Starting phenix.real_space_refine on Sun Feb 18 11:39:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tey_25855/02_2024/7tey_25855.pdb" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 92 5.16 5 C 13904 2.51 5 N 3584 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8091 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 11.92, per 1000 atoms: 0.55 Number of scatterers: 21867 At special positions: 0 Unit cell: (140, 147, 174, 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 92 16.00 O 4287 8.00 N 3584 7.00 C 13904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 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 C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG 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 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 8.96 Conformation dependent library (CDL) restraints added in 3.9 seconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5064 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 44 sheets defined 26.1% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.052A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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: 3.700A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.913A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.564A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.062A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.595A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.952A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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: 3.615A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.539A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.533A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.897A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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: 3.656A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.956A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.521A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.897A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.568A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 144 removed outlier: 7.067A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.650A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.006A 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 328 removed outlier: 5.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.283A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.660A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.324A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.114A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.741A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.713A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.560A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.146A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.021A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.452A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.857A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2793 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.99 Time building geometry restraints manager: 9.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6755 1.34 - 1.46: 5506 1.46 - 1.59: 9960 1.59 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22337 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 22332 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.12: 360 104.12 - 111.59: 10104 111.59 - 119.06: 7907 119.06 - 126.54: 11781 126.54 - 134.01: 249 Bond angle restraints: 30401 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.38 -5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.42 -4.49 1.20e+00 6.94e-01 1.40e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 12970 17.92 - 35.84: 867 35.84 - 53.76: 146 53.76 - 71.68: 56 71.68 - 89.60: 25 Dihedral angle restraints: 14064 sinusoidal: 6215 harmonic: 7849 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -58.25 -27.75 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 14061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.163: 539 0.163 - 0.244: 33 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 3647 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3644 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.016 2.00e-02 2.50e+03 1.63e-02 6.63e+00 pdb=" CG TRP C 886 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 886 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL C 551 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.014 2.00e-02 2.50e+03 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6022 2.81 - 3.34: 18440 3.34 - 3.86: 37594 3.86 - 4.38: 43056 4.38 - 4.90: 73807 Nonbonded interactions: 178919 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.293 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.297 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.303 2.440 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.303 2.440 ... (remaining 178914 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.850 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 61.740 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.005 0.068 22337 Z= 0.340 Angle : 0.819 9.430 30401 Z= 0.443 Chirality : 0.057 0.407 3647 Planarity : 0.006 0.054 3861 Dihedral : 12.951 89.598 8898 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 2651 helix: 1.22 (0.19), residues: 612 sheet: 0.75 (0.20), residues: 581 loop : -0.78 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 886 HIS 0.005 0.001 HIS C 66 PHE 0.036 0.002 PHE A 275 TYR 0.036 0.003 TYR C1067 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7771 (tp-100) REVERT: A 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8216 (m-30) REVERT: A 205 SER cc_start: 0.8476 (t) cc_final: 0.8242 (m) REVERT: A 591 SER cc_start: 0.8322 (m) cc_final: 0.7938 (p) REVERT: B 54 LEU cc_start: 0.7467 (mm) cc_final: 0.7187 (mp) REVERT: B 287 ASP cc_start: 0.7968 (t0) cc_final: 0.7668 (m-30) REVERT: B 553 THR cc_start: 0.6995 (p) cc_final: 0.6781 (p) REVERT: B 592 PHE cc_start: 0.7294 (p90) cc_final: 0.6884 (p90) REVERT: B 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8886 (tpp) REVERT: C 129 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6218 (mmtm) REVERT: C 347 PHE cc_start: 0.6661 (m-10) cc_final: 0.6396 (m-10) REVERT: C 396 TYR cc_start: 0.6830 (m-80) cc_final: 0.6586 (m-80) REVERT: C 421 TYR cc_start: 0.8323 (m-10) cc_final: 0.8022 (m-10) REVERT: C 436 TRP cc_start: 0.7005 (p90) cc_final: 0.6577 (p90) REVERT: C 437 ASN cc_start: 0.6398 (t0) cc_final: 0.6174 (m-40) REVERT: C 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6673 (p90) REVERT: C 508 TYR cc_start: 0.7844 (m-80) cc_final: 0.7041 (m-80) outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 1.2064 time to fit residues: 430.9712 Evaluate side-chains 156 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 81 optimal weight: 0.0470 chunk 128 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 244 optimal weight: 0.0980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 556 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22337 Z= 0.176 Angle : 0.536 13.171 30401 Z= 0.276 Chirality : 0.044 0.293 3647 Planarity : 0.004 0.046 3861 Dihedral : 6.248 59.351 4054 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.52 % Allowed : 7.31 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2651 helix: 2.24 (0.21), residues: 615 sheet: 0.78 (0.20), residues: 621 loop : -0.62 (0.15), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.003 0.001 HIS C1048 PHE 0.025 0.001 PHE C 238 TYR 0.022 0.001 TYR A1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7887 (tm-30) REVERT: A 205 SER cc_start: 0.8672 (t) cc_final: 0.8397 (m) REVERT: A 591 SER cc_start: 0.8468 (m) cc_final: 0.7559 (p) REVERT: A 1010 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: B 287 ASP cc_start: 0.7952 (t0) cc_final: 0.7682 (m-30) REVERT: B 592 PHE cc_start: 0.7399 (p90) cc_final: 0.6976 (p90) REVERT: C 129 LYS cc_start: 0.6877 (mtmt) cc_final: 0.6229 (mmtt) REVERT: C 421 TYR cc_start: 0.8304 (m-10) cc_final: 0.7928 (m-10) REVERT: C 436 TRP cc_start: 0.6893 (p90) cc_final: 0.6482 (p90) REVERT: C 453 TYR cc_start: 0.7126 (p90) cc_final: 0.6674 (p90) REVERT: C 508 TYR cc_start: 0.7695 (m-80) cc_final: 0.7156 (m-80) REVERT: C 740 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7335 (ttt) outliers start: 36 outliers final: 13 residues processed: 199 average time/residue: 1.0882 time to fit residues: 255.8715 Evaluate side-chains 155 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 264 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 239 GLN A 762 GLN A 955 ASN B 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN B1011 GLN C 121 ASN C 370 ASN C 824 ASN C 856 ASN C 926 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22337 Z= 0.384 Angle : 0.607 12.711 30401 Z= 0.311 Chirality : 0.049 0.385 3647 Planarity : 0.004 0.042 3861 Dihedral : 5.934 57.310 4052 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.94 % Allowed : 8.24 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2651 helix: 2.24 (0.20), residues: 627 sheet: 0.58 (0.20), residues: 630 loop : -0.62 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 886 HIS 0.004 0.001 HIS C1048 PHE 0.027 0.002 PHE C 238 TYR 0.025 0.002 TYR C1067 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 151 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 205 SER cc_start: 0.8793 (t) cc_final: 0.8531 (m) REVERT: A 858 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8693 (mt) REVERT: A 1010 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 565 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.6845 (p90) REVERT: C 129 LYS cc_start: 0.7036 (mtmt) cc_final: 0.6322 (mmtt) REVERT: C 389 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8429 (m-30) REVERT: C 436 TRP cc_start: 0.6811 (p90) cc_final: 0.6439 (p90) REVERT: C 509 ARG cc_start: 0.6024 (mtt180) cc_final: 0.5816 (mtt180) REVERT: C 740 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7427 (ttt) REVERT: C 1141 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7705 (tm) outliers start: 46 outliers final: 21 residues processed: 182 average time/residue: 1.0152 time to fit residues: 220.0530 Evaluate side-chains 163 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 127 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 260 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 901 GLN B1002 GLN C 856 ASN C 926 GLN C 978 ASN C1010 GLN C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22337 Z= 0.175 Angle : 0.527 11.434 30401 Z= 0.268 Chirality : 0.047 0.662 3647 Planarity : 0.004 0.039 3861 Dihedral : 5.483 56.484 4052 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.69 % Allowed : 9.17 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2651 helix: 2.59 (0.21), residues: 622 sheet: 0.58 (0.20), residues: 612 loop : -0.49 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 104 HIS 0.008 0.001 HIS A 66 PHE 0.027 0.001 PHE C 238 TYR 0.022 0.001 TYR C1067 ARG 0.006 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 145 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 964 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8308 (tttm) REVERT: B 565 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.6920 (p90) REVERT: B 983 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7331 (mtp180) REVERT: C 129 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6333 (mmtt) REVERT: C 238 PHE cc_start: 0.6495 (p90) cc_final: 0.5333 (p90) REVERT: C 436 TRP cc_start: 0.7015 (p90) cc_final: 0.6606 (p90) REVERT: C 740 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7371 (ttt) outliers start: 40 outliers final: 14 residues processed: 172 average time/residue: 1.0130 time to fit residues: 209.5816 Evaluate side-chains 151 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 221 optimal weight: 0.0050 chunk 179 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN A 762 GLN A 824 ASN B1002 GLN C 779 GLN C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22337 Z= 0.449 Angle : 0.626 10.610 30401 Z= 0.321 Chirality : 0.050 0.479 3647 Planarity : 0.004 0.044 3861 Dihedral : 5.689 53.701 4052 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.90 % Allowed : 9.04 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2651 helix: 2.08 (0.20), residues: 640 sheet: 0.19 (0.20), residues: 630 loop : -0.63 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 104 HIS 0.004 0.001 HIS A1058 PHE 0.022 0.002 PHE C 238 TYR 0.024 0.002 TYR C1067 ARG 0.004 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6609 (OUTLIER) cc_final: 0.6171 (m110) REVERT: A 200 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 858 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8717 (mt) REVERT: B 565 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6917 (p90) REVERT: B 902 MET cc_start: 0.8999 (mmt) cc_final: 0.8775 (mmt) REVERT: C 52 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8550 (tm-30) REVERT: C 129 LYS cc_start: 0.6990 (mtmt) cc_final: 0.6327 (mmtt) REVERT: C 238 PHE cc_start: 0.6333 (p90) cc_final: 0.5059 (p90) REVERT: C 347 PHE cc_start: 0.6558 (m-10) cc_final: 0.6110 (m-10) REVERT: C 389 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: C 740 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7433 (ttt) REVERT: C 748 GLU cc_start: 0.8056 (mp0) cc_final: 0.7845 (mp0) REVERT: C 1141 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7683 (tm) outliers start: 45 outliers final: 17 residues processed: 183 average time/residue: 0.9158 time to fit residues: 203.7090 Evaluate side-chains 161 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 260 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B 955 ASN B1002 GLN C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22337 Z= 0.163 Angle : 0.523 9.821 30401 Z= 0.268 Chirality : 0.046 0.583 3647 Planarity : 0.004 0.041 3861 Dihedral : 5.226 53.015 4052 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 10.39 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.16), residues: 2651 helix: 2.47 (0.21), residues: 635 sheet: 0.45 (0.21), residues: 568 loop : -0.50 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 104 HIS 0.002 0.000 HIS C 66 PHE 0.021 0.001 PHE B 194 TYR 0.021 0.001 TYR C1067 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 81 ASN cc_start: 0.6829 (OUTLIER) cc_final: 0.6377 (m-40) REVERT: A 200 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6609 (t80) REVERT: B 565 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6996 (p90) REVERT: B 983 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7353 (mtp180) REVERT: C 52 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8538 (tm-30) REVERT: C 129 LYS cc_start: 0.6993 (mtmt) cc_final: 0.6322 (mmtt) REVERT: C 238 PHE cc_start: 0.6290 (p90) cc_final: 0.5019 (p90) REVERT: C 347 PHE cc_start: 0.6563 (m-10) cc_final: 0.6234 (m-10) REVERT: C 516 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6520 (pp20) REVERT: C 740 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7371 (ttt) outliers start: 33 outliers final: 14 residues processed: 164 average time/residue: 1.0204 time to fit residues: 199.4506 Evaluate side-chains 148 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 162 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN A 762 GLN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22337 Z= 0.358 Angle : 0.580 11.046 30401 Z= 0.297 Chirality : 0.048 0.329 3647 Planarity : 0.004 0.044 3861 Dihedral : 5.277 53.656 4052 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.73 % Allowed : 10.60 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.16), residues: 2651 helix: 2.31 (0.20), residues: 641 sheet: 0.22 (0.21), residues: 613 loop : -0.58 (0.16), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS C1048 PHE 0.024 0.002 PHE A 168 TYR 0.022 0.002 TYR A1067 ARG 0.006 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 2.881 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 81 ASN cc_start: 0.6731 (OUTLIER) cc_final: 0.6259 (m110) REVERT: A 200 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7225 (t80) REVERT: A 231 ILE cc_start: 0.8742 (pt) cc_final: 0.8508 (pp) REVERT: A 858 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8725 (mt) REVERT: B 565 PHE cc_start: 0.7630 (OUTLIER) cc_final: 0.7132 (p90) REVERT: B 983 ARG cc_start: 0.7714 (ttm170) cc_final: 0.7450 (mtp180) REVERT: C 52 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 129 LYS cc_start: 0.6823 (mtmt) cc_final: 0.6171 (mmtt) REVERT: C 238 PHE cc_start: 0.6192 (p90) cc_final: 0.4915 (p90) REVERT: C 389 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8486 (m-30) REVERT: C 516 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6388 (pp20) REVERT: C 740 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7415 (ttt) outliers start: 41 outliers final: 18 residues processed: 162 average time/residue: 0.9738 time to fit residues: 190.7268 Evaluate side-chains 153 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 154 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22337 Z= 0.178 Angle : 0.518 9.972 30401 Z= 0.265 Chirality : 0.045 0.320 3647 Planarity : 0.004 0.045 3861 Dihedral : 4.985 53.262 4052 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.18 % Allowed : 11.07 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 635 sheet: 0.38 (0.21), residues: 572 loop : -0.50 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.002 0.000 HIS C 66 PHE 0.017 0.001 PHE B 238 TYR 0.022 0.001 TYR B 170 ARG 0.008 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7902 (tm-30) REVERT: A 200 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7265 (t80) REVERT: A 231 ILE cc_start: 0.8781 (pt) cc_final: 0.8549 (pp) REVERT: A 858 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8723 (mt) REVERT: B 551 VAL cc_start: 0.7502 (t) cc_final: 0.7209 (m) REVERT: B 565 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7220 (p90) REVERT: B 983 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7418 (mtp180) REVERT: C 52 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8552 (tm-30) REVERT: C 129 LYS cc_start: 0.6831 (mtmt) cc_final: 0.6168 (mmtt) REVERT: C 238 PHE cc_start: 0.6192 (p90) cc_final: 0.4930 (p90) REVERT: C 269 TYR cc_start: 0.6935 (m-80) cc_final: 0.6716 (m-80) REVERT: C 353 TRP cc_start: 0.7330 (p-90) cc_final: 0.7112 (p-90) REVERT: C 421 TYR cc_start: 0.8051 (m-80) cc_final: 0.7641 (m-80) REVERT: C 516 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6405 (pp20) REVERT: C 740 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7375 (ttt) outliers start: 28 outliers final: 14 residues processed: 157 average time/residue: 0.9982 time to fit residues: 188.4197 Evaluate side-chains 152 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 241 optimal weight: 0.0060 chunk 145 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 218 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN B1002 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22337 Z= 0.177 Angle : 0.512 10.043 30401 Z= 0.262 Chirality : 0.045 0.315 3647 Planarity : 0.004 0.058 3861 Dihedral : 4.774 53.601 4052 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.23 % Allowed : 11.24 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2651 helix: 2.64 (0.21), residues: 634 sheet: 0.40 (0.21), residues: 578 loop : -0.44 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 436 HIS 0.002 0.000 HIS A1048 PHE 0.022 0.001 PHE A 168 TYR 0.021 0.001 TYR C1067 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 2.641 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 200 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7135 (t80) REVERT: A 231 ILE cc_start: 0.8669 (pt) cc_final: 0.8438 (pp) REVERT: A 858 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8719 (mt) REVERT: B 565 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7227 (p90) REVERT: B 983 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7411 (mtp180) REVERT: C 52 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8566 (tm-30) REVERT: C 129 LYS cc_start: 0.6909 (mtmt) cc_final: 0.6257 (mmtt) REVERT: C 238 PHE cc_start: 0.6169 (p90) cc_final: 0.4924 (p90) REVERT: C 353 TRP cc_start: 0.7216 (p-90) cc_final: 0.6977 (p-90) REVERT: C 421 TYR cc_start: 0.8139 (m-80) cc_final: 0.7670 (m-80) REVERT: C 516 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6479 (pp20) REVERT: C 740 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7387 (ttt) outliers start: 29 outliers final: 17 residues processed: 157 average time/residue: 1.0354 time to fit residues: 194.9229 Evaluate side-chains 157 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 246 optimal weight: 0.0870 chunk 213 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 0.0570 chunk 169 optimal weight: 9.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22337 Z= 0.167 Angle : 0.506 10.143 30401 Z= 0.258 Chirality : 0.045 0.313 3647 Planarity : 0.004 0.061 3861 Dihedral : 4.650 53.620 4052 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.10 % Allowed : 11.49 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.16), residues: 2651 helix: 2.74 (0.21), residues: 627 sheet: 0.40 (0.21), residues: 572 loop : -0.42 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 104 HIS 0.002 0.000 HIS C 66 PHE 0.018 0.001 PHE B 238 TYR 0.024 0.001 TYR B 170 ARG 0.007 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 200 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.7130 (t80) REVERT: A 221 SER cc_start: 0.8629 (t) cc_final: 0.8291 (p) REVERT: A 231 ILE cc_start: 0.8704 (pt) cc_final: 0.8446 (pp) REVERT: A 858 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8685 (mt) REVERT: B 565 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7300 (p90) REVERT: B 983 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7405 (mtp180) REVERT: C 52 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8596 (tm-30) REVERT: C 129 LYS cc_start: 0.6846 (mtmt) cc_final: 0.6218 (mmtt) REVERT: C 190 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7214 (mmm160) REVERT: C 238 PHE cc_start: 0.6177 (p90) cc_final: 0.4931 (p90) REVERT: C 353 TRP cc_start: 0.7111 (p-90) cc_final: 0.6908 (p-90) REVERT: C 421 TYR cc_start: 0.8197 (m-80) cc_final: 0.7867 (m-10) REVERT: C 740 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7348 (ttt) outliers start: 26 outliers final: 16 residues processed: 162 average time/residue: 1.0027 time to fit residues: 194.2963 Evaluate side-chains 152 residues out of total 2367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 196 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 219 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 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 66 HIS A 196 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 856 ASN C 926 GLN C1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.151389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.089329 restraints weight = 33404.577| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.49 r_work: 0.3069 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22337 Z= 0.178 Angle : 0.510 10.993 30401 Z= 0.260 Chirality : 0.045 0.312 3647 Planarity : 0.004 0.056 3861 Dihedral : 4.634 53.636 4052 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.10 % Allowed : 11.66 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2651 helix: 2.72 (0.21), residues: 628 sheet: 0.39 (0.21), residues: 571 loop : -0.43 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 104 HIS 0.002 0.000 HIS C 519 PHE 0.029 0.001 PHE C 65 TYR 0.021 0.001 TYR C1067 ARG 0.007 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7041.05 seconds wall clock time: 126 minutes 42.37 seconds (7602.37 seconds total)