Starting phenix.real_space_refine on Tue Feb 20 05:07:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb4_25792/02_2024/7tb4_25792.pdb" } resolution = 3.29 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= 0.030 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 119 5.16 5 C 17138 2.51 5 N 4416 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 718": "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: 26897 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8601 Classifications: {'peptide': 1097} Link IDs: {'PTRANS': 57, 'TRANS': 1039} Chain breaks: 2 Chain: "B" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8715 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 2 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.48, per 1000 atoms: 0.50 Number of scatterers: 26897 At special positions: 0 Unit cell: (157.32, 153.045, 198.36, 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 119 16.00 O 5224 8.00 N 4416 7.00 C 17138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 234 " " NAG A1310 " - " ASN A 616 " " NAG A1311 " - " ASN A 603 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 61 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 343 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 234 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 122 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1074 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG L 1 " - " ASN B1134 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C1098 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 331 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 10.39 Conformation dependent library (CDL) restraints added in 5.4 seconds 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6238 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 54 sheets defined 22.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.956A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.615A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.335A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 620 through 625 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: 4.135A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.508A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.510A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.232A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.711A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.128A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.688A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.903A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.567A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.689A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.514A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.515A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.617A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.596A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.749A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.606A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.229A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 4.472A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.941A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.946A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B1004 " --> pdb=" O ARG B1000 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.024A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.032A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.515A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 4.273A pdb=" N TYR C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 757 removed outlier: 4.155A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 754 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.693A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.951A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 removed outlier: 3.505A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.664A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.542A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.133A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.006A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C1006 " --> pdb=" O GLN C1002 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.242A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.853A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.606A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.737A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.737A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N HIS A 146 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 312 removed outlier: 4.650A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 7.772A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 541 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 380 removed outlier: 3.509A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.649A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.103A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.212A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 722 removed outlier: 6.128A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.903A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.409A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.522A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.622A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.673A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.208A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.679A pdb=" N SER B 116 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.692A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.932A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 539 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.080A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.816A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 713 removed outlier: 3.885A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 719 Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 719 removed outlier: 3.643A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.222A 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 removed outlier: 3.628A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.947A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.605A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.490A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.677A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE7, first strand: chain 'C' and resid 133 through 135 removed outlier: 4.781A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 141 through 146 removed outlier: 3.547A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.038A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.510A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.757A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.757A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 712 through 722 removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AF8, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF9, first strand: chain 'C' and resid 1094 through 1097 828 hydrogen bonds defined for protein. 2265 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: 11.45 Time building geometry restraints manager: 11.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8544 1.35 - 1.48: 7227 1.48 - 1.61: 11602 1.61 - 1.73: 0 1.73 - 1.86: 149 Bond restraints: 27522 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.63e+00 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 27517 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.87: 832 106.87 - 113.70: 15267 113.70 - 120.54: 10200 120.54 - 127.37: 10922 127.37 - 134.21: 236 Bond angle restraints: 37457 Sorted by residual: angle pdb=" N ILE C 332 " pdb=" CA ILE C 332 " pdb=" C ILE C 332 " ideal model delta sigma weight residual 107.18 113.37 -6.19 1.73e+00 3.34e-01 1.28e+01 angle pdb=" C ASN C 717 " pdb=" CA ASN C 717 " pdb=" CB ASN C 717 " ideal model delta sigma weight residual 113.33 105.68 7.65 2.26e+00 1.96e-01 1.15e+01 angle pdb=" N THR C 333 " pdb=" CA THR C 333 " pdb=" C THR C 333 " ideal model delta sigma weight residual 110.91 114.81 -3.90 1.17e+00 7.31e-01 1.11e+01 angle pdb=" C ASN C 717 " pdb=" N PHE C 718 " pdb=" CA PHE C 718 " ideal model delta sigma weight residual 121.62 127.43 -5.81 1.83e+00 2.99e-01 1.01e+01 angle pdb=" N ASN C 370 " pdb=" CA ASN C 370 " pdb=" C ASN C 370 " ideal model delta sigma weight residual 112.57 109.06 3.51 1.13e+00 7.83e-01 9.64e+00 ... (remaining 37452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 16109 24.76 - 49.51: 905 49.51 - 74.27: 127 74.27 - 99.03: 30 99.03 - 123.78: 7 Dihedral angle restraints: 17178 sinusoidal: 7473 harmonic: 9705 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 8.81 84.19 1 1.00e+01 1.00e-02 8.63e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -17.46 -68.54 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 159.19 -66.19 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 17175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3828 0.073 - 0.146: 550 0.146 - 0.219: 16 0.219 - 0.292: 1 0.292 - 0.365: 3 Chirality restraints: 4398 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4395 not shown) Planarity restraints: 4815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.001 2.00e-02 2.50e+03 4.23e-02 2.23e+01 pdb=" CG ASN A 603 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 298 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU B 298 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU B 298 " 0.023 2.00e-02 2.50e+03 pdb=" N THR B 299 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 224 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 225 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 225 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 225 " -0.033 5.00e-02 4.00e+02 ... (remaining 4812 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1145 2.72 - 3.26: 26105 3.26 - 3.81: 40154 3.81 - 4.35: 47911 4.35 - 4.90: 85175 Nonbonded interactions: 200490 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.173 2.440 nonbonded pdb=" O GLY A 72 " pdb=" OG1 THR A 76 " model vdw 2.207 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O ASN A 450 " model vdw 2.211 2.440 nonbonded pdb=" O CYS A 617 " pdb=" OG1 THR A 618 " model vdw 2.212 2.440 nonbonded pdb=" O CYS C 15 " pdb=" N ASN C 17 " model vdw 2.220 2.520 ... (remaining 200485 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 213 or resid 215 through 676 or resid 691 throu \ gh 1145 or resid 1301 through 1308)) selection = (chain 'B' and (resid 14 through 676 or resid 691 through 827 or resid 848 throu \ gh 1145 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 213 or resid 215 through 676 or resid 691 throu \ gh 827 or resid 848 through 1145 or resid 1301 through 1308)) } 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' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.850 Check model and map are aligned: 0.000 Set scattering table: 0.100 Process input model: 71.610 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 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 : 0.003 0.069 27522 Z= 0.226 Angle : 0.612 8.645 37457 Z= 0.307 Chirality : 0.047 0.365 4398 Planarity : 0.004 0.060 4771 Dihedral : 14.803 123.783 10817 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.12 % Favored : 92.60 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3313 helix: 1.75 (0.22), residues: 632 sheet: -0.57 (0.21), residues: 632 loop : -1.84 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.000 HIS B1101 PHE 0.017 0.001 PHE B 906 TYR 0.013 0.001 TYR C1067 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8716 (m-80) cc_final: 0.8493 (m-80) REVERT: A 595 VAL cc_start: 0.7189 (p) cc_final: 0.6823 (p) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.4146 time to fit residues: 120.9842 Evaluate side-chains 100 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 279 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 259 optimal weight: 0.0270 chunk 100 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1002 GLN C 81 ASN C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27522 Z= 0.227 Angle : 0.592 9.740 37457 Z= 0.304 Chirality : 0.045 0.258 4398 Planarity : 0.004 0.072 4771 Dihedral : 9.316 112.222 4824 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.70 % Favored : 92.06 % Rotamer: Outliers : 0.48 % Allowed : 6.85 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3313 helix: 1.92 (0.22), residues: 652 sheet: -0.51 (0.21), residues: 634 loop : -1.84 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.014 0.001 PHE B 833 TYR 0.025 0.001 TYR A 369 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.7362 (tpp) cc_final: 0.7097 (ttm) outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 0.3778 time to fit residues: 68.6782 Evaluate side-chains 87 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 167 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 204 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 301 optimal weight: 20.0000 chunk 325 optimal weight: 4.9990 chunk 268 optimal weight: 0.0370 chunk 298 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 overall best weight: 2.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 81 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27522 Z= 0.243 Angle : 0.566 9.253 37457 Z= 0.290 Chirality : 0.044 0.265 4398 Planarity : 0.004 0.069 4771 Dihedral : 7.933 106.720 4824 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.46 % Favored : 92.27 % Rotamer: Outliers : 0.83 % Allowed : 9.99 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3313 helix: 2.01 (0.21), residues: 654 sheet: -0.48 (0.21), residues: 651 loop : -1.85 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 258 HIS 0.004 0.001 HIS A1088 PHE 0.026 0.001 PHE B 759 TYR 0.015 0.001 TYR A 369 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7965 (tpt-90) cc_final: 0.7570 (mmm-85) outliers start: 24 outliers final: 11 residues processed: 103 average time/residue: 0.3894 time to fit residues: 67.1901 Evaluate side-chains 89 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 297 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 319 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27522 Z= 0.361 Angle : 0.613 9.184 37457 Z= 0.315 Chirality : 0.045 0.272 4398 Planarity : 0.004 0.066 4771 Dihedral : 7.393 104.082 4824 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.39 % Favored : 91.34 % Rotamer: Outliers : 1.34 % Allowed : 12.09 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3313 helix: 1.89 (0.21), residues: 655 sheet: -0.54 (0.21), residues: 639 loop : -1.91 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.003 0.001 HIS B1064 PHE 0.020 0.001 PHE B 759 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 82 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7757 (p0) REVERT: B 129 LYS cc_start: 0.7624 (tptp) cc_final: 0.7219 (tptp) outliers start: 39 outliers final: 15 residues processed: 115 average time/residue: 0.3715 time to fit residues: 72.0027 Evaluate side-chains 89 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 221 optimal weight: 0.0470 chunk 0 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 overall best weight: 3.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN B 165 ASN B 207 HIS B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 81 ASN C 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27522 Z= 0.303 Angle : 0.582 9.284 37457 Z= 0.300 Chirality : 0.044 0.276 4398 Planarity : 0.004 0.061 4771 Dihedral : 7.069 103.215 4824 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.70 % Favored : 92.03 % Rotamer: Outliers : 1.55 % Allowed : 14.19 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3313 helix: 1.97 (0.21), residues: 655 sheet: -0.61 (0.21), residues: 644 loop : -1.87 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS A1088 PHE 0.023 0.001 PHE C 133 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 75 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7714 (p0) REVERT: B 129 LYS cc_start: 0.7535 (tptp) cc_final: 0.7236 (tptp) REVERT: C 660 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6902 (p90) outliers start: 45 outliers final: 23 residues processed: 112 average time/residue: 0.3673 time to fit residues: 69.4948 Evaluate side-chains 98 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 73 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 869 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 107 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 320 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 168 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27522 Z= 0.167 Angle : 0.554 11.307 37457 Z= 0.283 Chirality : 0.045 0.366 4398 Planarity : 0.004 0.060 4771 Dihedral : 6.697 102.626 4824 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.52 % Favored : 92.24 % Rotamer: Outliers : 1.24 % Allowed : 14.88 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.14), residues: 3313 helix: 2.16 (0.21), residues: 655 sheet: -0.44 (0.21), residues: 649 loop : -1.81 (0.13), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.000 HIS A1088 PHE 0.038 0.001 PHE B 759 TYR 0.017 0.001 TYR C1067 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 78 time to evaluate : 2.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 759 PHE cc_start: 0.6656 (m-80) cc_final: 0.6387 (m-80) REVERT: B 121 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7902 (p0) REVERT: B 129 LYS cc_start: 0.7545 (tptp) cc_final: 0.7209 (tptp) REVERT: C 660 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.6754 (p90) outliers start: 36 outliers final: 20 residues processed: 110 average time/residue: 0.3462 time to fit residues: 65.8322 Evaluate side-chains 95 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 308 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 269 optimal weight: 40.0000 chunk 178 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27522 Z= 0.299 Angle : 0.590 10.666 37457 Z= 0.301 Chirality : 0.045 0.322 4398 Planarity : 0.004 0.058 4771 Dihedral : 6.528 102.362 4824 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.06 % Favored : 91.67 % Rotamer: Outliers : 1.72 % Allowed : 15.29 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3313 helix: 2.07 (0.21), residues: 661 sheet: -0.52 (0.21), residues: 622 loop : -1.81 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS B1064 PHE 0.019 0.001 PHE B 759 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 71 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7920 (p0) REVERT: B 129 LYS cc_start: 0.7559 (tptp) cc_final: 0.7283 (tptp) REVERT: C 660 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6786 (p90) outliers start: 50 outliers final: 28 residues processed: 116 average time/residue: 0.3612 time to fit residues: 72.9463 Evaluate side-chains 100 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 70 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 61 optimal weight: 0.0870 chunk 202 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27522 Z= 0.186 Angle : 0.552 11.281 37457 Z= 0.282 Chirality : 0.044 0.315 4398 Planarity : 0.004 0.059 4771 Dihedral : 6.265 101.331 4824 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.58 % Favored : 92.15 % Rotamer: Outliers : 1.52 % Allowed : 15.57 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.15), residues: 3313 helix: 2.15 (0.21), residues: 661 sheet: -0.50 (0.21), residues: 659 loop : -1.76 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.003 0.000 HIS A1088 PHE 0.029 0.001 PHE C 201 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 76 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7918 (p0) REVERT: B 129 LYS cc_start: 0.7568 (tptp) cc_final: 0.7355 (tptp) REVERT: C 660 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6640 (p90) outliers start: 44 outliers final: 29 residues processed: 116 average time/residue: 0.3510 time to fit residues: 70.0383 Evaluate side-chains 105 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 290 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 chunk 233 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 296 optimal weight: 2.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27522 Z= 0.200 Angle : 0.566 15.446 37457 Z= 0.286 Chirality : 0.044 0.323 4398 Planarity : 0.004 0.059 4771 Dihedral : 6.162 100.628 4824 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.67 % Favored : 92.03 % Rotamer: Outliers : 1.31 % Allowed : 16.33 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.15), residues: 3313 helix: 2.14 (0.21), residues: 660 sheet: -0.49 (0.21), residues: 659 loop : -1.77 (0.13), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 633 HIS 0.003 0.000 HIS A1088 PHE 0.027 0.001 PHE C 201 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 77 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 LYS cc_start: 0.7575 (tptp) cc_final: 0.7349 (tptp) REVERT: C 660 TYR cc_start: 0.7612 (OUTLIER) cc_final: 0.6662 (p90) outliers start: 38 outliers final: 30 residues processed: 112 average time/residue: 0.3616 time to fit residues: 70.0939 Evaluate side-chains 105 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 195 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 218 optimal weight: 0.2980 chunk 329 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 262 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 49 HIS ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27522 Z= 0.267 Angle : 0.588 14.231 37457 Z= 0.298 Chirality : 0.045 0.323 4398 Planarity : 0.004 0.058 4771 Dihedral : 6.158 100.128 4824 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.03 % Favored : 91.67 % Rotamer: Outliers : 1.24 % Allowed : 16.47 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.97 (0.15), residues: 3313 helix: 2.12 (0.21), residues: 661 sheet: -0.45 (0.21), residues: 622 loop : -1.77 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 633 HIS 0.003 0.001 HIS A1088 PHE 0.027 0.001 PHE C 201 TYR 0.022 0.001 TYR C1067 ARG 0.003 0.000 ARG C 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6626 Ramachandran restraints generated. 3313 Oldfield, 0 Emsley, 3313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 74 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 660 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6660 (p90) outliers start: 36 outliers final: 28 residues processed: 108 average time/residue: 0.3641 time to fit residues: 67.5389 Evaluate side-chains 101 residues out of total 2903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 823 PHE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 208 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 263 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.066713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.039242 restraints weight = 120984.642| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 5.22 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27522 Z= 0.290 Angle : 0.599 12.886 37457 Z= 0.304 Chirality : 0.045 0.325 4398 Planarity : 0.004 0.058 4771 Dihedral : 6.178 99.729 4824 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.27 % Favored : 91.43 % Rotamer: Outliers : 1.24 % Allowed : 16.64 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.99 (0.15), residues: 3313 helix: 2.10 (0.21), residues: 661 sheet: -0.50 (0.21), residues: 631 loop : -1.77 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 633 HIS 0.003 0.001 HIS B1064 PHE 0.025 0.001 PHE C 201 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG C 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4426.58 seconds wall clock time: 82 minutes 45.71 seconds (4965.71 seconds total)