5487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " -0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO A 899 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.71e+01 pdb=" N PRO B 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO B 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 899 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 898 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO C 899 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO C 899 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 899 " 0.066 5.00e-02 4.00e+02 ... (remaining 5484 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9813 2.84 - 3.35: 24845 3.35 - 3.87: 49774 3.87 - 4.38: 54111 4.38 - 4.90: 93784 Nonbonded interactions: 232327 Sorted by model distance: nonbonded pdb=" O THR B1116 " pdb=" OG1 THR B1120 " model vdw 2.324 2.440 nonbonded pdb=" O THR C1116 " pdb=" OG1 THR C1120 " model vdw 2.325 2.440 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.326 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.326 2.440 ... (remaining 232322 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.440 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 76.610 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 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 : 0.004 0.058 31317 Z= 0.247 Angle : 0.732 12.706 42591 Z= 0.370 Chirality : 0.052 0.416 4920 Planarity : 0.007 0.130 5448 Dihedral : 13.999 88.155 11991 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -2.66 (0.12), residues: 3780 helix: -3.72 (0.09), residues: 603 sheet: -0.50 (0.18), residues: 831 loop : -1.75 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 47 HIS 0.003 0.000 HIS B1048 PHE 0.016 0.001 PHE G 49 TYR 0.010 0.001 TYR C 351 ARG 0.005 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 3.397 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 4 residues processed: 776 average time/residue: 1.2664 time to fit residues: 1176.1755 Evaluate side-chains 651 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 647 time to evaluate : 3.576 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 3 average time/residue: 1.2056 time to fit residues: 8.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 955 ASN A 957 GLN A 992 GLN A1010 GLN A1101 HIS L 27 GLN H 74 ASN B 317 ASN B 448 ASN B 540 ASN B 607 GLN B 804 GLN B 957 GLN B 960 ASN B 992 GLN B1101 HIS C 49 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C 992 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31317 Z= 0.308 Angle : 0.692 12.150 42591 Z= 0.348 Chirality : 0.049 0.491 4920 Planarity : 0.005 0.060 5448 Dihedral : 7.223 93.122 5199 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.04 % Allowed : 12.62 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.75 (0.13), residues: 3780 helix: -0.68 (0.19), residues: 615 sheet: -0.48 (0.17), residues: 885 loop : -1.62 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.007 0.001 HIS A 49 PHE 0.024 0.002 PHE B 490 TYR 0.027 0.002 TYR A 453 ARG 0.007 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 714 time to evaluate : 3.217 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 55 residues processed: 751 average time/residue: 1.2347 time to fit residues: 1114.7833 Evaluate side-chains 716 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 661 time to evaluate : 3.525 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 21 residues processed: 38 average time/residue: 0.5415 time to fit residues: 34.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 374 optimal weight: 0.0170 chunk 308 optimal weight: 0.8980 chunk 343 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 955 ASN A 992 GLN A1002 GLN A1101 HIS L 27 GLN B 49 HIS B 61 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN B 960 ASN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 31317 Z= 0.258 Angle : 0.649 15.208 42591 Z= 0.323 Chirality : 0.048 0.568 4920 Planarity : 0.005 0.065 5448 Dihedral : 6.592 63.772 5199 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.58 % Allowed : 16.74 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.40 (0.13), residues: 3780 helix: 0.46 (0.21), residues: 633 sheet: -0.50 (0.17), residues: 885 loop : -1.57 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 353 HIS 0.004 0.001 HIS G 30 PHE 0.027 0.002 PHE B 329 TYR 0.022 0.002 TYR E 32 ARG 0.006 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 671 time to evaluate : 3.652 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 65 residues processed: 716 average time/residue: 1.2402 time to fit residues: 1070.4797 Evaluate side-chains 707 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 642 time to evaluate : 3.082 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 24 residues processed: 44 average time/residue: 0.3654 time to fit residues: 31.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 3.9990 chunk 260 optimal weight: 0.3980 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 232 optimal weight: 1.9990 chunk 347 optimal weight: 0.6980 chunk 368 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 329 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 540 ASN B 607 GLN B 675 GLN B 907 ASN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN C 81 ASN C 207 HIS C 764 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 31317 Z= 0.251 Angle : 0.648 11.905 42591 Z= 0.319 Chirality : 0.047 0.354 4920 Planarity : 0.004 0.052 5448 Dihedral : 6.320 85.361 5199 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.76 % Allowed : 18.22 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.34 (0.13), residues: 3780 helix: 0.78 (0.21), residues: 651 sheet: -0.57 (0.17), residues: 876 loop : -1.59 (0.12), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 35 HIS 0.004 0.001 HIS A1083 PHE 0.025 0.002 PHE A 490 TYR 0.019 0.001 TYR B 204 ARG 0.005 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 676 time to evaluate : 3.632 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 69 residues processed: 727 average time/residue: 1.1713 time to fit residues: 1027.9725 Evaluate side-chains 718 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 649 time to evaluate : 2.947 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 32 residues processed: 40 average time/residue: 0.5391 time to fit residues: 36.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 0.1980 chunk 209 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 330 optimal weight: 0.0020 chunk 92 optimal weight: 0.9980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN H 39 GLN B 422 ASN B 540 ASN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS E 77 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31317 Z= 0.216 Angle : 0.634 12.163 42591 Z= 0.311 Chirality : 0.046 0.353 4920 Planarity : 0.004 0.050 5448 Dihedral : 6.519 116.237 5199 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.61 % Allowed : 20.33 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.27 (0.13), residues: 3780 helix: 1.27 (0.22), residues: 630 sheet: -0.64 (0.17), residues: 882 loop : -1.61 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 47 HIS 0.003 0.001 HIS A 207 PHE 0.026 0.002 PHE C 490 TYR 0.019 0.001 TYR D 32 ARG 0.009 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 657 time to evaluate : 3.050 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 77 residues processed: 719 average time/residue: 1.0812 time to fit residues: 938.5286 Evaluate side-chains 723 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 646 time to evaluate : 2.526 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 39 residues processed: 41 average time/residue: 0.3101 time to fit residues: 23.5408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 9.9990 chunk 331 optimal weight: 3.9990 chunk 72 optimal weight: 0.0010 chunk 216 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 368 optimal weight: 0.2980 chunk 306 optimal weight: 0.9980 chunk 170 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 540 ASN B 564 GLN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1010 GLN C1101 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31317 Z= 0.176 Angle : 0.630 11.448 42591 Z= 0.309 Chirality : 0.046 0.631 4920 Planarity : 0.004 0.052 5448 Dihedral : 6.326 116.861 5199 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.31 % Allowed : 21.71 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.20 (0.13), residues: 3780 helix: 1.37 (0.22), residues: 636 sheet: -0.53 (0.18), residues: 840 loop : -1.61 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.002 0.001 HIS A 207 PHE 0.031 0.001 PHE A 490 TYR 0.023 0.001 TYR E 103 ARG 0.009 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 659 time to evaluate : 3.786 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 73 residues processed: 716 average time/residue: 1.0981 time to fit residues: 951.2625 Evaluate side-chains 712 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 639 time to evaluate : 2.302 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 41 residues processed: 35 average time/residue: 0.3581 time to fit residues: 22.4866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 310 optimal weight: 0.0870 chunk 205 optimal weight: 3.9990 chunk 367 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 169 optimal weight: 0.0970 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN H 84 ASN B 540 ASN B 564 GLN B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 957 GLN B1005 GLN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31317 Z= 0.208 Angle : 0.646 12.142 42591 Z= 0.317 Chirality : 0.046 0.381 4920 Planarity : 0.004 0.063 5448 Dihedral : 6.307 114.884 5199 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.46 % Allowed : 22.07 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.20 (0.13), residues: 3780 helix: 1.40 (0.22), residues: 636 sheet: -0.51 (0.18), residues: 840 loop : -1.62 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 47 HIS 0.003 0.001 HIS A 207 PHE 0.025 0.001 PHE C 490 TYR 0.031 0.001 TYR B 453 ARG 0.015 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 657 time to evaluate : 3.780 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 84 residues processed: 712 average time/residue: 1.2432 time to fit residues: 1067.9121 Evaluate side-chains 734 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 650 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 43 residues processed: 42 average time/residue: 0.6601 time to fit residues: 43.6246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 181 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 288 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 540 ASN B 564 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS E 112 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31317 Z= 0.218 Angle : 0.660 11.022 42591 Z= 0.326 Chirality : 0.046 0.347 4920 Planarity : 0.004 0.055 5448 Dihedral : 6.294 113.914 5199 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.01 % Allowed : 23.22 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.25 (0.13), residues: 3780 helix: 1.42 (0.22), residues: 636 sheet: -0.56 (0.17), residues: 879 loop : -1.68 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 47 HIS 0.015 0.001 HIS C1101 PHE 0.031 0.002 PHE A 490 TYR 0.031 0.002 TYR B 453 ARG 0.015 0.001 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 641 time to evaluate : 3.442 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: 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 outliers start: 100 outliers final: 72 residues processed: 700 average time/residue: 1.2195 time to fit residues: 1032.4589 Evaluate side-chains 701 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 629 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 53 residues processed: 21 average time/residue: 0.5479 time to fit residues: 22.1872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 342 optimal weight: 0.2980 chunk 205 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 309 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 341 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 540 ASN B 564 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN E 112 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31317 Z= 0.198 Angle : 0.657 12.923 42591 Z= 0.322 Chirality : 0.046 0.344 4920 Planarity : 0.004 0.052 5448 Dihedral : 6.219 113.982 5199 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.01 % Allowed : 23.28 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.22 (0.13), residues: 3780 helix: 1.48 (0.22), residues: 636 sheet: -0.59 (0.17), residues: 882 loop : -1.66 (0.12), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.003 0.001 HIS C1101 PHE 0.025 0.001 PHE C 490 TYR 0.029 0.001 TYR B 453 ARG 0.010 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 635 time to evaluate : 3.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 79 residues processed: 694 average time/residue: 1.2381 time to fit residues: 1045.0172 Evaluate side-chains 711 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 632 time to evaluate : 3.370 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 51 residues processed: 29 average time/residue: 0.4848 time to fit residues: 26.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 0.8980 chunk 361 optimal weight: 0.0470 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 379 optimal weight: 0.9990 chunk 349 optimal weight: 0.4980 chunk 302 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 61 ASN B 540 ASN B 564 GLN B 607 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1005 GLN B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1101 HIS E 112 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31317 Z= 0.195 Angle : 0.665 13.831 42591 Z= 0.326 Chirality : 0.046 0.343 4920 Planarity : 0.004 0.057 5448 Dihedral : 6.168 113.933 5199 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.26 % Allowed : 24.24 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.17 (0.14), residues: 3780 helix: 1.52 (0.21), residues: 654 sheet: -0.50 (0.17), residues: 882 loop : -1.67 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 47 HIS 0.010 0.001 HIS C1101 PHE 0.066 0.001 PHE A 133 TYR 0.026 0.001 TYR B 453 ARG 0.009 0.001 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7560 Ramachandran restraints generated. 3780 Oldfield, 0 Emsley, 3780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 641 time to evaluate : 3.757 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 64 residues processed: 693 average time/residue: 1.2184 time to fit residues: 1032.1700 Evaluate side-chains 691 residues out of total 3321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 627 time to evaluate : 3.757 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 49 residues processed: 16 average time/residue: 0.6417 time to fit residues: 19.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 0.9990 chunk 321 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 310 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1010 GLN A1101 HIS L 27 GLN B 540 ASN B 564 GLN ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 755 GLN C 764 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN C1010 GLN C1101 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.201747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.180031 restraints weight = 58406.576| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 3.73 r_work: 0.4071 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31317 Z= 0.228 Angle : 0.678 12.346 42591 Z= 0.333 Chirality : 0.047 0.338 4920 Planarity : 0.004 0.053 5448 Dihedral : 6.360 113.913 5199 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.35 % Allowed : 24.57 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -1.20 (0.13), residues: 3780 helix: 1.50 (0.21), residues: 654 sheet: -0.51 (0.17), residues: 870 loop : -1.70 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.011 0.001 HIS C1101 PHE 0.029 0.002 PHE A 92 TYR 0.023 0.001 TYR C 369 ARG 0.013 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14653.45 seconds wall clock time: 303 minutes 42.48 seconds (18222.48 seconds total)