Starting phenix.real_space_refine on Tue Apr 16 17:57:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlp_27509/04_2024/8dlp_27509.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 198 5.16 5 C 25572 2.51 5 N 6546 2.21 5 O 7779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40095 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8139 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 55, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 19.59, per 1000 atoms: 0.49 Number of scatterers: 40095 At special positions: 0 Unit cell: (179, 158, 237, 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 198 16.00 O 7779 8.00 N 6546 7.00 C 25572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.04 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 701 " - " ASN F 53 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 322 " " NAG F 705 " - " ASN F 432 " " NAG F 706 " - " ASN F 546 " " NAG G 1 " - " ASN A 17 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 17 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 17 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1074 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 14.84 Conformation dependent library (CDL) restraints added in 6.9 seconds 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9228 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 58 sheets defined 41.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.500A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.099A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.900A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.082A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.718A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.084A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.621A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.891A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.035A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.512A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.722A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.071A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.638A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.898A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.013A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.707A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.658A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.812A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.070A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.722A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.738A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.814A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.572A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.720A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.295A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.622A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.409A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.542A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.805A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.411A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.873A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.714A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.630A pdb=" N GLN E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.800A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 4.079A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 145 through 155 removed outlier: 3.775A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 194 Proline residue: E 178 - end of helix removed outlier: 3.714A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.753A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 removed outlier: 3.817A pdb=" N TYR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 324 through 331 removed outlier: 3.564A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.680A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 397 through 413 removed outlier: 4.235A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.617A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.431A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.507A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 removed outlier: 3.792A pdb=" N SER E 502 " --> pdb=" O ASP E 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 499 through 502' Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.436A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.884A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.713A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.631A pdb=" N GLN F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.809A pdb=" N GLU F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.085A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 Proline residue: F 178 - end of helix removed outlier: 3.705A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.685A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.799A pdb=" N TYR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 318 Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.567A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.711A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 397 through 413 removed outlier: 4.250A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.601A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 465 removed outlier: 4.430A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.530A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 removed outlier: 3.789A pdb=" N SER F 502 " --> pdb=" O ASP F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 499 through 502' Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 533 removed outlier: 4.430A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.841A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.149A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.012A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.664A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 11.350A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.154A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.233A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.548A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.572A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.664A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 4.993A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.420A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.919A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.776A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.310A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.652A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.145A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.046A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.194A pdb=" N TYR B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N PHE B 157 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.669A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.744A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.261A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.069A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.787A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.759A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.507A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.065A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.544A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.208A pdb=" N TYR C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N PHE C 157 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 11.539A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.544A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.679A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.258A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.871A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.502A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.058A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.363A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.003A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.350A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 131 through 132 removed outlier: 3.669A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.068A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.369A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1959 hydrogen bonds defined for protein. 5532 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: 17.80 Time building geometry restraints manager: 16.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12627 1.34 - 1.47: 10498 1.47 - 1.59: 17666 1.59 - 1.72: 0 1.72 - 1.84: 288 Bond restraints: 41079 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1 NAG F 702 " pdb=" O5 NAG F 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.98e+00 bond pdb=" C1 NAG E 702 " pdb=" O5 NAG E 702 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.56e+00 ... (remaining 41074 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.12: 1101 106.12 - 113.10: 21776 113.10 - 120.09: 14506 120.09 - 127.07: 17974 127.07 - 134.06: 521 Bond angle restraints: 55878 Sorted by residual: angle pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " pdb=" CG TYR B 495 " ideal model delta sigma weight residual 113.90 123.16 -9.26 1.80e+00 3.09e-01 2.65e+01 angle pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " pdb=" CG TYR A 495 " ideal model delta sigma weight residual 113.90 122.79 -8.89 1.80e+00 3.09e-01 2.44e+01 angle pdb=" CA TYR C 495 " pdb=" CB TYR C 495 " pdb=" CG TYR C 495 " ideal model delta sigma weight residual 113.90 122.59 -8.69 1.80e+00 3.09e-01 2.33e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.22 -5.52 1.22e+00 6.72e-01 2.05e+01 angle pdb=" C SER C 359 " pdb=" N ASN C 360 " pdb=" CA ASN C 360 " ideal model delta sigma weight residual 122.82 129.24 -6.42 1.42e+00 4.96e-01 2.04e+01 ... (remaining 55873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 23260 17.72 - 35.44: 1699 35.44 - 53.16: 288 53.16 - 70.88: 93 70.88 - 88.60: 52 Dihedral angle restraints: 25392 sinusoidal: 11052 harmonic: 14340 Sorted by residual: dihedral pdb=" CA GLU E 145 " pdb=" C GLU E 145 " pdb=" N PRO E 146 " pdb=" CA PRO E 146 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CB CYS F 133 " pdb=" SG CYS F 133 " pdb=" SG CYS F 141 " pdb=" CB CYS F 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.22 -36.78 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS E 133 " pdb=" SG CYS E 133 " pdb=" SG CYS E 141 " pdb=" CB CYS E 141 " ideal model delta sinusoidal sigma weight residual -86.00 -49.70 -36.30 1 1.00e+01 1.00e-02 1.86e+01 ... (remaining 25389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4926 0.060 - 0.120: 1202 0.120 - 0.179: 214 0.179 - 0.239: 26 0.239 - 0.299: 4 Chirality restraints: 6372 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 6369 not shown) Planarity restraints: 7188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 169 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C ARG F 169 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG F 169 " -0.017 2.00e-02 2.50e+03 pdb=" N SER F 170 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " -0.030 2.00e-02 2.50e+03 1.90e-02 7.25e+00 pdb=" CG TYR B 495 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 169 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ARG D 169 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG D 169 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 170 " -0.015 2.00e-02 2.50e+03 ... (remaining 7185 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9955 2.80 - 3.33: 34919 3.33 - 3.85: 68717 3.85 - 4.38: 78818 4.38 - 4.90: 136249 Nonbonded interactions: 328658 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.276 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.294 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.314 2.440 ... (remaining 328653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 15.390 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 102.970 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 41079 Z= 0.300 Angle : 0.792 9.587 55878 Z= 0.431 Chirality : 0.054 0.299 6372 Planarity : 0.006 0.060 7128 Dihedral : 13.235 88.597 16020 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 0.12 % Allowed : 2.74 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 4854 helix: 0.49 (0.11), residues: 1751 sheet: 0.83 (0.18), residues: 747 loop : -0.79 (0.11), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 886 HIS 0.006 0.001 HIS D 378 PHE 0.027 0.002 PHE E 369 TYR 0.043 0.002 TYR B 495 ARG 0.008 0.001 ARG E 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 369 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.4380 (m-10) cc_final: 0.3847 (m-80) REVERT: A 532 ASN cc_start: 0.8558 (m-40) cc_final: 0.7980 (t0) REVERT: B 200 TYR cc_start: 0.8748 (m-10) cc_final: 0.8522 (t80) REVERT: B 378 LYS cc_start: 0.9219 (tptt) cc_final: 0.8879 (tptp) REVERT: B 387 LEU cc_start: 0.9029 (mt) cc_final: 0.8640 (mt) REVERT: B 517 LEU cc_start: 0.9274 (tt) cc_final: 0.9066 (mm) REVERT: C 1029 MET cc_start: 0.8751 (tpp) cc_final: 0.8402 (tpp) REVERT: D 117 ASN cc_start: 0.6612 (t0) cc_final: 0.6087 (p0) REVERT: D 269 ASP cc_start: 0.0773 (m-30) cc_final: 0.0561 (t0) REVERT: D 310 GLU cc_start: 0.4735 (mm-30) cc_final: 0.4103 (tm-30) REVERT: D 323 MET cc_start: 0.5366 (mmp) cc_final: 0.4113 (mmt) REVERT: D 332 MET cc_start: 0.2665 (ttp) cc_final: 0.1492 (ptm) REVERT: D 435 GLU cc_start: 0.1446 (mm-30) cc_final: 0.0575 (pt0) REVERT: D 577 LYS cc_start: 0.3685 (mtpt) cc_final: 0.2838 (pttm) REVERT: E 117 ASN cc_start: 0.7877 (t0) cc_final: 0.7666 (p0) REVERT: E 154 ASN cc_start: 0.6409 (m110) cc_final: 0.5824 (p0) REVERT: E 323 MET cc_start: 0.7588 (mmp) cc_final: 0.7359 (mmm) REVERT: E 332 MET cc_start: 0.5080 (ttp) cc_final: 0.4311 (ppp) REVERT: E 474 MET cc_start: 0.2080 (mmt) cc_final: 0.0453 (mmt) REVERT: F 234 LYS cc_start: 0.5297 (tttt) cc_final: 0.5020 (mttm) REVERT: F 291 ILE cc_start: 0.2581 (pt) cc_final: 0.2233 (mt) REVERT: F 383 MET cc_start: 0.2125 (mtp) cc_final: 0.0026 (tpt) REVERT: F 462 MET cc_start: 0.1806 (mtp) cc_final: 0.1602 (tpp) REVERT: F 480 MET cc_start: 0.3267 (mtp) cc_final: 0.2798 (mtt) REVERT: F 556 ASN cc_start: 0.6355 (m-40) cc_final: 0.6120 (p0) outliers start: 5 outliers final: 1 residues processed: 374 average time/residue: 1.7013 time to fit residues: 766.1844 Evaluate side-chains 184 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 383 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 444 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 519 HIS B 926 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS E 374 HIS ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 41079 Z= 0.286 Angle : 0.584 10.423 55878 Z= 0.300 Chirality : 0.044 0.292 6372 Planarity : 0.004 0.063 7128 Dihedral : 6.084 109.199 6911 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.41 % Allowed : 7.01 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 4854 helix: 1.48 (0.12), residues: 1775 sheet: 0.85 (0.18), residues: 737 loop : -0.54 (0.12), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 165 HIS 0.007 0.001 HIS D 505 PHE 0.019 0.002 PHE C 823 TYR 0.022 0.001 TYR A1067 ARG 0.014 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 3.370 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 532 ASN cc_start: 0.8707 (m-40) cc_final: 0.8222 (t0) REVERT: B 378 LYS cc_start: 0.9166 (tptt) cc_final: 0.8715 (tptp) REVERT: B 387 LEU cc_start: 0.8963 (mt) cc_final: 0.8633 (mt) REVERT: C 153 MET cc_start: 0.5977 (pp-130) cc_final: 0.5546 (ttm) REVERT: D 117 ASN cc_start: 0.6714 (t0) cc_final: 0.6148 (p0) REVERT: D 177 ARG cc_start: 0.0917 (tpt-90) cc_final: 0.0596 (ppt170) REVERT: D 310 GLU cc_start: 0.4624 (mm-30) cc_final: 0.4087 (tm-30) REVERT: D 332 MET cc_start: 0.2819 (ttp) cc_final: 0.1549 (ptm) REVERT: D 435 GLU cc_start: 0.1049 (mm-30) cc_final: 0.0437 (pt0) REVERT: D 510 TYR cc_start: -0.0112 (OUTLIER) cc_final: -0.0952 (m-80) REVERT: D 515 TYR cc_start: 0.0372 (m-80) cc_final: 0.0163 (m-80) REVERT: D 577 LYS cc_start: 0.3600 (mtpt) cc_final: 0.2792 (tttt) REVERT: E 332 MET cc_start: 0.5399 (ttp) cc_final: 0.4402 (ppp) REVERT: E 376 MET cc_start: 0.8402 (tpt) cc_final: 0.7025 (mmm) REVERT: E 383 MET cc_start: 0.8716 (tmm) cc_final: 0.7983 (mtm) REVERT: E 474 MET cc_start: 0.1638 (mmt) cc_final: 0.0788 (mmt) REVERT: F 234 LYS cc_start: 0.5512 (tttt) cc_final: 0.5177 (mttm) REVERT: F 291 ILE cc_start: 0.2778 (pt) cc_final: 0.2565 (mt) REVERT: F 295 ASP cc_start: 0.5960 (p0) cc_final: 0.5750 (m-30) REVERT: F 383 MET cc_start: 0.2328 (mtp) cc_final: 0.0728 (tpt) REVERT: F 462 MET cc_start: 0.1531 (mtp) cc_final: 0.1238 (tpp) REVERT: F 557 MET cc_start: 0.4227 (OUTLIER) cc_final: 0.3600 (ptm) outliers start: 61 outliers final: 14 residues processed: 219 average time/residue: 1.1732 time to fit residues: 314.5751 Evaluate side-chains 171 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 369 optimal weight: 20.0000 chunk 302 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 444 optimal weight: 10.0000 chunk 480 optimal weight: 30.0000 chunk 396 optimal weight: 5.9990 chunk 441 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 356 optimal weight: 20.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 824 ASN A 957 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 519 HIS B 755 GLN B 824 ASN B 926 GLN C 493 GLN C 824 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN E 552 GLN F 60 GLN F 96 GLN F 121 ASN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.131 41079 Z= 0.684 Angle : 0.780 11.869 55878 Z= 0.397 Chirality : 0.050 0.279 6372 Planarity : 0.005 0.073 7128 Dihedral : 6.456 83.226 6911 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.60 % Allowed : 9.19 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 4854 helix: 1.33 (0.12), residues: 1832 sheet: 0.39 (0.19), residues: 709 loop : -0.69 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 886 HIS 0.010 0.002 HIS A1083 PHE 0.028 0.003 PHE C 275 TYR 0.026 0.002 TYR C 265 ARG 0.011 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 169 time to evaluate : 4.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 ASN cc_start: 0.8863 (m-40) cc_final: 0.8444 (t0) REVERT: B 387 LEU cc_start: 0.8871 (mt) cc_final: 0.8544 (mt) REVERT: B 440 ASN cc_start: 0.9428 (OUTLIER) cc_final: 0.9164 (p0) REVERT: C 95 THR cc_start: 0.8089 (p) cc_final: 0.7879 (p) REVERT: C 153 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5605 (ttm) REVERT: D 117 ASN cc_start: 0.6461 (t0) cc_final: 0.5994 (p0) REVERT: D 310 GLU cc_start: 0.4575 (mm-30) cc_final: 0.3879 (tm-30) REVERT: D 332 MET cc_start: 0.2165 (ttp) cc_final: 0.1407 (ptm) REVERT: D 510 TYR cc_start: -0.0316 (OUTLIER) cc_final: -0.1210 (m-80) REVERT: D 555 PHE cc_start: 0.2498 (t80) cc_final: 0.2196 (t80) REVERT: D 577 LYS cc_start: 0.3892 (mtpt) cc_final: 0.2885 (tmmt) REVERT: E 323 MET cc_start: 0.7566 (mmm) cc_final: 0.7020 (tpt) REVERT: E 332 MET cc_start: 0.6014 (ttp) cc_final: 0.4233 (tmt) REVERT: E 474 MET cc_start: 0.2372 (mmt) cc_final: 0.1451 (mmt) REVERT: F 140 GLU cc_start: -0.0959 (OUTLIER) cc_final: -0.1243 (tt0) REVERT: F 234 LYS cc_start: 0.5303 (tttt) cc_final: 0.5011 (tptt) REVERT: F 249 MET cc_start: 0.4829 (mmt) cc_final: 0.2613 (tmt) REVERT: F 291 ILE cc_start: 0.3177 (pt) cc_final: 0.2889 (mt) REVERT: F 383 MET cc_start: 0.2563 (mtp) cc_final: 0.1049 (tpt) REVERT: F 462 MET cc_start: 0.1809 (mtp) cc_final: 0.1581 (mpp) REVERT: F 480 MET cc_start: 0.4040 (ptp) cc_final: 0.3303 (tpp) outliers start: 69 outliers final: 23 residues processed: 213 average time/residue: 1.5994 time to fit residues: 421.0626 Evaluate side-chains 173 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 5.9990 chunk 334 optimal weight: 40.0000 chunk 230 optimal weight: 0.0670 chunk 49 optimal weight: 4.9990 chunk 212 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 446 optimal weight: 8.9990 chunk 472 optimal weight: 40.0000 chunk 233 optimal weight: 0.8980 chunk 423 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 907 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN F 60 GLN F 121 ASN F 374 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41079 Z= 0.187 Angle : 0.538 9.571 55878 Z= 0.275 Chirality : 0.042 0.283 6372 Planarity : 0.004 0.054 7128 Dihedral : 5.893 115.088 6911 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.53 % Allowed : 10.09 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.12), residues: 4854 helix: 1.76 (0.12), residues: 1826 sheet: 0.55 (0.18), residues: 723 loop : -0.51 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 566 HIS 0.005 0.001 HIS F 374 PHE 0.019 0.001 PHE C 823 TYR 0.021 0.001 TYR A1067 ARG 0.018 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 157 time to evaluate : 4.608 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 245 HIS cc_start: 0.7847 (m-70) cc_final: 0.7639 (t70) REVERT: A 532 ASN cc_start: 0.8821 (m-40) cc_final: 0.8315 (t0) REVERT: A 565 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.7008 (m-10) REVERT: B 440 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.9080 (p0) REVERT: C 153 MET cc_start: 0.6095 (pp-130) cc_final: 0.5621 (ttm) REVERT: D 117 ASN cc_start: 0.6533 (t0) cc_final: 0.6094 (p0) REVERT: D 310 GLU cc_start: 0.4614 (mm-30) cc_final: 0.3909 (tm-30) REVERT: D 332 MET cc_start: 0.1928 (ttp) cc_final: 0.1226 (ptm) REVERT: D 455 MET cc_start: 0.1339 (OUTLIER) cc_final: 0.0971 (tpt) REVERT: D 497 TYR cc_start: 0.3407 (OUTLIER) cc_final: 0.2979 (t80) REVERT: D 510 TYR cc_start: -0.0037 (OUTLIER) cc_final: -0.0828 (m-80) REVERT: D 555 PHE cc_start: 0.2377 (t80) cc_final: 0.2104 (t80) REVERT: D 577 LYS cc_start: 0.3869 (mtpt) cc_final: 0.2870 (ttpt) REVERT: E 323 MET cc_start: 0.7647 (mmm) cc_final: 0.6553 (tpt) REVERT: E 332 MET cc_start: 0.5902 (ttp) cc_final: 0.4230 (tmt) REVERT: E 383 MET cc_start: 0.8882 (tmm) cc_final: 0.8166 (mtm) REVERT: E 474 MET cc_start: 0.2074 (mmt) cc_final: 0.1627 (mmp) REVERT: E 579 MET cc_start: 0.2486 (OUTLIER) cc_final: 0.0883 (mtt) REVERT: F 140 GLU cc_start: -0.0840 (OUTLIER) cc_final: -0.1081 (tt0) REVERT: F 234 LYS cc_start: 0.5281 (tttt) cc_final: 0.5008 (tptt) REVERT: F 249 MET cc_start: 0.4802 (mmt) cc_final: 0.2668 (tmt) REVERT: F 291 ILE cc_start: 0.3227 (pt) cc_final: 0.2927 (mt) REVERT: F 383 MET cc_start: 0.2523 (mtp) cc_final: 0.0938 (tpt) REVERT: F 460 ARG cc_start: 0.0298 (mtm180) cc_final: -0.1127 (mmt-90) REVERT: F 462 MET cc_start: 0.1820 (mtp) cc_final: 0.1509 (mpp) REVERT: F 480 MET cc_start: 0.4258 (ptp) cc_final: 0.3134 (tpp) outliers start: 66 outliers final: 19 residues processed: 198 average time/residue: 1.4757 time to fit residues: 365.3538 Evaluate side-chains 169 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 5.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 20.0000 chunk 268 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 351 optimal weight: 30.0000 chunk 195 optimal weight: 1.9990 chunk 403 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 241 optimal weight: 2.9990 chunk 424 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 498 GLN C 907 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 535 HIS E 154 ASN E 330 ASN E 442 GLN F 60 GLN F 121 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 41079 Z= 0.538 Angle : 0.674 9.560 55878 Z= 0.340 Chirality : 0.047 0.282 6372 Planarity : 0.004 0.061 7128 Dihedral : 6.094 95.162 6911 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.06 % Allowed : 10.69 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.12), residues: 4854 helix: 1.60 (0.12), residues: 1820 sheet: 0.11 (0.19), residues: 684 loop : -0.57 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 566 HIS 0.007 0.002 HIS E 378 PHE 0.025 0.002 PHE C 823 TYR 0.032 0.002 TYR F 587 ARG 0.004 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 146 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.7756 (m-70) cc_final: 0.7488 (t-90) REVERT: A 532 ASN cc_start: 0.8917 (m-40) cc_final: 0.8514 (t0) REVERT: B 200 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8507 (t80) REVERT: B 440 ASN cc_start: 0.9408 (OUTLIER) cc_final: 0.9154 (p0) REVERT: C 100 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6969 (mp) REVERT: C 153 MET cc_start: 0.6206 (pp-130) cc_final: 0.5719 (ttm) REVERT: D 117 ASN cc_start: 0.6550 (t0) cc_final: 0.6094 (p0) REVERT: D 310 GLU cc_start: 0.4530 (mm-30) cc_final: 0.3687 (tm-30) REVERT: D 332 MET cc_start: 0.1970 (ttp) cc_final: 0.1270 (ptm) REVERT: D 358 ILE cc_start: -0.0565 (OUTLIER) cc_final: -0.1323 (mt) REVERT: D 455 MET cc_start: 0.1655 (OUTLIER) cc_final: 0.1289 (tpt) REVERT: D 497 TYR cc_start: 0.3294 (OUTLIER) cc_final: 0.2789 (t80) REVERT: D 510 TYR cc_start: -0.0137 (OUTLIER) cc_final: -0.1013 (m-80) REVERT: D 555 PHE cc_start: 0.2560 (t80) cc_final: 0.2221 (t80) REVERT: E 323 MET cc_start: 0.7661 (mmm) cc_final: 0.6946 (tpt) REVERT: E 383 MET cc_start: 0.8887 (tmm) cc_final: 0.8674 (ppp) REVERT: E 474 MET cc_start: 0.2476 (mmt) cc_final: 0.1634 (tpp) REVERT: E 510 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7614 (t80) REVERT: E 579 MET cc_start: 0.2820 (OUTLIER) cc_final: 0.0834 (mtp) REVERT: F 140 GLU cc_start: -0.0674 (OUTLIER) cc_final: -0.0893 (tt0) REVERT: F 208 GLU cc_start: 0.1144 (OUTLIER) cc_final: 0.0384 (tp30) REVERT: F 234 LYS cc_start: 0.5114 (tttt) cc_final: 0.4787 (mttm) REVERT: F 249 MET cc_start: 0.5246 (mmt) cc_final: 0.2897 (tmt) REVERT: F 291 ILE cc_start: 0.3108 (pt) cc_final: 0.2843 (mt) REVERT: F 383 MET cc_start: 0.2367 (mtp) cc_final: 0.0802 (tpt) REVERT: F 394 ASN cc_start: 0.1370 (OUTLIER) cc_final: 0.0555 (OUTLIER) REVERT: F 462 MET cc_start: 0.1751 (mtp) cc_final: 0.1500 (mpp) REVERT: F 480 MET cc_start: 0.4165 (ptp) cc_final: 0.2761 (mmm) outliers start: 89 outliers final: 28 residues processed: 209 average time/residue: 1.4075 time to fit residues: 370.9475 Evaluate side-chains 183 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 144 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 449 TYR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 0.8980 chunk 425 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 277 optimal weight: 0.0070 chunk 116 optimal weight: 10.0000 chunk 473 optimal weight: 30.0000 chunk 392 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 39 optimal weight: 40.0000 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1010 GLN C 907 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 121 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 41079 Z= 0.184 Angle : 0.530 11.151 55878 Z= 0.268 Chirality : 0.042 0.294 6372 Planarity : 0.004 0.064 7128 Dihedral : 5.555 71.810 6911 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.41 % Allowed : 11.88 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.12), residues: 4854 helix: 1.92 (0.12), residues: 1798 sheet: 0.32 (0.19), residues: 661 loop : -0.44 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 203 HIS 0.005 0.001 HIS E 378 PHE 0.019 0.001 PHE C 823 TYR 0.020 0.001 TYR A1067 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.7776 (m-70) cc_final: 0.7496 (t-90) REVERT: A 532 ASN cc_start: 0.8864 (m-40) cc_final: 0.8442 (t0) REVERT: A 565 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7231 (m-10) REVERT: B 200 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8405 (t80) REVERT: B 440 ASN cc_start: 0.9352 (OUTLIER) cc_final: 0.9041 (p0) REVERT: C 153 MET cc_start: 0.6221 (pp-130) cc_final: 0.5730 (ttm) REVERT: D 117 ASN cc_start: 0.6521 (t0) cc_final: 0.6072 (p0) REVERT: D 310 GLU cc_start: 0.4532 (mm-30) cc_final: 0.3723 (tm-30) REVERT: D 332 MET cc_start: 0.1921 (ttp) cc_final: 0.1193 (ptm) REVERT: D 358 ILE cc_start: -0.0155 (OUTLIER) cc_final: -0.0953 (mt) REVERT: D 455 MET cc_start: 0.1479 (OUTLIER) cc_final: 0.1045 (tpt) REVERT: D 510 TYR cc_start: -0.0155 (OUTLIER) cc_final: -0.1020 (m-80) REVERT: D 555 PHE cc_start: 0.2595 (t80) cc_final: 0.2268 (t80) REVERT: E 21 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6594 (pp) REVERT: E 323 MET cc_start: 0.7682 (mmm) cc_final: 0.6855 (ttt) REVERT: E 332 MET cc_start: 0.5589 (ttp) cc_final: 0.4258 (tmt) REVERT: E 455 MET cc_start: 0.2834 (tmt) cc_final: 0.2204 (pp-130) REVERT: E 474 MET cc_start: 0.2452 (mmt) cc_final: 0.1627 (tpp) REVERT: E 510 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7721 (t80) REVERT: E 579 MET cc_start: 0.2556 (OUTLIER) cc_final: 0.0541 (mtt) REVERT: F 208 GLU cc_start: 0.1429 (OUTLIER) cc_final: 0.0692 (tp30) REVERT: F 234 LYS cc_start: 0.5232 (tttt) cc_final: 0.4990 (ttmm) REVERT: F 249 MET cc_start: 0.5053 (mmt) cc_final: 0.2863 (tmt) REVERT: F 291 ILE cc_start: 0.3140 (pt) cc_final: 0.2884 (mt) REVERT: F 314 PHE cc_start: 0.1321 (t80) cc_final: 0.1115 (t80) REVERT: F 383 MET cc_start: 0.1911 (mtp) cc_final: 0.0385 (tpt) REVERT: F 394 ASN cc_start: 0.1368 (OUTLIER) cc_final: 0.0562 (OUTLIER) REVERT: F 462 MET cc_start: 0.1746 (mtp) cc_final: 0.1468 (mpp) REVERT: F 480 MET cc_start: 0.4103 (ptp) cc_final: 0.2924 (mmm) outliers start: 61 outliers final: 22 residues processed: 196 average time/residue: 1.5302 time to fit residues: 371.5705 Evaluate side-chains 173 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 394 ASN Chi-restraints excluded: chain F residue 417 HIS Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 269 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 chunk 267 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 471 optimal weight: 20.0000 chunk 294 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS D 524 GLN E 417 HIS F 121 ASN F 241 HIS ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 41079 Z= 0.470 Angle : 0.655 10.423 55878 Z= 0.330 Chirality : 0.046 0.297 6372 Planarity : 0.004 0.063 7128 Dihedral : 5.954 106.843 6911 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.69 % Allowed : 12.34 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.12), residues: 4854 helix: 1.69 (0.12), residues: 1816 sheet: 0.15 (0.19), residues: 678 loop : -0.57 (0.12), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 203 HIS 0.007 0.001 HIS E 378 PHE 0.024 0.002 PHE C 823 TYR 0.023 0.002 TYR C 265 ARG 0.010 0.001 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 160 time to evaluate : 4.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.7642 (m-70) cc_final: 0.7355 (t-90) REVERT: A 532 ASN cc_start: 0.9021 (m-40) cc_final: 0.8610 (t0) REVERT: A 565 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: B 440 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.9145 (p0) REVERT: C 100 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6998 (mp) REVERT: C 153 MET cc_start: 0.6366 (pp-130) cc_final: 0.5818 (ttm) REVERT: D 117 ASN cc_start: 0.6492 (t0) cc_final: 0.6032 (p0) REVERT: D 332 MET cc_start: 0.1688 (ttp) cc_final: 0.0990 (ptm) REVERT: D 455 MET cc_start: 0.1560 (OUTLIER) cc_final: 0.1194 (tpt) REVERT: D 510 TYR cc_start: -0.0106 (OUTLIER) cc_final: -0.0999 (m-80) REVERT: D 555 PHE cc_start: 0.2709 (t80) cc_final: 0.2350 (t80) REVERT: E 67 ASP cc_start: 0.8958 (m-30) cc_final: 0.8663 (t0) REVERT: E 267 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5079 (tp) REVERT: E 323 MET cc_start: 0.7734 (mmm) cc_final: 0.6778 (ttt) REVERT: E 376 MET cc_start: 0.8127 (tpt) cc_final: 0.6954 (tpp) REVERT: E 383 MET cc_start: 0.8386 (ppp) cc_final: 0.7724 (mtm) REVERT: E 408 MET cc_start: 0.8539 (mmp) cc_final: 0.8078 (mmm) REVERT: E 474 MET cc_start: 0.2236 (OUTLIER) cc_final: 0.2035 (tpp) REVERT: E 510 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7672 (t80) REVERT: E 579 MET cc_start: 0.2977 (OUTLIER) cc_final: 0.1021 (mtp) REVERT: F 196 TYR cc_start: 0.4502 (OUTLIER) cc_final: 0.4279 (m-10) REVERT: F 208 GLU cc_start: 0.1272 (OUTLIER) cc_final: 0.0576 (tp30) REVERT: F 249 MET cc_start: 0.5190 (mmt) cc_final: 0.2880 (tmt) REVERT: F 291 ILE cc_start: 0.3256 (pt) cc_final: 0.2978 (mt) REVERT: F 383 MET cc_start: 0.1875 (mtp) cc_final: 0.0393 (tpt) REVERT: F 480 MET cc_start: 0.4109 (ptp) cc_final: 0.3017 (mtt) outliers start: 73 outliers final: 30 residues processed: 213 average time/residue: 1.4065 time to fit residues: 376.8349 Evaluate side-chains 180 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 139 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 196 TYR Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 ASP Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 281 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 299 optimal weight: 0.7980 chunk 321 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 370 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN E 417 HIS F 60 GLN F 250 ASN ** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 41079 Z= 0.152 Angle : 0.540 13.599 55878 Z= 0.270 Chirality : 0.042 0.305 6372 Planarity : 0.004 0.064 7128 Dihedral : 5.400 83.521 6911 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.25 % Allowed : 13.06 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 4854 helix: 1.98 (0.12), residues: 1797 sheet: 0.33 (0.19), residues: 652 loop : -0.40 (0.12), residues: 2405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 566 HIS 0.004 0.001 HIS D 378 PHE 0.021 0.001 PHE F 314 TYR 0.020 0.001 TYR A1067 ARG 0.010 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9708 Ramachandran restraints generated. 4854 Oldfield, 0 Emsley, 4854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 156 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5324 (pmm) cc_final: 0.4966 (pmm) REVERT: A 245 HIS cc_start: 0.7708 (m-70) cc_final: 0.7416 (t-90) REVERT: A 532 ASN cc_start: 0.8943 (m-40) cc_final: 0.8522 (t0) REVERT: A 565 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7338 (m-10) REVERT: B 200 TYR cc_start: 0.8655 (t80) cc_final: 0.8349 (t80) REVERT: B 378 LYS cc_start: 0.9220 (tptt) cc_final: 0.8911 (tptp) REVERT: C 100 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6901 (mp) REVERT: C 153 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5824 (ttm) REVERT: D 117 ASN cc_start: 0.6453 (t0) cc_final: 0.6017 (p0) REVERT: D 310 GLU cc_start: 0.4532 (mm-30) cc_final: 0.3692 (tm-30) REVERT: D 332 MET cc_start: 0.1491 (ttp) cc_final: 0.0853 (ptm) REVERT: D 358 ILE cc_start: -0.0333 (OUTLIER) cc_final: -0.0854 (mm) REVERT: D 455 MET cc_start: 0.1545 (OUTLIER) cc_final: 0.1214 (tpt) REVERT: D 489 GLU cc_start: 0.1399 (pm20) cc_final: 0.0945 (pm20) REVERT: D 510 TYR cc_start: 0.0007 (OUTLIER) cc_final: -0.0870 (m-80) REVERT: D 555 PHE cc_start: 0.2746 (t80) cc_final: 0.2345 (t80) REVERT: E 267 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5126 (tp) REVERT: E 323 MET cc_start: 0.7605 (mmm) cc_final: 0.7305 (mtp) REVERT: E 383 MET cc_start: 0.8518 (ppp) cc_final: 0.7940 (mtm) REVERT: E 408 MET cc_start: 0.8491 (mmp) cc_final: 0.8190 (mmm) REVERT: E 455 MET cc_start: 0.2707 (tmt) cc_final: 0.2261 (ttp) REVERT: E 474 MET cc_start: 0.2426 (OUTLIER) cc_final: 0.1985 (tpp) REVERT: E 510 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7683 (t80) REVERT: E 579 MET cc_start: 0.2678 (OUTLIER) cc_final: 0.0581 (mtt) REVERT: E 600 LYS cc_start: 0.4347 (mmmt) cc_final: 0.2791 (mttt) REVERT: F 196 TYR cc_start: 0.4698 (OUTLIER) cc_final: 0.4478 (m-10) REVERT: F 208 GLU cc_start: 0.1328 (OUTLIER) cc_final: 0.0796 (tp30) REVERT: F 249 MET cc_start: 0.5117 (mmt) cc_final: 0.2939 (tmt) REVERT: F 291 ILE cc_start: 0.3232 (pt) cc_final: 0.2957 (mt) REVERT: F 332 MET cc_start: 0.1140 (ppp) cc_final: -0.1417 (mpm) REVERT: F 383 MET cc_start: 0.1919 (mtp) cc_final: 0.0365 (tpt) REVERT: F 460 ARG cc_start: 0.0327 (mtm180) cc_final: -0.1054 (mmt180) REVERT: F 480 MET cc_start: 0.3947 (ptp) cc_final: 0.3089 (mtt) outliers start: 54 outliers final: 22 residues processed: 195 average time/residue: 1.3797 time to fit residues: 336.2525 Evaluate side-chains 180 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 146 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain E residue 510 TYR Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 196 TYR Chi-restraints excluded: chain F residue 208 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 560 LEU Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 411 optimal weight: 10.0000 chunk 439 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 396 optimal weight: 8.9990 chunk 415 optimal weight: 7.9990 chunk 437 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: