Starting phenix.real_space_refine on Tue Feb 20 03:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s6i_24876/02_2024/7s6i_24876.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 126 5.16 5 C 17013 2.51 5 N 4383 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26772 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "B" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "C" Number of atoms: 8616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8616 Classifications: {'peptide': 1103} Link IDs: {'PTRANS': 57, 'TRANS': 1045} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "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: "C" 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 Time building chain proxies: 14.37, per 1000 atoms: 0.54 Number of scatterers: 26772 At special positions: 0 Unit cell: (150.65, 146.05, 179.4, 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 126 16.00 O 5250 8.00 N 4383 7.00 C 17013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS B 985 " distance=2.15 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.09 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.08 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A 985 " - pdb=" SG CYS C 383 " distance=2.15 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.08 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS C 985 " distance=2.15 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 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=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 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=2.08 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.08 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.08 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 17 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 149 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 17 " " NAG B1306 " - " ASN B1134 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 149 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 343 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 17 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C1074 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 616 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN B 616 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 616 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " Time building additional restraints: 11.65 Conformation dependent library (CDL) restraints added in 4.9 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 25.3% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.878A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.245A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.502A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.160A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 147 through 150 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.879A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.246A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.503A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.159A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 147 through 150 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.919A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.878A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.246A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.693A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.503A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU C 959 " --> pdb=" O ASN C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.160A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.733A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.665A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.448A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.504A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.534A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.471A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.734A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 188 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 210 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR B 208 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE B 192 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS B 206 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE B 194 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR B 204 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN B 196 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS B 202 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.449A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.505A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.534A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.470A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.508A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.734A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.355A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.162A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.449A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.427A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.535A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.997A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.596A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.510A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1097 hydrogen bonds defined for protein. 2967 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: 13.30 Time building geometry restraints manager: 12.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5522 1.32 - 1.46: 9866 1.46 - 1.60: 11822 1.60 - 1.75: 33 1.75 - 1.89: 141 Bond restraints: 27384 Sorted by residual: bond pdb=" CB ILE C 312 " pdb=" CG1 ILE C 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CB ILE A 312 " pdb=" CG1 ILE A 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" CB ILE B 312 " pdb=" CG1 ILE B 312 " ideal model delta sigma weight residual 1.530 1.421 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" CB HIS B1058 " pdb=" CG HIS B1058 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.79e+01 bond pdb=" CB HIS A1058 " pdb=" CG HIS A1058 " ideal model delta sigma weight residual 1.497 1.423 0.074 1.40e-02 5.10e+03 2.77e+01 ... (remaining 27379 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.71: 868 105.71 - 112.87: 13462 112.87 - 120.04: 11427 120.04 - 127.21: 11347 127.21 - 134.38: 177 Bond angle restraints: 37281 Sorted by residual: angle pdb=" C LYS B 811 " pdb=" N PRO B 812 " pdb=" CA PRO B 812 " ideal model delta sigma weight residual 119.56 127.66 -8.10 1.02e+00 9.61e-01 6.30e+01 angle pdb=" C PRO C 862 " pdb=" N PRO C 863 " pdb=" CA PRO C 863 " ideal model delta sigma weight residual 120.03 127.87 -7.84 9.90e-01 1.02e+00 6.27e+01 angle pdb=" C LYS C 811 " pdb=" N PRO C 812 " pdb=" CA PRO C 812 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.02e+00 9.61e-01 6.26e+01 angle pdb=" C PRO B 862 " pdb=" N PRO B 863 " pdb=" CA PRO B 863 " ideal model delta sigma weight residual 120.03 127.86 -7.83 9.90e-01 1.02e+00 6.26e+01 angle pdb=" C LYS A 811 " pdb=" N PRO A 812 " pdb=" CA PRO A 812 " ideal model delta sigma weight residual 119.56 127.61 -8.05 1.02e+00 9.61e-01 6.23e+01 ... (remaining 37276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 16616 17.77 - 35.53: 394 35.53 - 53.30: 117 53.30 - 71.06: 42 71.06 - 88.83: 24 Dihedral angle restraints: 17193 sinusoidal: 7563 harmonic: 9630 Sorted by residual: dihedral pdb=" N PHE A 898 " pdb=" C PHE A 898 " pdb=" CA PHE A 898 " pdb=" CB PHE A 898 " ideal model delta harmonic sigma weight residual 122.80 130.62 -7.82 0 2.50e+00 1.60e-01 9.77e+00 dihedral pdb=" N PHE B 898 " pdb=" C PHE B 898 " pdb=" CA PHE B 898 " pdb=" CB PHE B 898 " ideal model delta harmonic sigma weight residual 122.80 130.59 -7.79 0 2.50e+00 1.60e-01 9.72e+00 dihedral pdb=" N PHE C 898 " pdb=" C PHE C 898 " pdb=" CA PHE C 898 " pdb=" CB PHE C 898 " ideal model delta harmonic sigma weight residual 122.80 130.57 -7.77 0 2.50e+00 1.60e-01 9.65e+00 ... (remaining 17190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3068 0.104 - 0.208: 983 0.208 - 0.312: 205 0.312 - 0.417: 89 0.417 - 0.521: 56 Chirality restraints: 4401 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 ... (remaining 4398 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " 0.066 2.00e-02 2.50e+03 7.01e-02 6.15e+01 pdb=" CG ASN B 17 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " -0.110 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 17 " 0.066 2.00e-02 2.50e+03 7.01e-02 6.13e+01 pdb=" CG ASN C 17 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 17 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 17 " -0.110 2.00e-02 2.50e+03 pdb=" C1 NAG C1305 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 17 " -0.066 2.00e-02 2.50e+03 6.99e-02 6.11e+01 pdb=" CG ASN A 17 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 17 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 17 " 0.110 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.085 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 10841 2.90 - 3.40: 24286 3.40 - 3.90: 45386 3.90 - 4.40: 53646 4.40 - 4.90: 86360 Nonbonded interactions: 220519 Sorted by model distance: nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.394 2.496 nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.395 2.496 nonbonded pdb=" N PRO C 600 " pdb=" O PRO C 600 " model vdw 2.395 2.496 nonbonded pdb=" OE1 GLU C 340 " pdb=" NZ LYS C 356 " model vdw 2.415 2.520 nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.415 2.520 ... (remaining 220514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 13.430 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 76.730 Find NCS groups from input model: 1.640 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.022 0.146 27384 Z= 1.424 Angle : 1.734 12.084 37281 Z= 1.167 Chirality : 0.124 0.521 4401 Planarity : 0.008 0.049 4749 Dihedral : 9.814 88.826 10863 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 0.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 3285 helix: -0.36 (0.17), residues: 777 sheet: 1.39 (0.19), residues: 699 loop : 0.11 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.009 TRP A 886 HIS 0.009 0.002 HIS A 66 PHE 0.038 0.005 PHE B 58 TYR 0.063 0.009 TYR B 837 ARG 0.009 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 369 time to evaluate : 3.207 Fit side-chains REVERT: B 900 MET cc_start: 0.8617 (mtp) cc_final: 0.8377 (mtm) outliers start: 3 outliers final: 0 residues processed: 372 average time/residue: 0.4568 time to fit residues: 254.9953 Evaluate side-chains 135 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 133 optimal weight: 0.7980 chunk 258 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN B 354 ASN B 914 ASN C 354 ASN C 804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27384 Z= 0.218 Angle : 0.654 10.694 37281 Z= 0.348 Chirality : 0.047 0.277 4401 Planarity : 0.004 0.031 4749 Dihedral : 5.736 51.578 4944 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.92 % Favored : 97.99 % Rotamer: Outliers : 1.07 % Allowed : 4.15 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3285 helix: 1.10 (0.19), residues: 780 sheet: 0.85 (0.19), residues: 696 loop : -0.16 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 886 HIS 0.004 0.001 HIS C 66 PHE 0.017 0.002 PHE A 55 TYR 0.020 0.002 TYR B1067 ARG 0.008 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 LEU cc_start: 0.7632 (mt) cc_final: 0.7316 (mp) REVERT: B 994 ASP cc_start: 0.7885 (t0) cc_final: 0.7659 (t0) REVERT: C 979 ASP cc_start: 0.7720 (m-30) cc_final: 0.7505 (m-30) REVERT: C 988 GLU cc_start: 0.7897 (tp30) cc_final: 0.7621 (tp30) REVERT: C 994 ASP cc_start: 0.7776 (t70) cc_final: 0.7553 (t70) outliers start: 31 outliers final: 15 residues processed: 220 average time/residue: 0.3731 time to fit residues: 134.3029 Evaluate side-chains 155 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 901 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 324 optimal weight: 0.9990 chunk 267 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1048 HIS B1048 HIS C1048 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27384 Z= 0.405 Angle : 0.678 14.019 37281 Z= 0.349 Chirality : 0.049 0.297 4401 Planarity : 0.005 0.055 4749 Dihedral : 5.694 48.388 4944 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 1.49 % Allowed : 5.02 % Favored : 93.49 % 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: 3285 helix: 1.11 (0.19), residues: 759 sheet: 0.43 (0.18), residues: 765 loop : -0.59 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 886 HIS 0.009 0.002 HIS A 66 PHE 0.020 0.002 PHE C 275 TYR 0.025 0.002 TYR A 495 ARG 0.011 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 3.100 Fit side-chains REVERT: A 569 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8734 (mp) REVERT: A 1001 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8698 (tt) REVERT: A 1029 MET cc_start: 0.8687 (tpp) cc_final: 0.8398 (ttm) REVERT: B 994 ASP cc_start: 0.8033 (t0) cc_final: 0.7821 (t0) outliers start: 43 outliers final: 26 residues processed: 178 average time/residue: 0.3619 time to fit residues: 110.9679 Evaluate side-chains 155 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 828 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 0.0170 chunk 225 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 201 optimal weight: 0.9990 chunk 301 optimal weight: 0.0070 chunk 318 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A1142 GLN C1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27384 Z= 0.151 Angle : 0.543 13.358 37281 Z= 0.276 Chirality : 0.044 0.252 4401 Planarity : 0.004 0.034 4749 Dihedral : 5.139 51.074 4944 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.37 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 6.09 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3285 helix: 1.48 (0.19), residues: 759 sheet: 0.46 (0.18), residues: 741 loop : -0.60 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE B 55 TYR 0.016 0.001 TYR B1067 ARG 0.011 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8715 (tpp) cc_final: 0.8310 (ttm) REVERT: C 556 ASN cc_start: 0.7792 (t0) cc_final: 0.7525 (t0) outliers start: 36 outliers final: 18 residues processed: 173 average time/residue: 0.3725 time to fit residues: 107.2381 Evaluate side-chains 139 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27384 Z= 0.346 Angle : 0.619 15.305 37281 Z= 0.313 Chirality : 0.047 0.280 4401 Planarity : 0.004 0.043 4749 Dihedral : 5.247 48.528 4944 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.70 % Allowed : 6.51 % Favored : 91.80 % 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: 3285 helix: 1.38 (0.19), residues: 759 sheet: 0.18 (0.18), residues: 756 loop : -0.76 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 886 HIS 0.006 0.001 HIS C1064 PHE 0.016 0.002 PHE B 898 TYR 0.020 0.002 TYR A1067 ARG 0.008 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 3.003 Fit side-chains REVERT: C 111 ASP cc_start: 0.6972 (t70) cc_final: 0.6754 (t0) REVERT: C 556 ASN cc_start: 0.7813 (t0) cc_final: 0.7555 (t0) outliers start: 49 outliers final: 39 residues processed: 170 average time/residue: 0.3578 time to fit residues: 102.9440 Evaluate side-chains 169 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 886 TRP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 319 optimal weight: 0.0770 chunk 265 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 167 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 ASN A1142 GLN B 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27384 Z= 0.151 Angle : 0.529 14.034 37281 Z= 0.266 Chirality : 0.044 0.251 4401 Planarity : 0.004 0.036 4749 Dihedral : 4.881 50.360 4944 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 1.07 % Allowed : 7.30 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3285 helix: 1.64 (0.20), residues: 759 sheet: 0.36 (0.19), residues: 711 loop : -0.78 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 886 HIS 0.003 0.001 HIS A 66 PHE 0.012 0.001 PHE A1121 TYR 0.016 0.001 TYR A1067 ARG 0.006 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 3.149 Fit side-chains REVERT: A 1029 MET cc_start: 0.8755 (tpp) cc_final: 0.8129 (ttm) REVERT: B 675 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7439 (pp30) REVERT: C 111 ASP cc_start: 0.6927 (t70) cc_final: 0.6666 (t0) REVERT: C 556 ASN cc_start: 0.7857 (t0) cc_final: 0.7617 (t0) outliers start: 31 outliers final: 23 residues processed: 167 average time/residue: 0.3425 time to fit residues: 98.4421 Evaluate side-chains 154 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 268 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN B 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 27384 Z= 0.389 Angle : 0.621 16.165 37281 Z= 0.312 Chirality : 0.047 0.287 4401 Planarity : 0.004 0.048 4749 Dihedral : 5.150 48.467 4944 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.70 % Allowed : 6.96 % Favored : 91.35 % 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: -0.13 (0.14), residues: 3285 helix: 1.43 (0.19), residues: 759 sheet: 0.09 (0.18), residues: 747 loop : -0.82 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 886 HIS 0.006 0.001 HIS C1064 PHE 0.016 0.002 PHE B 238 TYR 0.020 0.002 TYR A1067 ARG 0.004 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 2.788 Fit side-chains REVERT: A 1029 MET cc_start: 0.8887 (tpp) cc_final: 0.8142 (ttm) REVERT: B 675 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7515 (pp30) REVERT: C 111 ASP cc_start: 0.7080 (t70) cc_final: 0.6851 (t0) REVERT: C 556 ASN cc_start: 0.7923 (t0) cc_final: 0.7688 (t0) outliers start: 49 outliers final: 38 residues processed: 170 average time/residue: 0.3393 time to fit residues: 98.2738 Evaluate side-chains 169 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 130 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 216 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 250 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 556 ASN A 779 GLN C 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27384 Z= 0.192 Angle : 0.539 15.038 37281 Z= 0.269 Chirality : 0.044 0.261 4401 Planarity : 0.004 0.039 4749 Dihedral : 4.870 49.936 4944 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 1.25 % Allowed : 7.48 % Favored : 91.28 % 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: -0.04 (0.14), residues: 3285 helix: 1.63 (0.19), residues: 759 sheet: 0.28 (0.19), residues: 714 loop : -0.89 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 886 HIS 0.004 0.001 HIS A 66 PHE 0.013 0.001 PHE A1121 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 3.028 Fit side-chains REVERT: A 1029 MET cc_start: 0.8757 (tpp) cc_final: 0.8097 (ttm) REVERT: B 675 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: C 111 ASP cc_start: 0.6899 (t70) cc_final: 0.6668 (t0) REVERT: C 556 ASN cc_start: 0.7870 (t0) cc_final: 0.7619 (t0) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 0.3463 time to fit residues: 96.9286 Evaluate side-chains 157 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 3.9990 chunk 304 optimal weight: 0.0570 chunk 278 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1142 GLN C 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27384 Z= 0.334 Angle : 0.588 16.011 37281 Z= 0.295 Chirality : 0.046 0.278 4401 Planarity : 0.004 0.040 4749 Dihedral : 4.992 49.124 4944 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.45 % Allowed : 7.34 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3285 helix: 1.55 (0.19), residues: 762 sheet: 0.06 (0.18), residues: 753 loop : -0.88 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 886 HIS 0.005 0.001 HIS C1064 PHE 0.014 0.002 PHE B 238 TYR 0.019 0.001 TYR A1067 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 2.934 Fit side-chains REVERT: A 1029 MET cc_start: 0.8830 (tpp) cc_final: 0.8098 (ttm) REVERT: B 197 ILE cc_start: 0.8793 (mm) cc_final: 0.8588 (mm) REVERT: B 675 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7518 (pp30) REVERT: C 111 ASP cc_start: 0.6982 (t70) cc_final: 0.6757 (t0) REVERT: C 556 ASN cc_start: 0.7837 (t0) cc_final: 0.7637 (t0) outliers start: 42 outliers final: 37 residues processed: 164 average time/residue: 0.3610 time to fit residues: 100.5286 Evaluate side-chains 166 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 607 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.0040 chunk 313 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 328 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 202 optimal weight: 0.0770 chunk 160 optimal weight: 2.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A1142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27384 Z= 0.162 Angle : 0.527 14.419 37281 Z= 0.265 Chirality : 0.044 0.258 4401 Planarity : 0.004 0.039 4749 Dihedral : 4.788 50.042 4944 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 1.07 % Allowed : 7.75 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3285 helix: 1.72 (0.19), residues: 762 sheet: 0.27 (0.19), residues: 714 loop : -0.90 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 886 HIS 0.003 0.001 HIS C 66 PHE 0.013 0.001 PHE A1121 TYR 0.017 0.001 TYR A1067 ARG 0.005 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 3.385 Fit side-chains REVERT: A 1029 MET cc_start: 0.8755 (tpp) cc_final: 0.8070 (ttm) REVERT: B 675 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7538 (pp30) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.3531 time to fit residues: 95.9406 Evaluate side-chains 162 residues out of total 2889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 481 ASN Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 269 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085547 restraints weight = 48041.131| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.48 r_work: 0.3105 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 27384 Z= 0.227 Angle : 0.663 59.168 37281 Z= 0.360 Chirality : 0.045 0.564 4401 Planarity : 0.004 0.039 4749 Dihedral : 4.787 50.047 4944 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.14 % Favored : 96.77 % Rotamer: Outliers : 1.25 % Allowed : 7.82 % Favored : 90.93 % Cbeta Deviations : 0.03 % 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: 3285 helix: 1.71 (0.19), residues: 762 sheet: 0.27 (0.19), residues: 714 loop : -0.90 (0.13), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 886 HIS 0.003 0.001 HIS C 66 PHE 0.012 0.001 PHE A1121 TYR 0.017 0.001 TYR A1067 ARG 0.004 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.29 seconds wall clock time: 92 minutes 33.56 seconds (5553.56 seconds total)