Starting phenix.real_space_refine on Fri Feb 23 04:28:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wgb_32482/02_2024/7wgb_32482.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 23421 2.51 5 N 6003 2.21 5 O 7120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 509": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36719 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "D" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "F" Number of atoms: 4852 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 566} bond proxies already assigned to first conformer: 4972 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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: "F" 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 Time building chain proxies: 23.71, per 1000 atoms: 0.65 Number of scatterers: 36719 At special positions: 0 Unit cell: (138.03, 163.71, 263.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 7120 8.00 N 6003 7.00 C 23421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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 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 163 " 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 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 F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 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 K 2 " - " BMA K 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A1303 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 145 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 53 " " NAG F 701 " - " ASN F 546 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 322 " " NAG F 704 " - " ASN F 53 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B 331 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " NAG-SER " NAG C1302 " - " SER C 254 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.01 Conformation dependent library (CDL) restraints added in 8.7 seconds 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8450 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 43 sheets defined 36.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.681A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.997A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.614A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.588A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.704A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.352A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.641A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.618A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 4.216A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.149A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.750A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.177A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.946A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1032 removed outlier: 4.398A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 4.346A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.137A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.574A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.342A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.666A pdb=" N TYR B 636 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.587A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.056A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 882 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.522A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 4.151A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.757A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.029A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.764A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.945A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.639A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.759A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.824A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.337A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.669A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.795A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.599A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.712A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.898A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.058A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.847A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A 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 removed outlier: 3.566A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.082A pdb=" N GLU C 990 " --> pdb=" O LYS C 986 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1160 removed outlier: 4.231A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.592A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.699A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.178A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 176 through 194 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.720A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.333A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (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 277 through 283 removed outlier: 4.024A pdb=" N VAL D 283 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.999A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.534A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 4.179A pdb=" N LEU D 418 " --> pdb=" O THR D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.718A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 471 through 474 removed outlier: 3.841A pdb=" N MET D 474 " --> pdb=" O ASP D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.914A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.687A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 558 Processing helix chain 'D' and resid 565 through 574 removed outlier: 4.130A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 4.605A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.952A pdb=" N MET F 82 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.503A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.778A pdb=" N SER F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.713A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 173 removed outlier: 4.329A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 218 through 250 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.592A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.724A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 325 through 330 removed outlier: 4.181A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.876A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 removed outlier: 4.072A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 removed outlier: 3.623A pdb=" N LEU F 418 " --> pdb=" O THR F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 472 through 485 removed outlier: 3.861A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.555A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 513 through 531 Processing helix chain 'F' and resid 532 through 534 No H-bonds generated for 'chain 'F' and resid 532 through 534' Processing helix chain 'F' and resid 547 through 561 removed outlier: 4.001A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 Processing helix chain 'F' and resid 581 through 586 Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.984A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 203 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 229 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER A 205 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.762A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.622A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.587A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.868A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.392A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.913A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB3, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.689A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.787A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.251A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N VAL B 126 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N GLU B 166 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.277A pdb=" N ILE B 128 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR B 164 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL B 130 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ASN B 162 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU B 132 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 160 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN B 134 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.551A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.581A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.607A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.904A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'B' and resid 551 through 554 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.800A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 656 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.536A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.678A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AC8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.724A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE C 201 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP C 230 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 203 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 226 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.647A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD3, first strand: chain 'C' and resid 116 through 122 Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.883A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AD6, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.509A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.741A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.899A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.585A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.735A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.320A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 347 through 349 1480 hydrogen bonds defined for protein. 4153 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: 14.68 Time building geometry restraints manager: 16.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11588 1.34 - 1.46: 9491 1.46 - 1.59: 16284 1.59 - 1.71: 0 1.71 - 1.84: 247 Bond restraints: 37610 Sorted by residual: bond pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.13e+00 bond pdb=" C ASP B 138 " pdb=" N PRO B 139 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.19e-02 7.06e+03 6.83e+00 bond pdb=" N HIS B 143 " pdb=" CA HIS B 143 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N PHE B 140 " pdb=" CA PHE B 140 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.44e+00 bond pdb=" N SER B 148 " pdb=" CA SER B 148 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.37e+00 ... (remaining 37605 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.16: 931 106.16 - 113.17: 20539 113.17 - 120.19: 13218 120.19 - 127.20: 16042 127.20 - 134.22: 408 Bond angle restraints: 51138 Sorted by residual: angle pdb=" N GLY B 103 " pdb=" CA GLY B 103 " pdb=" C GLY B 103 " ideal model delta sigma weight residual 111.14 117.60 -6.46 1.46e+00 4.69e-01 1.96e+01 angle pdb=" CA LYS B 144 " pdb=" C LYS B 144 " pdb=" O LYS B 144 " ideal model delta sigma weight residual 122.31 116.70 5.61 1.31e+00 5.83e-01 1.84e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.53 109.42 4.11 9.80e-01 1.04e+00 1.76e+01 angle pdb=" N HIS B 143 " pdb=" CA HIS B 143 " pdb=" C HIS B 143 " ideal model delta sigma weight residual 108.41 114.80 -6.39 1.61e+00 3.86e-01 1.58e+01 angle pdb=" N LEU B 141 " pdb=" CA LEU B 141 " pdb=" C LEU B 141 " ideal model delta sigma weight residual 113.38 108.61 4.77 1.23e+00 6.61e-01 1.50e+01 ... (remaining 51133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 21499 22.06 - 44.12: 1663 44.12 - 66.18: 175 66.18 - 88.24: 70 88.24 - 110.29: 26 Dihedral angle restraints: 23433 sinusoidal: 10316 harmonic: 13117 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 -177.99 -89.01 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.66 84.34 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 165.66 -72.66 1 1.00e+01 1.00e-02 6.74e+01 ... (remaining 23430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5212 0.075 - 0.149: 631 0.149 - 0.224: 20 0.224 - 0.298: 11 0.298 - 0.373: 3 Chirality restraints: 5877 Sorted by residual: chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 5874 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 329 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO C 330 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 83 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.47e+00 pdb=" N PRO D 84 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 214 " -0.046 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO A 215 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.039 5.00e-02 4.00e+02 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 925 2.68 - 3.24: 37003 3.24 - 3.79: 56762 3.79 - 4.35: 72179 4.35 - 4.90: 117190 Nonbonded interactions: 284059 Sorted by model distance: nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR D 55 " pdb=" OD1 ASN D 58 " model vdw 2.152 2.440 nonbonded pdb=" OH TYR B 489 " pdb=" OH TYR F 83 " model vdw 2.157 2.440 nonbonded pdb=" OG1 THR C 581 " pdb=" OE1 GLU C 583 " model vdw 2.166 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 2.440 ... (remaining 284054 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 1162 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 1162 or resid 1301 through 1308)) } ncs_group { reference = (chain 'D' and (resid 19 through 227 or resid 229 through 612 or resid 701 throu \ gh 704)) selection = (chain 'F' and (resid 19 through 227 or resid 229 through 612 or resid 701 throu \ gh 704)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.860 Check model and map are aligned: 0.490 Set scattering table: 0.390 Process input model: 105.360 Find NCS groups from input model: 2.630 Set up NCS constraints: 0.530 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37610 Z= 0.254 Angle : 0.654 11.460 51138 Z= 0.332 Chirality : 0.047 0.373 5877 Planarity : 0.004 0.076 6494 Dihedral : 15.286 110.294 14848 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -0.98 (0.13), residues: 4450 helix: 0.82 (0.14), residues: 1423 sheet: 0.22 (0.21), residues: 606 loop : -1.87 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 566 HIS 0.006 0.001 HIS B1159 PHE 0.030 0.001 PHE F 452 TYR 0.032 0.001 TYR D 199 ARG 0.004 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1017 GLU cc_start: 0.8233 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 759 PHE cc_start: 0.7236 (t80) cc_final: 0.6891 (t80) REVERT: D 69 TRP cc_start: 0.2001 (t-100) cc_final: 0.1018 (t60) REVERT: D 249 MET cc_start: 0.3632 (mtt) cc_final: 0.3431 (mmt) REVERT: F 498 CYS cc_start: 0.6573 (t) cc_final: 0.6248 (t) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.4376 time to fit residues: 127.7264 Evaluate side-chains 126 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 375 optimal weight: 10.0000 chunk 337 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 227 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 404 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 508 ASN F 42 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 37610 Z= 0.452 Angle : 0.731 11.066 51138 Z= 0.373 Chirality : 0.048 0.439 5877 Planarity : 0.005 0.076 6494 Dihedral : 9.188 76.432 6508 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 0.66 % Allowed : 9.91 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4450 helix: 0.52 (0.14), residues: 1429 sheet: -0.09 (0.21), residues: 601 loop : -2.05 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 203 HIS 0.006 0.001 HIS C 49 PHE 0.035 0.002 PHE D 369 TYR 0.024 0.002 TYR A 453 ARG 0.008 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 217 TYR cc_start: 0.1117 (OUTLIER) cc_final: 0.0907 (m-80) REVERT: F 498 CYS cc_start: 0.6245 (t) cc_final: 0.5881 (t) REVERT: F 579 MET cc_start: 0.4129 (ttt) cc_final: 0.3878 (ttt) outliers start: 25 outliers final: 14 residues processed: 152 average time/residue: 0.4306 time to fit residues: 116.4585 Evaluate side-chains 141 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 224 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 chunk 275 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 404 optimal weight: 20.0000 chunk 437 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 324 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 37610 Z= 0.305 Angle : 0.633 9.703 51138 Z= 0.323 Chirality : 0.045 0.404 5877 Planarity : 0.005 0.074 6494 Dihedral : 8.123 59.279 6508 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer: Outliers : 1.24 % Allowed : 13.36 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -1.21 (0.12), residues: 4450 helix: 0.63 (0.14), residues: 1429 sheet: 0.03 (0.22), residues: 586 loop : -2.00 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 203 HIS 0.006 0.001 HIS C 146 PHE 0.034 0.001 PHE D 369 TYR 0.022 0.001 TYR D 385 ARG 0.008 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 135 time to evaluate : 4.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1010 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: B 87 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7426 (p0) REVERT: B 259 THR cc_start: 0.4702 (m) cc_final: 0.4491 (m) REVERT: C 190 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6415 (mmm-85) REVERT: D 217 TYR cc_start: 0.1388 (OUTLIER) cc_final: 0.0894 (m-80) REVERT: D 249 MET cc_start: 0.3370 (mmt) cc_final: 0.2102 (tpt) REVERT: F 498 CYS cc_start: 0.6148 (t) cc_final: 0.5920 (t) outliers start: 48 outliers final: 26 residues processed: 178 average time/residue: 0.4317 time to fit residues: 136.2363 Evaluate side-chains 156 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 399 optimal weight: 6.9990 chunk 304 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 193 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 chunk 406 optimal weight: 20.0000 chunk 430 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 chunk 385 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 508 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37610 Z= 0.204 Angle : 0.575 9.679 51138 Z= 0.293 Chirality : 0.043 0.391 5877 Planarity : 0.004 0.073 6494 Dihedral : 7.120 59.849 6508 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.15 % Favored : 92.76 % Rotamer: Outliers : 1.50 % Allowed : 14.83 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -1.00 (0.13), residues: 4450 helix: 0.83 (0.14), residues: 1431 sheet: 0.14 (0.21), residues: 597 loop : -1.89 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP F 477 HIS 0.008 0.001 HIS F 540 PHE 0.029 0.001 PHE D 369 TYR 0.022 0.001 TYR D 385 ARG 0.007 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: A 1010 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: B 87 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 259 THR cc_start: 0.4687 (m) cc_final: 0.4453 (m) REVERT: C 87 ASN cc_start: 0.5578 (OUTLIER) cc_final: 0.5348 (p0) REVERT: C 303 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8328 (tt) REVERT: D 217 TYR cc_start: 0.1584 (OUTLIER) cc_final: 0.0360 (m-80) REVERT: D 249 MET cc_start: 0.3403 (mmt) cc_final: 0.2063 (tpt) REVERT: D 579 MET cc_start: -0.0962 (mpp) cc_final: -0.2396 (mtm) outliers start: 58 outliers final: 30 residues processed: 191 average time/residue: 0.4184 time to fit residues: 143.0307 Evaluate side-chains 161 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 358 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 320 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 367 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 chunk 386 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 37610 Z= 0.263 Angle : 0.600 13.008 51138 Z= 0.304 Chirality : 0.044 0.399 5877 Planarity : 0.004 0.074 6494 Dihedral : 6.819 58.278 6508 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.36 % Rotamer: Outliers : 1.88 % Allowed : 16.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -1.04 (0.13), residues: 4450 helix: 0.82 (0.14), residues: 1433 sheet: 0.07 (0.21), residues: 605 loop : -1.92 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP F 477 HIS 0.008 0.001 HIS C 146 PHE 0.032 0.001 PHE A 133 TYR 0.020 0.001 TYR D 385 ARG 0.005 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 131 time to evaluate : 4.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 271 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: A 660 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: A 822 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9412 (mm) REVERT: A 1010 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: B 87 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 259 THR cc_start: 0.4786 (m) cc_final: 0.4513 (m) REVERT: C 190 ARG cc_start: 0.7645 (mtp180) cc_final: 0.6391 (mmm160) REVERT: C 303 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8300 (tt) REVERT: D 217 TYR cc_start: 0.1636 (OUTLIER) cc_final: 0.0272 (m-80) REVERT: D 579 MET cc_start: -0.0969 (mpp) cc_final: -0.2413 (mtm) outliers start: 73 outliers final: 44 residues processed: 202 average time/residue: 0.4219 time to fit residues: 150.9957 Evaluate side-chains 175 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 123 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 144 optimal weight: 4.9990 chunk 387 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 357 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 762 GLN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 37610 Z= 0.487 Angle : 0.747 13.349 51138 Z= 0.381 Chirality : 0.048 0.425 5877 Planarity : 0.005 0.074 6494 Dihedral : 7.469 56.360 6508 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer: Outliers : 2.79 % Allowed : 17.75 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % 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: -1.45 (0.12), residues: 4450 helix: 0.45 (0.14), residues: 1430 sheet: -0.20 (0.21), residues: 609 loop : -2.15 (0.12), residues: 2411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP F 477 HIS 0.013 0.002 HIS F 540 PHE 0.040 0.002 PHE D 369 TYR 0.020 0.002 TYR A 170 ARG 0.006 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 130 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: A 271 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: A 660 TYR cc_start: 0.8065 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: A 1010 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: B 87 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7388 (p0) REVERT: B 909 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8476 (tp) REVERT: C 190 ARG cc_start: 0.7629 (mtp180) cc_final: 0.6624 (mmm160) REVERT: C 303 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8407 (tt) REVERT: D 217 TYR cc_start: 0.1703 (OUTLIER) cc_final: 0.0789 (m-80) REVERT: D 249 MET cc_start: 0.3238 (mmt) cc_final: 0.1870 (tpt) outliers start: 109 outliers final: 66 residues processed: 230 average time/residue: 0.4116 time to fit residues: 169.5702 Evaluate side-chains 200 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 126 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 817 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 249 MET Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 415 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 245 optimal weight: 3.9990 chunk 314 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 362 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 428 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 37610 Z= 0.217 Angle : 0.611 11.881 51138 Z= 0.310 Chirality : 0.044 0.390 5877 Planarity : 0.004 0.071 6494 Dihedral : 6.778 57.151 6508 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 1.77 % Allowed : 19.37 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.12), residues: 4450 helix: 0.74 (0.14), residues: 1439 sheet: 0.15 (0.22), residues: 589 loop : -2.00 (0.12), residues: 2422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP F 477 HIS 0.007 0.001 HIS C 146 PHE 0.031 0.001 PHE D 369 TYR 0.058 0.001 TYR D 237 ARG 0.005 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 133 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: A 660 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: A 1010 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8418 (mp10) REVERT: B 87 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7337 (p0) REVERT: B 259 THR cc_start: 0.4897 (m) cc_final: 0.4613 (m) REVERT: C 190 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6390 (mmm160) REVERT: C 303 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8292 (tt) REVERT: C 1074 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.8088 (p0) REVERT: D 217 TYR cc_start: 0.1731 (OUTLIER) cc_final: 0.0945 (m-80) REVERT: D 249 MET cc_start: 0.3523 (mmt) cc_final: 0.2034 (tpt) REVERT: F 332 MET cc_start: -0.0758 (tpt) cc_final: -0.1048 (mmm) outliers start: 69 outliers final: 49 residues processed: 198 average time/residue: 0.4221 time to fit residues: 147.5755 Evaluate side-chains 182 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 265 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 256 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 337 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 37610 Z= 0.352 Angle : 0.668 11.789 51138 Z= 0.339 Chirality : 0.045 0.408 5877 Planarity : 0.005 0.074 6494 Dihedral : 6.902 56.237 6508 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.95 % Favored : 90.94 % Rotamer: Outliers : 2.16 % Allowed : 19.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.12), residues: 4450 helix: 0.64 (0.14), residues: 1438 sheet: -0.01 (0.21), residues: 600 loop : -2.06 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP F 477 HIS 0.016 0.001 HIS C 146 PHE 0.035 0.002 PHE D 369 TYR 0.041 0.002 TYR D 237 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 124 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: A 660 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: A 1010 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: B 87 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7335 (p0) REVERT: B 259 THR cc_start: 0.4898 (m) cc_final: 0.4637 (m) REVERT: B 909 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8335 (tp) REVERT: C 190 ARG cc_start: 0.7624 (mtp180) cc_final: 0.6573 (mmm160) REVERT: C 303 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8338 (tt) REVERT: D 217 TYR cc_start: 0.1765 (OUTLIER) cc_final: 0.1017 (m-80) REVERT: D 249 MET cc_start: 0.3347 (mmt) cc_final: 0.2037 (tpt) REVERT: F 464 PHE cc_start: 0.3891 (OUTLIER) cc_final: 0.3598 (t80) outliers start: 84 outliers final: 63 residues processed: 202 average time/residue: 0.4076 time to fit residues: 146.9446 Evaluate side-chains 192 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 121 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 390 optimal weight: 9.9990 chunk 410 optimal weight: 30.0000 chunk 374 optimal weight: 20.0000 chunk 399 optimal weight: 30.0000 chunk 240 optimal weight: 7.9990 chunk 174 optimal weight: 3.9990 chunk 313 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 361 optimal weight: 0.4980 chunk 378 optimal weight: 9.9990 chunk 398 optimal weight: 7.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 37610 Z= 0.338 Angle : 0.663 11.581 51138 Z= 0.337 Chirality : 0.045 0.404 5877 Planarity : 0.005 0.072 6494 Dihedral : 6.892 55.453 6508 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.54 % Favored : 91.32 % Rotamer: Outliers : 2.23 % Allowed : 19.90 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4450 helix: 0.66 (0.14), residues: 1432 sheet: -0.01 (0.21), residues: 605 loop : -2.07 (0.12), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP F 477 HIS 0.013 0.001 HIS C 146 PHE 0.035 0.002 PHE D 369 TYR 0.037 0.002 TYR D 237 ARG 0.004 0.000 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 124 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: A 660 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: A 1010 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: B 87 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7340 (p0) REVERT: B 259 THR cc_start: 0.4857 (m) cc_final: 0.4598 (m) REVERT: B 909 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8318 (tp) REVERT: C 190 ARG cc_start: 0.7637 (mtp180) cc_final: 0.6573 (mmm160) REVERT: C 303 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8312 (tt) REVERT: D 217 TYR cc_start: 0.1716 (OUTLIER) cc_final: 0.0951 (m-80) REVERT: D 249 MET cc_start: 0.3273 (mmt) cc_final: 0.2013 (tpt) REVERT: F 464 PHE cc_start: 0.4074 (OUTLIER) cc_final: 0.3741 (t80) outliers start: 87 outliers final: 70 residues processed: 206 average time/residue: 0.4172 time to fit residues: 152.5805 Evaluate side-chains 199 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 121 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 262 optimal weight: 30.0000 chunk 422 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 443 optimal weight: 6.9990 chunk 408 optimal weight: 8.9990 chunk 353 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 37610 Z= 0.392 Angle : 0.695 11.633 51138 Z= 0.354 Chirality : 0.046 0.412 5877 Planarity : 0.005 0.073 6494 Dihedral : 7.049 56.553 6508 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.49 % Favored : 90.38 % Rotamer: Outliers : 2.33 % Allowed : 20.01 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4450 helix: 0.54 (0.14), residues: 1438 sheet: -0.11 (0.21), residues: 602 loop : -2.14 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP F 477 HIS 0.012 0.001 HIS C 146 PHE 0.037 0.002 PHE D 369 TYR 0.035 0.002 TYR D 237 ARG 0.008 0.001 ARG A 634 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8900 Ramachandran restraints generated. 4450 Oldfield, 0 Emsley, 4450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 125 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6918 (pm20) REVERT: A 660 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 1010 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8290 (mp10) REVERT: A 1144 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8767 (tp30) REVERT: B 87 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7331 (p0) REVERT: B 909 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8374 (tp) REVERT: C 190 ARG cc_start: 0.7651 (mtp180) cc_final: 0.6597 (mmm-85) REVERT: C 303 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8344 (tt) REVERT: D 217 TYR cc_start: 0.1789 (OUTLIER) cc_final: 0.0523 (m-80) REVERT: D 249 MET cc_start: 0.3283 (mmt) cc_final: 0.2033 (tpt) REVERT: D 579 MET cc_start: -0.0345 (mpp) cc_final: -0.1380 (mtm) REVERT: F 464 PHE cc_start: 0.4281 (OUTLIER) cc_final: 0.3964 (t80) outliers start: 91 outliers final: 73 residues processed: 211 average time/residue: 0.4242 time to fit residues: 159.5745 Evaluate side-chains 205 residues out of total 3940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 124 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 PHE Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 445 random chunks: chunk 280 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 325 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 363 optimal weight: 7.9990 chunk 44 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.117918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.082932 restraints weight = 193559.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085013 restraints weight = 88499.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.085077 restraints weight = 50128.956| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37610 Z= 0.205 Angle : 0.605 10.987 51138 Z= 0.306 Chirality : 0.044 0.382 5877 Planarity : 0.004 0.069 6494 Dihedral : 6.473 56.331 6508 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.86 % Favored : 92.99 % Rotamer: Outliers : 1.90 % Allowed : 20.59 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4450 helix: 0.84 (0.14), residues: 1426 sheet: 0.18 (0.22), residues: 580 loop : -1.98 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP F 477 HIS 0.014 0.001 HIS F 540 PHE 0.031 0.001 PHE D 369 TYR 0.036 0.001 TYR D 237 ARG 0.008 0.000 ARG A 634 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6050.71 seconds wall clock time: 113 minutes 20.07 seconds (6800.07 seconds total)