Starting phenix.real_space_refine on Tue Feb 20 19:40:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g75_29797/02_2024/8g75_29797.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18226 2.51 5 N 4748 2.21 5 O 5608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28711 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 8367 Classifications: {'peptide': 1071} Link IDs: {'PTRANS': 57, 'TRANS': 1013} Chain breaks: 4 Chain: "B" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "D" Number of atoms: 8382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8382 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 57, 'TRANS': 1015} Chain breaks: 4 Chain: "E" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "G" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "F" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 974 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} 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: "C" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.65, per 1000 atoms: 0.51 Number of scatterers: 28711 At special positions: 0 Unit cell: (156.704, 164.672, 196.544, 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 129 16.00 O 5608 8.00 N 4748 7.00 C 18226 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 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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 C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1074 " " NAG C 1 " - " ASN A 801 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 616 " " NAG D1304 " - " ASN D 657 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN D 717 " " NAG O 1 " - " ASN D 801 " " NAG P 1 " - " ASN D1098 " " NAG Q 1 " - " ASN D1134 " Time building additional restraints: 10.90 Conformation dependent library (CDL) restraints added in 4.9 seconds 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.5% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.165A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.810A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.824A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.569A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 6.940A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.578A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.507A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.595A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.501A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.871A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.807A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (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 Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.032A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.704A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.787A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.315A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.742A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.649A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.748A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.546A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.778A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.614A pdb=" N LYS D 386 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 383 through 387' Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.783A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.600A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.749A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 919 removed outlier: 4.339A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.441A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1147 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.922A pdb=" N TYR E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.717A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.952A pdb=" N TYR F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR F 32 " --> pdb=" O LEU F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.616A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.216A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.738A pdb=" N ARG D 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY D 566 " --> pdb=" O ASP D 574 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.780A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 68 through 70 removed outlier: 3.782A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.587A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.662A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.852A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.405A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.164A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.573A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.512A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.552A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.647A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.367A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.350A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.765A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 70 removed outlier: 3.682A pdb=" N ARG B 78 " --> pdb=" O HIS B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.654A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.773A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.975A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.883A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B 565 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.635A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.020A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.652A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.653A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 7.990A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.741A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.588A pdb=" N ARG D 78 " --> pdb=" O HIS D 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 84 through 85 removed outlier: 12.725A pdb=" N PHE D 135 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 12.622A pdb=" N THR D 240 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N ASN D 137 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N LEU D 242 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU D 244 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N ASP D 138 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR D 160 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 140 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.594A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 172 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 318 removed outlier: 5.206A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 593 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D 649 " --> pdb=" O TYR D 612 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE D 643 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.680A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.644A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 711 through 715 removed outlier: 4.145A pdb=" N THR D1076 " --> pdb=" O SER D1097 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.625A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.330A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.296A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG E 38 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.737A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG G 38 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLY G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.562A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG F 38 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 12 1153 hydrogen bonds defined for protein. 3090 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: 13.19 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8742 1.34 - 1.46: 7711 1.46 - 1.59: 12759 1.59 - 1.72: 0 1.72 - 1.85: 162 Bond restraints: 29374 Sorted by residual: bond pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" C1 NAG D1303 " pdb=" O5 NAG D1303 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.69e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" N LYS B 811 " pdb=" CA LYS B 811 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 8.75e+00 bond pdb=" N VAL B1104 " pdb=" CA VAL B1104 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.10e+00 ... (remaining 29369 not shown) Histogram of bond angle deviations from ideal: 93.61 - 101.76: 40 101.76 - 109.92: 4431 109.92 - 118.08: 17854 118.08 - 126.23: 17304 126.23 - 134.39: 347 Bond angle restraints: 39976 Sorted by residual: angle pdb=" CA PRO B1143 " pdb=" N PRO B1143 " pdb=" CD PRO B1143 " ideal model delta sigma weight residual 112.00 103.38 8.62 1.40e+00 5.10e-01 3.79e+01 angle pdb=" CA TRP D 436 " pdb=" CB TRP D 436 " pdb=" CG TRP D 436 " ideal model delta sigma weight residual 113.60 122.91 -9.31 1.90e+00 2.77e-01 2.40e+01 angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 123.35 -8.95 2.30e+00 1.89e-01 1.51e+01 angle pdb=" N GLY A 485 " pdb=" CA GLY A 485 " pdb=" C GLY A 485 " ideal model delta sigma weight residual 113.18 122.26 -9.08 2.37e+00 1.78e-01 1.47e+01 angle pdb=" C TRP E 104 " pdb=" N TYR E 105 " pdb=" CA TYR E 105 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 ... (remaining 39971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15958 17.94 - 35.89: 1582 35.89 - 53.83: 431 53.83 - 71.77: 66 71.77 - 89.72: 33 Dihedral angle restraints: 18070 sinusoidal: 7636 harmonic: 10434 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 7.59 85.41 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 170.19 -77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.99 76.99 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 18067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4537 0.126 - 0.251: 71 0.251 - 0.377: 9 0.377 - 0.503: 0 0.503 - 0.628: 2 Chirality restraints: 4619 Sorted by residual: chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 282 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" C1 NAG D1303 " pdb=" ND2 ASN D 616 " pdb=" C2 NAG D1303 " pdb=" O5 NAG D1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.96 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 4616 not shown) Planarity restraints: 5169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.062 2.00e-02 2.50e+03 5.11e-02 3.27e+01 pdb=" C7 NAG A1309 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.082 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1142 " 0.060 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO B1143 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B1143 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B1143 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 400 " 0.030 2.00e-02 2.50e+03 2.60e-02 1.19e+01 pdb=" CG PHE D 400 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE D 400 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 400 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 400 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 400 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 400 " 0.008 2.00e-02 2.50e+03 ... (remaining 5166 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 230 2.59 - 3.17: 23753 3.17 - 3.75: 43519 3.75 - 4.32: 60537 4.32 - 4.90: 99210 Nonbonded interactions: 227249 Sorted by model distance: nonbonded pdb=" NZ LYS A 417 " pdb=" OH TYR A 495 " model vdw 2.017 2.520 nonbonded pdb=" OG1 THR D 323 " pdb=" OE1 GLU D 324 " model vdw 2.102 2.440 nonbonded pdb=" O SER G 52 " pdb=" NH2 ARG G 72 " model vdw 2.105 2.520 nonbonded pdb=" OD1 ASN B 616 " pdb=" N CYS B 617 " model vdw 2.110 2.520 nonbonded pdb=" OH TYR B 37 " pdb=" OD1 ASP B 53 " model vdw 2.116 2.440 ... (remaining 227244 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 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) selection = (chain 'D' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'C' 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' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.900 Check model and map are aligned: 0.420 Set scattering table: 0.270 Process input model: 75.650 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.310 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29374 Z= 0.266 Angle : 0.697 11.385 39976 Z= 0.365 Chirality : 0.050 0.628 4619 Planarity : 0.006 0.096 5133 Dihedral : 15.318 89.718 11252 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 0.61 % Allowed : 19.09 % Favored : 80.30 % 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: -0.29 (0.13), residues: 3562 helix: 0.95 (0.20), residues: 687 sheet: 0.47 (0.17), residues: 811 loop : -0.87 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 104 HIS 0.006 0.001 HIS A 655 PHE 0.058 0.002 PHE D 400 TYR 0.049 0.002 TYR A 453 ARG 0.011 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.6198 (p0) cc_final: 0.5973 (p0) REVERT: A 821 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8273 (tm) REVERT: B 900 MET cc_start: 0.8477 (ttm) cc_final: 0.8255 (mtm) REVERT: D 153 MET cc_start: 0.0085 (ptp) cc_final: -0.1163 (pmm) REVERT: D 602 THR cc_start: 0.7495 (p) cc_final: 0.7288 (p) outliers start: 19 outliers final: 8 residues processed: 233 average time/residue: 0.3699 time to fit residues: 144.4543 Evaluate side-chains 208 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 150 optimal weight: 50.0000 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 chunk 279 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 856 ASN A 926 GLN A 935 GLN A1010 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN D 564 GLN D 764 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29374 Z= 0.268 Angle : 0.652 9.938 39976 Z= 0.339 Chirality : 0.048 0.509 4619 Planarity : 0.005 0.079 5133 Dihedral : 6.263 58.302 4874 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.49 % Allowed : 17.08 % Favored : 80.43 % 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: -0.20 (0.14), residues: 3562 helix: 1.36 (0.20), residues: 710 sheet: 0.52 (0.17), residues: 831 loop : -0.99 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 436 HIS 0.005 0.001 HIS B1064 PHE 0.034 0.002 PHE D 400 TYR 0.027 0.002 TYR B 369 ARG 0.008 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 221 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: -0.0487 (OUTLIER) cc_final: -0.1583 (mmm) REVERT: A 428 ASP cc_start: 0.6139 (p0) cc_final: 0.5939 (p0) REVERT: B 153 MET cc_start: 0.2200 (tpt) cc_final: -0.1049 (ptp) REVERT: B 314 GLN cc_start: 0.8019 (tt0) cc_final: 0.7754 (tt0) REVERT: B 1081 ILE cc_start: 0.8492 (mt) cc_final: 0.8178 (mt) REVERT: B 1127 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5229 (m-30) REVERT: D 153 MET cc_start: 0.0181 (ptp) cc_final: -0.1262 (pmm) REVERT: D 420 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6759 (t0) REVERT: D 950 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7910 (t0) REVERT: D 985 ASP cc_start: 0.6532 (t0) cc_final: 0.6287 (m-30) outliers start: 78 outliers final: 27 residues processed: 285 average time/residue: 0.3532 time to fit residues: 170.1223 Evaluate side-chains 215 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 950 ASP Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain G residue 94 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 269 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 289 optimal weight: 0.9990 chunk 322 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 260 optimal weight: 9.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 926 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN D 437 ASN D 613 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29374 Z= 0.294 Angle : 0.639 9.195 39976 Z= 0.334 Chirality : 0.048 0.441 4619 Planarity : 0.005 0.054 5133 Dihedral : 5.713 55.372 4862 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.96 % Favored : 95.93 % Rotamer: Outliers : 3.26 % Allowed : 16.66 % Favored : 80.08 % 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: -0.23 (0.14), residues: 3562 helix: 1.58 (0.20), residues: 717 sheet: 0.43 (0.17), residues: 830 loop : -1.09 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 436 HIS 0.012 0.002 HIS D1083 PHE 0.052 0.002 PHE D 400 TYR 0.031 0.002 TYR A 351 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 204 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.6306 (p0) cc_final: 0.6053 (p0) REVERT: A 753 LEU cc_start: 0.7490 (tp) cc_final: 0.7235 (tp) REVERT: B 269 TYR cc_start: 0.7270 (m-10) cc_final: 0.7039 (m-10) REVERT: B 902 MET cc_start: 0.8300 (tpt) cc_final: 0.7711 (tpt) REVERT: B 1127 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: D 153 MET cc_start: -0.0076 (ptp) cc_final: -0.1569 (pmm) REVERT: D 565 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: D 823 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: D 900 MET cc_start: 0.8491 (mtm) cc_final: 0.8131 (mtm) outliers start: 102 outliers final: 53 residues processed: 291 average time/residue: 0.3636 time to fit residues: 176.4859 Evaluate side-chains 219 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 1037 SER Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 218 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 345 optimal weight: 40.0000 chunk 170 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 926 GLN A1011 GLN B 99 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29374 Z= 0.238 Angle : 0.590 10.718 39976 Z= 0.304 Chirality : 0.046 0.431 4619 Planarity : 0.005 0.058 5133 Dihedral : 5.433 57.886 4862 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 3.26 % Allowed : 17.56 % Favored : 79.18 % 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: -0.21 (0.14), residues: 3562 helix: 1.80 (0.20), residues: 712 sheet: 0.28 (0.17), residues: 812 loop : -1.06 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 436 HIS 0.006 0.001 HIS D1083 PHE 0.040 0.002 PHE D 400 TYR 0.020 0.001 TYR B 674 ARG 0.005 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 181 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.6681 (m-80) cc_final: 0.6454 (m-80) REVERT: A 753 LEU cc_start: 0.7768 (tp) cc_final: 0.7556 (tp) REVERT: A 921 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8325 (mttt) REVERT: B 269 TYR cc_start: 0.7279 (m-10) cc_final: 0.6996 (m-10) REVERT: B 902 MET cc_start: 0.8311 (tpt) cc_final: 0.7740 (tpt) REVERT: D 153 MET cc_start: -0.0207 (ptp) cc_final: -0.1607 (pmm) REVERT: D 420 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6797 (t0) REVERT: D 565 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: D 823 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: D 900 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: G 83 MET cc_start: 0.1293 (mpp) cc_final: -0.0479 (tpt) outliers start: 102 outliers final: 55 residues processed: 266 average time/residue: 0.3457 time to fit residues: 158.3257 Evaluate side-chains 221 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 161 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 420 ASP Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 294 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 309 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN D 437 ASN D 613 GLN D 655 HIS D 784 GLN D1083 HIS E 3 GLN F 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 29374 Z= 0.452 Angle : 0.735 10.089 39976 Z= 0.382 Chirality : 0.051 0.441 4619 Planarity : 0.005 0.062 5133 Dihedral : 6.302 59.218 4862 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.36 % Favored : 94.58 % Rotamer: Outliers : 4.41 % Allowed : 17.68 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3562 helix: 1.25 (0.20), residues: 695 sheet: 0.13 (0.17), residues: 839 loop : -1.28 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 436 HIS 0.048 0.003 HIS D1083 PHE 0.027 0.003 PHE A 970 TYR 0.027 0.002 TYR B 279 ARG 0.005 0.001 ARG B1014 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 160 time to evaluate : 3.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.7316 (t80) REVERT: A 787 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: A 804 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: A 935 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.6841 (tt0) REVERT: A 960 ASN cc_start: 0.8296 (OUTLIER) cc_final: 0.7991 (t0) REVERT: B 131 CYS cc_start: 0.2026 (OUTLIER) cc_final: 0.1826 (m) REVERT: D 153 MET cc_start: -0.0359 (ptp) cc_final: -0.1854 (pmm) REVERT: D 565 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7115 (m-80) REVERT: D 673 SER cc_start: 0.8601 (p) cc_final: 0.8229 (m) REVERT: D 823 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: D 900 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8304 (mtt) outliers start: 138 outliers final: 76 residues processed: 281 average time/residue: 0.3715 time to fit residues: 174.5317 Evaluate side-chains 228 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 143 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 584 ILE Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 202 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 345 optimal weight: 40.0000 chunk 286 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 690 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29374 Z= 0.196 Angle : 0.587 11.444 39976 Z= 0.302 Chirality : 0.046 0.440 4619 Planarity : 0.005 0.059 5133 Dihedral : 5.748 59.730 4862 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 2.97 % Allowed : 18.74 % Favored : 78.29 % 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: -0.26 (0.14), residues: 3562 helix: 1.89 (0.20), residues: 688 sheet: 0.25 (0.17), residues: 840 loop : -1.13 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 436 HIS 0.006 0.001 HIS D1083 PHE 0.027 0.002 PHE D 400 TYR 0.035 0.001 TYR A 351 ARG 0.009 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 155 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7278 (t80) REVERT: A 613 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7948 (mm110) REVERT: A 921 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8350 (mttt) REVERT: B 105 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 210 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6536 (tp) REVERT: B 988 GLU cc_start: 0.7392 (tp30) cc_final: 0.7180 (tp30) REVERT: D 153 MET cc_start: -0.0472 (ptp) cc_final: -0.0698 (pmm) REVERT: D 565 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: D 673 SER cc_start: 0.8498 (p) cc_final: 0.8139 (m) REVERT: D 823 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: D 900 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8177 (mtp) outliers start: 93 outliers final: 63 residues processed: 233 average time/residue: 0.3704 time to fit residues: 146.3343 Evaluate side-chains 213 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 142 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 613 GLN Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 252 optimal weight: 20.0000 chunk 195 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 344 optimal weight: 40.0000 chunk 215 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 158 optimal weight: 0.2980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 29374 Z= 0.268 Angle : 0.598 9.370 39976 Z= 0.308 Chirality : 0.047 0.444 4619 Planarity : 0.005 0.079 5133 Dihedral : 5.641 59.511 4862 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 3.29 % Allowed : 18.61 % Favored : 78.09 % 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: -0.26 (0.14), residues: 3562 helix: 1.88 (0.20), residues: 693 sheet: 0.22 (0.17), residues: 849 loop : -1.13 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 436 HIS 0.004 0.001 HIS A1058 PHE 0.023 0.002 PHE D 400 TYR 0.026 0.001 TYR A 351 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 147 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (t80) REVERT: A 921 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8412 (mttt) REVERT: B 105 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 210 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6514 (tp) REVERT: B 902 MET cc_start: 0.8348 (tpt) cc_final: 0.7557 (tpt) REVERT: D 153 MET cc_start: 0.0210 (ptp) cc_final: -0.0578 (pmm) REVERT: D 265 TYR cc_start: 0.6910 (p90) cc_final: 0.6645 (p90) REVERT: D 565 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: D 580 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: D 673 SER cc_start: 0.8531 (p) cc_final: 0.8180 (m) REVERT: D 823 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: D 900 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8148 (mtt) outliers start: 103 outliers final: 74 residues processed: 233 average time/residue: 0.3701 time to fit residues: 143.9062 Evaluate side-chains 223 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 141 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 423 TYR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 921 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 565 PHE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 750 SER Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1145 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 205 optimal weight: 0.5980 chunk 103 optimal weight: 0.0060 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 32 optimal weight: 0.0170 chunk 270 optimal weight: 1.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 641 ASN A 690 GLN A 804 GLN A 935 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29374 Z= 0.152 Angle : 0.536 9.332 39976 Z= 0.277 Chirality : 0.045 0.435 4619 Planarity : 0.004 0.057 5133 Dihedral : 5.070 59.491 4860 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.62 % Allowed : 19.19 % Favored : 78.19 % 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: 3562 helix: 2.44 (0.21), residues: 667 sheet: 0.22 (0.17), residues: 856 loop : -1.00 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 436 HIS 0.005 0.001 HIS D 66 PHE 0.022 0.001 PHE D 400 TYR 0.022 0.001 TYR D1138 ARG 0.012 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 157 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 ASN cc_start: 0.8065 (t0) cc_final: 0.7745 (m-40) REVERT: B 210 ILE cc_start: 0.6809 (OUTLIER) cc_final: 0.6543 (tp) REVERT: B 646 ARG cc_start: 0.6696 (tpm170) cc_final: 0.6486 (tpm170) REVERT: B 902 MET cc_start: 0.8213 (tpt) cc_final: 0.7731 (tpt) REVERT: D 153 MET cc_start: -0.0165 (ptp) cc_final: -0.0856 (pmm) REVERT: D 265 TYR cc_start: 0.6655 (p90) cc_final: 0.6451 (p90) REVERT: D 673 SER cc_start: 0.8455 (p) cc_final: 0.8096 (m) REVERT: D 823 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 900 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8003 (mtt) outliers start: 82 outliers final: 55 residues processed: 222 average time/residue: 0.3705 time to fit residues: 140.4241 Evaluate side-chains 206 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 3.9990 chunk 329 optimal weight: 30.0000 chunk 300 optimal weight: 0.9980 chunk 320 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 319 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 690 GLN A1005 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29374 Z= 0.282 Angle : 0.589 9.358 39976 Z= 0.302 Chirality : 0.046 0.446 4619 Planarity : 0.005 0.058 5133 Dihedral : 5.188 58.856 4860 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 2.49 % Allowed : 19.60 % Favored : 77.90 % 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: -0.12 (0.14), residues: 3562 helix: 2.17 (0.21), residues: 673 sheet: 0.20 (0.17), residues: 865 loop : -1.02 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 436 HIS 0.005 0.001 HIS A1058 PHE 0.019 0.002 PHE A 338 TYR 0.023 0.001 TYR A1138 ARG 0.006 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 146 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6652 (tp) REVERT: D 153 MET cc_start: -0.0096 (ptp) cc_final: -0.0783 (pmm) REVERT: D 580 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7510 (mp-120) REVERT: D 673 SER cc_start: 0.8536 (p) cc_final: 0.8195 (m) REVERT: D 823 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: D 900 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8187 (mtt) outliers start: 78 outliers final: 63 residues processed: 212 average time/residue: 0.3624 time to fit residues: 130.8346 Evaluate side-chains 209 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 142 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.8980 chunk 339 optimal weight: 30.0000 chunk 206 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 355 optimal weight: 0.0000 chunk 327 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 218 optimal weight: 0.0070 chunk 173 optimal weight: 0.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A 613 GLN A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29374 Z= 0.149 Angle : 0.539 9.535 39976 Z= 0.277 Chirality : 0.044 0.439 4619 Planarity : 0.004 0.056 5133 Dihedral : 4.921 58.769 4860 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.69 % Rotamer: Outliers : 2.24 % Allowed : 20.15 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3562 helix: 2.38 (0.21), residues: 678 sheet: 0.29 (0.17), residues: 850 loop : -0.92 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 436 HIS 0.005 0.001 HIS D 66 PHE 0.019 0.001 PHE D 400 TYR 0.020 0.001 TYR D1138 ARG 0.005 0.000 ARG A 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7124 Ramachandran restraints generated. 3562 Oldfield, 0 Emsley, 3562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 161 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.6026 (mtm110) cc_final: 0.5783 (mtm110) REVERT: A 759 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7279 (t80) REVERT: A 900 MET cc_start: 0.8370 (mtp) cc_final: 0.8143 (mtp) REVERT: A 960 ASN cc_start: 0.8052 (t0) cc_final: 0.7735 (m-40) REVERT: B 105 ILE cc_start: 0.8695 (pt) cc_final: 0.8295 (mt) REVERT: B 210 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6615 (tp) REVERT: B 902 MET cc_start: 0.8177 (tpt) cc_final: 0.7864 (tpt) REVERT: D 153 MET cc_start: -0.0175 (ptp) cc_final: -0.0615 (pmm) REVERT: D 580 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7528 (mp-120) REVERT: D 673 SER cc_start: 0.8443 (p) cc_final: 0.8122 (m) REVERT: D 823 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: D 900 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8038 (mtt) outliers start: 70 outliers final: 55 residues processed: 216 average time/residue: 0.3566 time to fit residues: 130.3645 Evaluate side-chains 205 residues out of total 3127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 145 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 731 MET Chi-restraints excluded: chain D residue 784 GLN Chi-restraints excluded: chain D residue 804 GLN Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 912 THR Chi-restraints excluded: chain D residue 949 GLN Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1119 ASN Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain G residue 94 TYR Chi-restraints excluded: chain F residue 94 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 7.9990 chunk 301 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 283 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 291 optimal weight: 0.0980 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 690 GLN B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 GLN F 122 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.203887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.148628 restraints weight = 42520.600| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.68 r_work: 0.3594 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29374 Z= 0.222 Angle : 0.568 10.341 39976 Z= 0.290 Chirality : 0.045 0.450 4619 Planarity : 0.004 0.057 5133 Dihedral : 4.959 57.456 4860 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.21 % Allowed : 19.92 % Favored : 77.87 % 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: -0.01 (0.14), residues: 3562 helix: 2.30 (0.21), residues: 673 sheet: 0.31 (0.17), residues: 832 loop : -0.97 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 436 HIS 0.005 0.001 HIS A1058 PHE 0.017 0.002 PHE D 400 TYR 0.022 0.001 TYR A1138 ARG 0.004 0.000 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.33 seconds wall clock time: 98 minutes 54.01 seconds (5934.01 seconds total)