Starting phenix.real_space_refine on Mon Feb 19 15:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dli_27502/02_2024/8dli_27502.pdb" } resolution = 2.56 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= 0.039 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 111 5.16 5 C 16013 2.51 5 N 4115 2.21 5 O 4915 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 "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "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: 25154 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8107 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 7 Chain: "B" Number of atoms: 8107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8107 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8100 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 8 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "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: 13.38, per 1000 atoms: 0.53 Number of scatterers: 25154 At special positions: 0 Unit cell: (140, 144, 196, 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 111 16.00 O 4915 8.00 N 4115 7.00 C 16013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " 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 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " 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: 10.01 Conformation dependent library (CDL) restraints added in 4.4 seconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 24.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.048A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.665A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.736A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.044A 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: 3.613A 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: 3.961A 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 966 removed outlier: 3.733A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.109A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.129A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.883A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.650A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.994A 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: 3.523A 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 removed outlier: 3.502A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.925A 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 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: 4.025A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.534A 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: 3.894A 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 386 through 390 removed outlier: 3.775A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.827A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.873A 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: 3.605A 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: 3.953A 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: 3.516A 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: 4.334A 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 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.672A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.986A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 11.376A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.674A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.004A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.818A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.575A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.027A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.743A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.900A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.311A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.786A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.238A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.940A 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: 4.089A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.798A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.746A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.519A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.647A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.904A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.341A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.122A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.664A 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: 4.109A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.977A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 156 through 163 removed outlier: 9.921A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.190A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.876A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.744A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 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: 3.528A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.929A 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: 6.228A 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: 6.415A 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 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.840A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 924 hydrogen bonds defined for protein. 2571 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: 10.83 Time building geometry restraints manager: 10.76 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: 7878 1.34 - 1.46: 6408 1.46 - 1.59: 11293 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25717 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.31e+00 ... (remaining 25712 not shown) Histogram of bond angle deviations from ideal: 96.97 - 104.38: 479 104.38 - 111.79: 12025 111.79 - 119.21: 8732 119.21 - 126.62: 13480 126.62 - 134.03: 287 Bond angle restraints: 35003 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 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.96 -5.26 1.22e+00 6.72e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.87 -5.17 1.22e+00 6.72e-01 1.80e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 ... (remaining 34998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14830 17.80 - 35.60: 1021 35.60 - 53.39: 178 53.39 - 71.19: 66 71.19 - 88.99: 28 Dihedral angle restraints: 16123 sinusoidal: 7079 harmonic: 9044 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 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+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 -57.45 -28.55 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 16120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3195 0.065 - 0.130: 826 0.130 - 0.195: 114 0.195 - 0.260: 9 0.260 - 0.325: 3 Chirality restraints: 4147 Sorted by residual: 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 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+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 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 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 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 4144 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 716 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE B 716 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE B 716 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN B 717 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 716 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ILE C 716 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 716 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN C 717 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 716 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ILE A 716 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE A 716 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN A 717 " 0.023 2.00e-02 2.50e+03 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6444 2.80 - 3.32: 21194 3.32 - 3.85: 43005 3.85 - 4.37: 49555 4.37 - 4.90: 85019 Nonbonded interactions: 205217 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.274 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR C 369 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.288 2.440 ... (remaining 205212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 552 or resid 554 through 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 552 or resid 554 through 1147 or resid 1301 thr \ ough 1308)) selection = chain 'C' } 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: 3.650 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: 0.020 Extract box with map and model: 15.090 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 68.220 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 25717 Z= 0.330 Angle : 0.828 9.209 35003 Z= 0.454 Chirality : 0.057 0.325 4147 Planarity : 0.006 0.058 4459 Dihedral : 12.958 88.988 10173 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % 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: -0.02 (0.14), residues: 3060 helix: 1.01 (0.18), residues: 675 sheet: 0.81 (0.19), residues: 686 loop : -0.78 (0.13), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 886 HIS 0.006 0.001 HIS B1118 PHE 0.031 0.002 PHE C 275 TYR 0.029 0.002 TYR A1067 ARG 0.009 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7984 (t80) cc_final: 0.7254 (t80) REVERT: A 1029 MET cc_start: 0.9325 (tpp) cc_final: 0.9042 (tpp) REVERT: B 201 PHE cc_start: 0.8955 (t80) cc_final: 0.8299 (t80) REVERT: B 239 GLN cc_start: 0.8316 (tt0) cc_final: 0.7788 (tp40) REVERT: B 387 LEU cc_start: 0.8247 (mt) cc_final: 0.7753 (mp) REVERT: B 1029 MET cc_start: 0.9310 (tpp) cc_final: 0.8931 (tpp) REVERT: C 229 LEU cc_start: 0.7935 (tp) cc_final: 0.7707 (tt) REVERT: C 392 PHE cc_start: 0.7192 (m-80) cc_final: 0.6861 (m-80) REVERT: C 453 TYR cc_start: 0.6072 (p90) cc_final: 0.5653 (p90) outliers start: 2 outliers final: 1 residues processed: 252 average time/residue: 1.3771 time to fit residues: 402.6444 Evaluate side-chains 104 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 7.9990 chunk 234 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN B 239 GLN B 370 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 960 ASN C1005 GLN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25717 Z= 0.199 Angle : 0.526 10.105 35003 Z= 0.271 Chirality : 0.043 0.252 4147 Planarity : 0.004 0.060 4459 Dihedral : 6.560 59.678 4590 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.84 % Allowed : 7.86 % Favored : 91.30 % 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: 0.45 (0.14), residues: 3060 helix: 1.90 (0.20), residues: 680 sheet: 0.82 (0.20), residues: 641 loop : -0.55 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 353 HIS 0.003 0.001 HIS B 519 PHE 0.022 0.001 PHE B 342 TYR 0.016 0.001 TYR B 265 ARG 0.008 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 2.627 Fit side-chains revert: symmetry clash REVERT: A 988 GLU cc_start: 0.8886 (mp0) cc_final: 0.8383 (mp0) REVERT: B 201 PHE cc_start: 0.8744 (t80) cc_final: 0.8227 (t80) REVERT: B 387 LEU cc_start: 0.8206 (mt) cc_final: 0.7733 (mp) REVERT: B 950 ASP cc_start: 0.8177 (m-30) cc_final: 0.7959 (m-30) REVERT: B 1029 MET cc_start: 0.9246 (tpp) cc_final: 0.8756 (tpp) REVERT: C 453 TYR cc_start: 0.6613 (p90) cc_final: 0.6367 (p90) REVERT: C 1145 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7142 (tm) outliers start: 23 outliers final: 9 residues processed: 131 average time/residue: 1.2651 time to fit residues: 196.7908 Evaluate side-chains 102 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 281 optimal weight: 0.0000 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN C 207 HIS C 824 ASN C 856 ASN C1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25717 Z= 0.224 Angle : 0.510 10.410 35003 Z= 0.261 Chirality : 0.043 0.265 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.817 57.768 4588 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.40 % Allowed : 8.59 % Favored : 90.01 % 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: 0.50 (0.15), residues: 3060 helix: 2.02 (0.20), residues: 691 sheet: 0.56 (0.20), residues: 637 loop : -0.44 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 104 HIS 0.003 0.001 HIS C1088 PHE 0.014 0.001 PHE C 898 TYR 0.028 0.001 TYR C 265 ARG 0.011 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7503 (p0) cc_final: 0.7023 (p0) REVERT: A 1002 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: B 201 PHE cc_start: 0.8840 (t80) cc_final: 0.8295 (t80) REVERT: B 237 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6686 (mtm-85) REVERT: B 387 LEU cc_start: 0.8316 (mt) cc_final: 0.7720 (mp) REVERT: B 950 ASP cc_start: 0.8201 (m-30) cc_final: 0.7954 (m-30) REVERT: B 1029 MET cc_start: 0.9195 (tpp) cc_final: 0.8912 (tpp) REVERT: C 229 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7820 (tm) REVERT: C 1145 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7129 (tm) outliers start: 38 outliers final: 9 residues processed: 130 average time/residue: 1.0225 time to fit residues: 165.2866 Evaluate side-chains 101 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 755 GLN A 824 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 955 ASN B1002 GLN C 856 ASN C 969 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25717 Z= 0.411 Angle : 0.584 9.312 35003 Z= 0.297 Chirality : 0.045 0.263 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.733 53.027 4588 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.54 % Allowed : 9.95 % Favored : 88.51 % 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: 0.33 (0.15), residues: 3060 helix: 1.87 (0.20), residues: 699 sheet: 0.34 (0.21), residues: 607 loop : -0.49 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 886 HIS 0.004 0.001 HIS C1058 PHE 0.019 0.002 PHE B 515 TYR 0.026 0.002 TYR C 453 ARG 0.006 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 3.186 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8314 (tpt) REVERT: A 985 ASP cc_start: 0.7500 (p0) cc_final: 0.7180 (p0) REVERT: A 1002 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7965 (tm-30) REVERT: B 108 THR cc_start: 0.4347 (OUTLIER) cc_final: 0.3452 (m) REVERT: B 189 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (tm) REVERT: B 201 PHE cc_start: 0.8865 (t80) cc_final: 0.8319 (t80) REVERT: B 237 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6758 (mtm-85) REVERT: B 342 PHE cc_start: 0.7377 (m-80) cc_final: 0.7165 (t80) REVERT: B 950 ASP cc_start: 0.8290 (m-30) cc_final: 0.8036 (m-30) REVERT: C 229 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (tm) REVERT: C 540 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7941 (p0) REVERT: C 1145 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7136 (tm) outliers start: 42 outliers final: 10 residues processed: 130 average time/residue: 1.1094 time to fit residues: 175.6456 Evaluate side-chains 107 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 20.0000 chunk 169 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 957 GLN C 856 ASN C 913 GLN C 955 ASN C1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25717 Z= 0.274 Angle : 0.526 8.969 35003 Z= 0.267 Chirality : 0.044 0.259 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.453 52.819 4588 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.32 % Allowed : 11.05 % Favored : 87.62 % 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: 0.38 (0.15), residues: 3060 helix: 2.01 (0.20), residues: 699 sheet: 0.29 (0.21), residues: 594 loop : -0.47 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.004 0.001 HIS C1088 PHE 0.018 0.001 PHE A 175 TYR 0.021 0.001 TYR C 265 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 2.673 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8196 (tp) cc_final: 0.7941 (tt) REVERT: A 740 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8324 (tpt) REVERT: A 1002 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: B 108 THR cc_start: 0.4617 (OUTLIER) cc_final: 0.3785 (m) REVERT: B 189 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (tm) REVERT: B 201 PHE cc_start: 0.8897 (t80) cc_final: 0.8376 (t80) REVERT: B 237 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6748 (mtm-85) REVERT: B 950 ASP cc_start: 0.8258 (m-30) cc_final: 0.7998 (m-30) REVERT: C 229 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8068 (tm) REVERT: C 353 TRP cc_start: 0.7679 (p-90) cc_final: 0.7370 (p-90) REVERT: C 540 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7855 (p0) REVERT: C 1145 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7130 (tm) outliers start: 36 outliers final: 10 residues processed: 121 average time/residue: 1.1264 time to fit residues: 165.8316 Evaluate side-chains 108 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN A1011 GLN B 52 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 901 GLN B 926 GLN C 856 ASN C 913 GLN C1005 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25717 Z= 0.152 Angle : 0.487 9.043 35003 Z= 0.246 Chirality : 0.043 0.262 4147 Planarity : 0.003 0.052 4459 Dihedral : 5.033 53.701 4588 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.36 % Allowed : 11.53 % Favored : 87.11 % 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: 0.54 (0.15), residues: 3060 helix: 2.18 (0.20), residues: 691 sheet: 0.39 (0.21), residues: 628 loop : -0.38 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.002 0.000 HIS C1088 PHE 0.021 0.001 PHE B 374 TYR 0.019 0.001 TYR C 265 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 3.015 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8311 (tp) cc_final: 0.8064 (tt) REVERT: A 1002 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: B 108 THR cc_start: 0.4557 (OUTLIER) cc_final: 0.3711 (m) REVERT: B 191 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: B 201 PHE cc_start: 0.8817 (t80) cc_final: 0.8288 (t80) REVERT: B 237 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6675 (mtm-85) REVERT: B 245 HIS cc_start: 0.2356 (OUTLIER) cc_final: 0.1597 (m90) REVERT: B 950 ASP cc_start: 0.8240 (m-30) cc_final: 0.7987 (m-30) REVERT: B 1145 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7782 (tp) REVERT: C 229 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8110 (tm) REVERT: C 358 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 1145 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7126 (tm) outliers start: 37 outliers final: 9 residues processed: 128 average time/residue: 1.2133 time to fit residues: 188.2136 Evaluate side-chains 107 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 251 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 137 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 856 ASN C 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25717 Z= 0.157 Angle : 0.486 8.995 35003 Z= 0.247 Chirality : 0.043 0.262 4147 Planarity : 0.003 0.053 4459 Dihedral : 4.797 53.543 4588 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.25 % Allowed : 11.60 % Favored : 87.15 % 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: 0.61 (0.15), residues: 3060 helix: 2.31 (0.20), residues: 685 sheet: 0.37 (0.21), residues: 629 loop : -0.34 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 353 HIS 0.002 0.000 HIS C1088 PHE 0.020 0.001 PHE B 374 TYR 0.027 0.001 TYR C 453 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 3.274 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8279 (tp) cc_final: 0.8059 (tt) REVERT: A 1002 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 108 THR cc_start: 0.4360 (OUTLIER) cc_final: 0.3486 (m) REVERT: B 191 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: B 201 PHE cc_start: 0.8831 (t80) cc_final: 0.8268 (t80) REVERT: B 237 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6723 (mtm-85) REVERT: B 245 HIS cc_start: 0.2160 (OUTLIER) cc_final: 0.1454 (m90) REVERT: B 731 MET cc_start: 0.9015 (ptm) cc_final: 0.8794 (ptm) REVERT: B 950 ASP cc_start: 0.8188 (m-30) cc_final: 0.7935 (m-30) REVERT: B 1145 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7780 (tp) REVERT: C 153 MET cc_start: 0.6218 (tpt) cc_final: 0.5975 (tpp) REVERT: C 229 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8115 (tm) REVERT: C 358 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 1145 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7119 (tm) outliers start: 34 outliers final: 8 residues processed: 123 average time/residue: 1.0992 time to fit residues: 164.9296 Evaluate side-chains 105 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A 957 GLN A1011 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 580 GLN C 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25717 Z= 0.349 Angle : 0.567 10.591 35003 Z= 0.287 Chirality : 0.045 0.263 4147 Planarity : 0.004 0.051 4459 Dihedral : 5.084 53.363 4588 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.18 % Allowed : 11.83 % Favored : 87.00 % 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: 0.45 (0.15), residues: 3060 helix: 2.11 (0.20), residues: 685 sheet: 0.21 (0.20), residues: 644 loop : -0.39 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 353 HIS 0.005 0.001 HIS C1088 PHE 0.022 0.001 PHE B 374 TYR 0.019 0.001 TYR C 265 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 2.666 Fit side-chains revert: symmetry clash REVERT: A 740 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8373 (tpp) REVERT: A 1002 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: B 108 THR cc_start: 0.4661 (OUTLIER) cc_final: 0.3541 (m) REVERT: B 201 PHE cc_start: 0.8870 (t80) cc_final: 0.8311 (t80) REVERT: B 237 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.7115 (mpp80) REVERT: B 245 HIS cc_start: 0.2402 (OUTLIER) cc_final: 0.1679 (m90) REVERT: B 950 ASP cc_start: 0.8283 (m-30) cc_final: 0.8028 (m-30) REVERT: B 1029 MET cc_start: 0.9149 (tpp) cc_final: 0.8925 (tpp) REVERT: B 1145 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7886 (OUTLIER) REVERT: C 104 TRP cc_start: 0.7859 (m-90) cc_final: 0.7618 (m-90) REVERT: C 153 MET cc_start: 0.6138 (tpt) cc_final: 0.5847 (tpp) REVERT: C 229 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8043 (tm) REVERT: C 358 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (mp) REVERT: C 1145 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7238 (tm) outliers start: 32 outliers final: 13 residues processed: 116 average time/residue: 1.1205 time to fit residues: 157.8466 Evaluate side-chains 106 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 1.9990 chunk 285 optimal weight: 0.6980 chunk 260 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 120 optimal weight: 0.0270 chunk 217 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 262 optimal weight: 0.9980 chunk 276 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 955 ASN A1011 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 856 ASN C 913 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25717 Z= 0.148 Angle : 0.502 10.717 35003 Z= 0.253 Chirality : 0.043 0.266 4147 Planarity : 0.003 0.053 4459 Dihedral : 4.781 53.852 4588 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.95 % Allowed : 12.38 % Favored : 86.67 % 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 (0.15), residues: 3060 helix: 2.38 (0.20), residues: 673 sheet: 0.22 (0.21), residues: 631 loop : -0.30 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 104 HIS 0.002 0.000 HIS C1088 PHE 0.021 0.001 PHE B 456 TYR 0.029 0.001 TYR C 453 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 2.699 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: B 108 THR cc_start: 0.4641 (OUTLIER) cc_final: 0.3604 (m) REVERT: B 201 PHE cc_start: 0.8855 (t80) cc_final: 0.8281 (t80) REVERT: B 237 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7206 (mpp80) REVERT: B 245 HIS cc_start: 0.2399 (OUTLIER) cc_final: 0.1695 (m90) REVERT: B 731 MET cc_start: 0.9025 (ptm) cc_final: 0.8804 (ptm) REVERT: B 950 ASP cc_start: 0.8239 (m-30) cc_final: 0.7985 (m-30) REVERT: B 1145 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7881 (OUTLIER) REVERT: C 104 TRP cc_start: 0.7700 (m-90) cc_final: 0.7449 (m-90) REVERT: C 153 MET cc_start: 0.6072 (tpt) cc_final: 0.5846 (tpp) REVERT: C 229 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8018 (tm) REVERT: C 358 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8238 (mp) REVERT: C 1145 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7203 (tm) outliers start: 26 outliers final: 11 residues processed: 110 average time/residue: 1.1809 time to fit residues: 162.9074 Evaluate side-chains 103 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 440 ASN Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 139 optimal weight: 0.0570 chunk 204 optimal weight: 0.8980 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B 957 GLN C 856 ASN C 913 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25717 Z= 0.199 Angle : 0.509 10.736 35003 Z= 0.257 Chirality : 0.043 0.259 4147 Planarity : 0.004 0.055 4459 Dihedral : 4.718 53.385 4588 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.77 % Allowed : 12.63 % Favored : 86.60 % 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: 0.62 (0.15), residues: 3060 helix: 2.39 (0.20), residues: 673 sheet: 0.21 (0.21), residues: 633 loop : -0.27 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 353 HIS 0.003 0.001 HIS C1088 PHE 0.019 0.001 PHE C 192 TYR 0.018 0.001 TYR C 265 ARG 0.004 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 3.214 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: B 108 THR cc_start: 0.4661 (OUTLIER) cc_final: 0.3610 (m) REVERT: B 201 PHE cc_start: 0.8870 (t80) cc_final: 0.8326 (t80) REVERT: B 237 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7225 (mpp80) REVERT: B 245 HIS cc_start: 0.2425 (OUTLIER) cc_final: 0.1718 (m90) REVERT: B 950 ASP cc_start: 0.8207 (m-30) cc_final: 0.7954 (m-30) REVERT: B 1145 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7857 (OUTLIER) REVERT: C 104 TRP cc_start: 0.7730 (m-90) cc_final: 0.7455 (m-90) REVERT: C 229 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8073 (tm) REVERT: C 358 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 1145 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7150 (tm) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 1.1226 time to fit residues: 146.0304 Evaluate side-chains 99 residues out of total 2723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1011 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1005 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077616 restraints weight = 67094.474| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.79 r_work: 0.3113 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.122 25717 Z= 0.156 Angle : 0.632 48.146 35003 Z= 0.342 Chirality : 0.043 0.261 4147 Planarity : 0.004 0.054 4459 Dihedral : 4.651 53.417 4588 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.70 % Allowed : 13.00 % Favored : 86.30 % 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 (0.15), residues: 3060 helix: 2.45 (0.21), residues: 673 sheet: 0.22 (0.21), residues: 631 loop : -0.24 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 353 HIS 0.002 0.000 HIS A 245 PHE 0.043 0.001 PHE B 238 TYR 0.029 0.001 TYR C 453 ARG 0.006 0.000 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.02 seconds wall clock time: 118 minutes 18.26 seconds (7098.26 seconds total)