Starting phenix.real_space_refine on Mon Mar 25 17:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xch_33120/03_2024/7xch_33120.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14449 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 172 5.16 5 C 22821 2.51 5 N 5857 2.21 5 O 6897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35749 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "B" Number of atoms: 8357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8357 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 59, 'TRANS': 1005} Chain breaks: 7 Chain: "C" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8336 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "E" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "Y" 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: "Z" 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: 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: "b" 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 22.61, per 1000 atoms: 0.63 Number of scatterers: 35749 At special positions: 0 Unit cell: (172.92, 143.22, 242.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 172 16.00 O 6897 8.00 N 5857 7.00 C 22821 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=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A 616 " " 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 B1074 " " NAG B1308 " - " ASN B 616 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 616 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 103 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 53 " " NAG E 704 " - " ASN E 90 " " NAG E 705 " - " ASN E 322 " " NAG E 706 " - " ASN E 103 " " NAG F 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN D 546 " " NAG b 1 " - " ASN E 546 " Time building additional restraints: 15.77 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 374 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 378 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 374 " 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8260 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 49 sheets defined 36.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 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 349 through 353 removed outlier: 4.076A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.722A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.633A pdb=" N ASN A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.704A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.572A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.087A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' 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 1032 removed outlier: 3.611A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.505A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.196A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.066A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.578A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.517A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 751 removed outlier: 3.991A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 746 through 751' Processing helix chain 'B' and resid 752 through 757 removed outlier: 3.621A pdb=" N GLN B 755 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 757 " --> pdb=" O LEU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.257A 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 removed outlier: 4.355A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.800A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.124A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.025A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.700A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.510A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.694A pdb=" N LYS C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 941 removed outlier: 7.130A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.579A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.187A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.363A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.392A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 removed outlier: 4.165A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.879A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.587A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.491A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.865A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (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 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.032A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.697A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (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 399 through 412 removed outlier: 3.664A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.743A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 465 removed outlier: 3.604A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix 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: 5.234A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 484 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing helix 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: 3.801A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.818A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.943A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.514A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.704A pdb=" N LYS E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.516A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 83 No H-bonds generated for 'chain 'E' and resid 82 through 83' Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.503A pdb=" N GLU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE E 88 " --> pdb=" O LEU E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.849A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.648A 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 146 through 155 Processing helix chain 'E' and resid 157 through 172 removed outlier: 3.601A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 250 removed outlier: 3.749A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.014A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 303 through 317 Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.309A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.552A pdb=" N PHE E 369 " --> pdb=" O THR E 365 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS E 374 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.613A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA E 413 " --> pdb=" O SER E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 removed outlier: 3.976A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.333A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 473 removed outlier: 3.783A pdb=" N TRP E 473 " --> pdb=" O LYS E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.393A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 3.578A pdb=" N SER E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 534 removed outlier: 4.418A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.677A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.531A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.639A pdb=" N THR E 593 " --> pdb=" O GLU E 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.978A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.225A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.643A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.553A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.611A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.911A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.573A pdb=" N ILE A 587 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.876A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.669A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.497A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 8.424A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.388A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.623A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.569A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.207A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.310A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.010A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.076A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.500A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.614A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.709A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.012A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.605A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.967A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.580A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.610A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.784A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.367A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.027A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.598A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.702A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.927A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.673A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.478A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.149A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.717A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF3, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.844A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.234A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1516 hydrogen bonds defined for protein. 4270 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: 14.96 Time building geometry restraints manager: 16.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9162 1.33 - 1.46: 8794 1.46 - 1.58: 18425 1.58 - 1.71: 0 1.71 - 1.83: 241 Bond restraints: 36622 Sorted by residual: bond pdb=" N PHE A 374 " pdb=" CA PHE A 374 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.26e-02 6.30e+03 7.37e+00 bond pdb=" N GLN C 675 " pdb=" CA GLN C 675 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.25e-02 6.40e+03 7.33e+00 bond pdb=" N THR C 376 " pdb=" CA THR C 376 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.87e+00 bond pdb=" N PHE A 375 " pdb=" CA PHE A 375 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.80e+00 bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.335 1.366 -0.031 1.30e-02 5.92e+03 5.58e+00 ... (remaining 36617 not shown) Histogram of bond angle deviations from ideal: 97.21 - 104.59: 609 104.59 - 111.96: 17983 111.96 - 119.34: 12101 119.34 - 126.72: 18602 126.72 - 134.09: 526 Bond angle restraints: 49821 Sorted by residual: angle pdb=" N ASN B 370 " pdb=" CA ASN B 370 " pdb=" C ASN B 370 " ideal model delta sigma weight residual 113.50 104.53 8.97 1.23e+00 6.61e-01 5.32e+01 angle pdb=" C SER B 637 " pdb=" CA SER B 637 " pdb=" CB SER B 637 " ideal model delta sigma weight residual 117.23 109.93 7.30 1.36e+00 5.41e-01 2.88e+01 angle pdb=" C SER B 640 " pdb=" N ASN B 641 " pdb=" CA ASN B 641 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" N ILE A 624 " pdb=" CA ILE A 624 " pdb=" C ILE A 624 " ideal model delta sigma weight residual 111.48 107.00 4.48 9.40e-01 1.13e+00 2.27e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 108.87 4.66 9.80e-01 1.04e+00 2.27e+01 ... (remaining 49816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20527 17.95 - 35.89: 1727 35.89 - 53.84: 340 53.84 - 71.78: 82 71.78 - 89.73: 40 Dihedral angle restraints: 22716 sinusoidal: 9900 harmonic: 12816 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -29.80 -56.20 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -35.09 -50.91 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 140.01 -47.01 1 1.00e+01 1.00e-02 3.05e+01 ... (remaining 22713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 5002 0.067 - 0.135: 694 0.135 - 0.202: 22 0.202 - 0.269: 3 0.269 - 0.337: 2 Chirality restraints: 5723 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5720 not shown) Planarity restraints: 6391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 371 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C LEU A 371 " -0.050 2.00e-02 2.50e+03 pdb=" O LEU A 371 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 710 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C ASN A 710 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN A 710 " -0.018 2.00e-02 2.50e+03 pdb=" N SER A 711 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 25 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.031 5.00e-02 4.00e+02 ... (remaining 6388 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 293 2.58 - 3.16: 28794 3.16 - 3.74: 54676 3.74 - 4.32: 73199 4.32 - 4.90: 122850 Nonbonded interactions: 279812 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 701 " model vdw 2.001 2.230 nonbonded pdb=" OE2 GLU E 402 " pdb="ZN ZN E 701 " model vdw 2.004 2.230 nonbonded pdb=" OD1 ASN E 103 " pdb=" OG SER E 106 " model vdw 2.149 2.440 nonbonded pdb=" OD1 ASP C 53 " pdb=" N LEU C 54 " model vdw 2.159 2.520 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.208 2.440 ... (remaining 279807 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' and (resid 14 through 827 or resid 848 through 1147 or resid 1301 thr \ ough 1304)) selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 19 through 227 or resid 229 through 614 or resid 701 throu \ gh 704)) selection = (chain 'E' and (resid 19 through 227 or resid 229 through 614 or resid 701 throu \ gh 704)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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=0.49 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: 10.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.030 Extract box with map and model: 32.510 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 104.500 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36622 Z= 0.204 Angle : 0.585 9.659 49821 Z= 0.311 Chirality : 0.044 0.337 5723 Planarity : 0.004 0.057 6345 Dihedral : 13.971 89.730 14312 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.86 % Favored : 95.93 % Rotamer: Outliers : 0.29 % Allowed : 0.26 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4331 helix: 1.95 (0.15), residues: 1341 sheet: 0.91 (0.19), residues: 732 loop : -0.72 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 566 HIS 0.008 0.001 HIS C 954 PHE 0.022 0.001 PHE E 438 TYR 0.015 0.001 TYR B1067 ARG 0.007 0.000 ARG E 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 246 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.8090 (mm) cc_final: 0.7471 (mm) REVERT: B 113 LYS cc_start: 0.9046 (mtmm) cc_final: 0.8838 (mmtt) REVERT: B 170 TYR cc_start: 0.8584 (t80) cc_final: 0.8351 (t80) REVERT: B 370 ASN cc_start: 0.4992 (OUTLIER) cc_final: 0.4111 (t0) REVERT: B 676 THR cc_start: 0.4359 (OUTLIER) cc_final: 0.4135 (p) REVERT: C 242 LEU cc_start: 0.8375 (mt) cc_final: 0.7931 (tt) REVERT: C 258 TRP cc_start: 0.1588 (p-90) cc_final: 0.1144 (p-90) REVERT: D 152 MET cc_start: -0.0306 (mtm) cc_final: -0.0511 (mtt) REVERT: E 360 MET cc_start: -0.0250 (mtt) cc_final: -0.0915 (tpt) REVERT: E 568 LEU cc_start: 0.3968 (mp) cc_final: 0.3727 (mp) outliers start: 11 outliers final: 3 residues processed: 256 average time/residue: 0.4297 time to fit residues: 191.5706 Evaluate side-chains 178 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 40.0000 chunk 330 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 222 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 341 optimal weight: 0.0170 chunk 132 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 395 optimal weight: 20.0000 overall best weight: 3.1024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 949 GLN A1142 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 580 GLN B 628 GLN E 394 ASN E 524 GLN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36622 Z= 0.252 Angle : 0.576 13.285 49821 Z= 0.290 Chirality : 0.044 0.253 5723 Planarity : 0.004 0.069 6345 Dihedral : 7.416 58.458 6186 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.60 % Favored : 95.22 % Rotamer: Outliers : 0.93 % Allowed : 6.46 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: 0.53 (0.13), residues: 4331 helix: 1.93 (0.15), residues: 1362 sheet: 0.90 (0.19), residues: 674 loop : -0.82 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 165 HIS 0.015 0.001 HIS D 378 PHE 0.020 0.001 PHE C 515 TYR 0.024 0.001 TYR B 636 ARG 0.010 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6468 (t80) cc_final: 0.6124 (t80) REVERT: A 185 ASN cc_start: 0.4106 (OUTLIER) cc_final: 0.3770 (p0) REVERT: B 170 TYR cc_start: 0.8721 (t80) cc_final: 0.8495 (t80) REVERT: B 370 ASN cc_start: 0.4971 (OUTLIER) cc_final: 0.4301 (t0) REVERT: B 987 PRO cc_start: 0.8157 (OUTLIER) cc_final: 0.7905 (Cg_endo) REVERT: C 258 TRP cc_start: 0.1642 (p-90) cc_final: 0.1221 (p-90) REVERT: D 152 MET cc_start: -0.0752 (mtm) cc_final: -0.1082 (mtt) REVERT: D 270 MET cc_start: 0.2201 (mtm) cc_final: 0.1929 (mtm) REVERT: D 376 MET cc_start: 0.2251 (tpp) cc_final: 0.1766 (mtt) REVERT: E 360 MET cc_start: -0.0513 (mtt) cc_final: -0.1093 (tpt) outliers start: 36 outliers final: 19 residues processed: 220 average time/residue: 0.3860 time to fit residues: 149.7970 Evaluate side-chains 188 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 166 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 987 PRO Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 329 optimal weight: 0.8980 chunk 269 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 396 optimal weight: 7.9990 chunk 428 optimal weight: 20.0000 chunk 353 optimal weight: 40.0000 chunk 393 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 318 optimal weight: 40.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 185 ASN A 343 ASN A 370 ASN A 901 GLN A1106 GLN A1135 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B1106 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 394 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 36622 Z= 0.472 Angle : 0.731 12.094 49821 Z= 0.370 Chirality : 0.048 0.363 5723 Planarity : 0.005 0.068 6345 Dihedral : 7.771 59.847 6183 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 1.43 % Allowed : 10.85 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.10 (0.13), residues: 4331 helix: 1.42 (0.14), residues: 1350 sheet: 0.49 (0.19), residues: 685 loop : -1.20 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 165 HIS 0.009 0.002 HIS A 207 PHE 0.032 0.002 PHE C 906 TYR 0.027 0.002 TYR B 636 ARG 0.006 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 170 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6688 (t80) cc_final: 0.6425 (t80) REVERT: A 984 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7171 (mm) REVERT: C 546 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7221 (tp) REVERT: E 360 MET cc_start: -0.0305 (mtt) cc_final: -0.0778 (tpt) outliers start: 55 outliers final: 36 residues processed: 216 average time/residue: 0.4074 time to fit residues: 155.9936 Evaluate side-chains 195 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 238 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 30.0000 chunk 298 optimal weight: 0.9980 chunk 205 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 189 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 398 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 377 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1106 GLN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36622 Z= 0.278 Angle : 0.602 11.905 49821 Z= 0.302 Chirality : 0.045 0.258 5723 Planarity : 0.004 0.065 6345 Dihedral : 7.249 59.829 6179 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.13 % Favored : 94.71 % Rotamer: Outliers : 1.58 % Allowed : 12.92 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4331 helix: 1.68 (0.14), residues: 1342 sheet: 0.49 (0.19), residues: 704 loop : -1.16 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 165 HIS 0.009 0.001 HIS C1083 PHE 0.032 0.001 PHE B 375 TYR 0.018 0.001 TYR A1067 ARG 0.003 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 173 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 PHE cc_start: 0.6712 (t80) cc_final: 0.6500 (t80) REVERT: A 945 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 258 TRP cc_start: 0.1870 (p-90) cc_final: 0.1408 (p-90) REVERT: D 376 MET cc_start: 0.2102 (tpp) cc_final: 0.1664 (mtt) outliers start: 61 outliers final: 39 residues processed: 222 average time/residue: 0.4247 time to fit residues: 168.8451 Evaluate side-chains 197 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 238 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 291 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 378 optimal weight: 8.9990 chunk 106 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 175 GLN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36622 Z= 0.195 Angle : 0.565 10.095 49821 Z= 0.281 Chirality : 0.044 0.252 5723 Planarity : 0.004 0.059 6345 Dihedral : 6.822 59.855 6179 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 1.79 % Allowed : 13.93 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.13), residues: 4331 helix: 1.85 (0.15), residues: 1342 sheet: 0.48 (0.19), residues: 715 loop : -1.07 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 165 HIS 0.008 0.001 HIS E 417 PHE 0.029 0.001 PHE B 375 TYR 0.017 0.001 TYR A1067 ARG 0.002 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 172 time to evaluate : 4.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8352 (mp) REVERT: A 984 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7120 (mm) REVERT: C 258 TRP cc_start: 0.1871 (p-90) cc_final: 0.1371 (p-90) REVERT: D 376 MET cc_start: 0.2288 (tpp) cc_final: 0.1925 (mtt) REVERT: E 190 MET cc_start: 0.0517 (mmm) cc_final: 0.0261 (mmm) outliers start: 69 outliers final: 48 residues processed: 227 average time/residue: 0.3902 time to fit residues: 158.8565 Evaluate side-chains 207 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 157 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 238 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 0.0040 chunk 379 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 247 optimal weight: 30.0000 chunk 104 optimal weight: 8.9990 chunk 421 optimal weight: 9.9990 chunk 350 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 388 ASN ** C 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 HIS ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 36622 Z= 0.354 Angle : 0.654 11.404 49821 Z= 0.328 Chirality : 0.046 0.266 5723 Planarity : 0.005 0.060 6345 Dihedral : 7.151 59.982 6179 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 2.31 % Allowed : 14.48 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.11 (0.13), residues: 4331 helix: 1.57 (0.14), residues: 1350 sheet: 0.33 (0.19), residues: 682 loop : -1.26 (0.13), residues: 2299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 165 HIS 0.011 0.001 HIS E 417 PHE 0.033 0.002 PHE B 375 TYR 0.027 0.002 TYR B 636 ARG 0.004 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 164 time to evaluate : 4.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8440 (mp) REVERT: A 984 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7247 (mm) REVERT: B 516 GLU cc_start: 0.7044 (pm20) cc_final: 0.6585 (pm20) REVERT: C 1050 MET cc_start: 0.7613 (ptm) cc_final: 0.7411 (ptm) REVERT: D 297 MET cc_start: -0.2230 (mtt) cc_final: -0.2591 (ttp) REVERT: D 376 MET cc_start: 0.2104 (tpp) cc_final: 0.1800 (mtt) outliers start: 88 outliers final: 70 residues processed: 242 average time/residue: 0.3947 time to fit residues: 169.2891 Evaluate side-chains 225 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 153 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 7.9990 chunk 47 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 420 optimal weight: 20.0000 chunk 262 optimal weight: 0.0040 chunk 256 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 644 GLN B 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 175 GLN E 394 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36622 Z= 0.267 Angle : 0.599 10.179 49821 Z= 0.300 Chirality : 0.045 0.263 5723 Planarity : 0.004 0.059 6345 Dihedral : 7.001 59.973 6179 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 2.13 % Allowed : 15.23 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.05 (0.13), residues: 4331 helix: 1.59 (0.14), residues: 1363 sheet: 0.30 (0.19), residues: 708 loop : -1.21 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 165 HIS 0.013 0.001 HIS E 417 PHE 0.032 0.001 PHE B 375 TYR 0.022 0.001 TYR E 497 ARG 0.007 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 162 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 984 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7271 (mm) REVERT: C 258 TRP cc_start: 0.1771 (p-90) cc_final: 0.1272 (p-90) REVERT: D 297 MET cc_start: -0.2229 (mtt) cc_final: -0.2528 (ttp) REVERT: D 376 MET cc_start: 0.2196 (tpp) cc_final: 0.1908 (mtt) REVERT: E 190 MET cc_start: 0.0872 (mmm) cc_final: 0.0633 (mmm) REVERT: E 504 PHE cc_start: -0.0088 (OUTLIER) cc_final: -0.0516 (m-80) outliers start: 81 outliers final: 64 residues processed: 231 average time/residue: 0.3938 time to fit residues: 162.7554 Evaluate side-chains 226 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 20.0000 chunk 167 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 126 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 330 optimal weight: 9.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN B 644 GLN B 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36622 Z= 0.289 Angle : 0.618 12.580 49821 Z= 0.309 Chirality : 0.045 0.295 5723 Planarity : 0.004 0.065 6345 Dihedral : 7.017 59.731 6179 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.63 % Favored : 93.23 % Rotamer: Outliers : 2.41 % Allowed : 15.39 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.11 (0.13), residues: 4331 helix: 1.58 (0.14), residues: 1359 sheet: 0.31 (0.20), residues: 679 loop : -1.26 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 165 HIS 0.017 0.001 HIS E 417 PHE 0.033 0.002 PHE B 375 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 165 time to evaluate : 4.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 945 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 984 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7294 (mm) REVERT: C 258 TRP cc_start: 0.1739 (p-90) cc_final: 0.1218 (p-90) REVERT: D 297 MET cc_start: -0.2033 (mtt) cc_final: -0.2320 (ttp) REVERT: D 376 MET cc_start: 0.2217 (tpp) cc_final: 0.1975 (mtt) REVERT: D 480 MET cc_start: 0.0230 (tpp) cc_final: 0.0014 (tpp) REVERT: E 190 MET cc_start: 0.0712 (mmm) cc_final: 0.0442 (mmm) REVERT: E 504 PHE cc_start: -0.0323 (OUTLIER) cc_final: -0.0815 (m-80) outliers start: 91 outliers final: 74 residues processed: 244 average time/residue: 0.4085 time to fit residues: 177.5991 Evaluate side-chains 231 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 154 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 555 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 20.0000 chunk 402 optimal weight: 20.0000 chunk 367 optimal weight: 30.0000 chunk 391 optimal weight: 30.0000 chunk 235 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 353 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 chunk 390 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1005 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 394 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 580 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 36622 Z= 0.547 Angle : 0.796 13.953 49821 Z= 0.401 Chirality : 0.050 0.285 5723 Planarity : 0.005 0.075 6345 Dihedral : 7.893 58.150 6179 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 2.67 % Allowed : 15.54 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.72 (0.12), residues: 4331 helix: 1.02 (0.14), residues: 1364 sheet: 0.02 (0.20), residues: 677 loop : -1.63 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 104 HIS 0.012 0.002 HIS E 417 PHE 0.035 0.002 PHE B 375 TYR 0.021 0.002 TYR D 158 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 155 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A 945 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 984 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7367 (mm) REVERT: B 1115 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8518 (mm) REVERT: D 297 MET cc_start: -0.1819 (mtt) cc_final: -0.2108 (ttp) REVERT: D 376 MET cc_start: 0.1788 (tpp) cc_final: 0.1588 (mtt) REVERT: E 504 PHE cc_start: -0.0453 (OUTLIER) cc_final: -0.0973 (m-80) outliers start: 101 outliers final: 82 residues processed: 244 average time/residue: 0.4002 time to fit residues: 173.3160 Evaluate side-chains 234 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 147 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1084 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 0.9990 chunk 414 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 chunk 434 optimal weight: 3.9990 chunk 399 optimal weight: 30.0000 chunk 345 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36622 Z= 0.220 Angle : 0.613 14.116 49821 Z= 0.306 Chirality : 0.045 0.263 5723 Planarity : 0.004 0.070 6345 Dihedral : 7.199 59.906 6177 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.20 % Rotamer: Outliers : 1.89 % Allowed : 16.50 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % 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: -0.28 (0.13), residues: 4331 helix: 1.45 (0.14), residues: 1365 sheet: 0.21 (0.19), residues: 694 loop : -1.40 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 104 HIS 0.006 0.001 HIS D 374 PHE 0.032 0.001 PHE B 375 TYR 0.021 0.001 TYR D 385 ARG 0.004 0.000 ARG B 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 162 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 984 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7380 (mm) REVERT: C 258 TRP cc_start: 0.1899 (p-90) cc_final: 0.1308 (p-90) REVERT: D 297 MET cc_start: -0.1905 (mtt) cc_final: -0.2180 (ttp) REVERT: D 376 MET cc_start: 0.2115 (tpp) cc_final: 0.1869 (mtt) REVERT: D 480 MET cc_start: 0.0433 (tpp) cc_final: 0.0114 (tpt) REVERT: E 504 PHE cc_start: -0.0408 (OUTLIER) cc_final: -0.0899 (m-80) outliers start: 71 outliers final: 57 residues processed: 226 average time/residue: 0.4268 time to fit residues: 170.5379 Evaluate side-chains 213 residues out of total 3850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 153 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 708 SER Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 375 GLU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain E residue 238 GLU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 431 ASP Chi-restraints excluded: chain E residue 504 PHE Chi-restraints excluded: chain E residue 536 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 0.7980 chunk 368 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 346 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 355 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.129117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090227 restraints weight = 173582.675| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 6.65 r_work: 0.3230 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36622 Z= 0.232 Angle : 0.610 13.712 49821 Z= 0.303 Chirality : 0.045 0.261 5723 Planarity : 0.004 0.070 6345 Dihedral : 6.972 59.742 6177 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.54 % Favored : 93.30 % Rotamer: Outliers : 2.02 % Allowed : 16.50 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4331 helix: 1.55 (0.14), residues: 1367 sheet: 0.28 (0.20), residues: 673 loop : -1.36 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 275 HIS 0.006 0.001 HIS D 374 PHE 0.033 0.001 PHE B 375 TYR 0.018 0.001 TYR D 385 ARG 0.007 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8308.27 seconds wall clock time: 151 minutes 12.88 seconds (9072.88 seconds total)