Starting phenix.real_space_refine on Wed Feb 14 07:15:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ya0_33698/02_2024/7ya0_33698.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19431 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 201 5.16 5 C 25521 2.51 5 N 6570 2.21 5 O 7701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 775": "OD1" <-> "OD2" Residue "C PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 299": "OD1" <-> "OD2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 367": "OD1" <-> "OD2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 589": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 39996 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8167 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 8180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8180 Classifications: {'peptide': 1045} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 988} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Chain: "C" Number of atoms: 8157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8157 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "E" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "F" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 19.79, per 1000 atoms: 0.49 Number of scatterers: 39996 At special positions: 0 Unit cell: (168.08, 189.2, 247.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 201 16.00 O 7701 8.00 N 6570 7.00 C 25521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 701 " - " ASN E 53 " " NAG E 702 " - " ASN E 90 " " NAG E 703 " - " ASN E 322 " " NAG E 705 " - " ASN E 432 " " NAG E 706 " - " ASN E 546 " " NAG F 701 " - " ASN F 53 " " NAG F 702 " - " ASN F 90 " " NAG F 703 " - " ASN F 322 " " NAG F 705 " - " ASN F 432 " " NAG F 706 " - " ASN F 546 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 331 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 12.20 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 374 " pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 378 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 704 " pdb="ZN ZN F 704 " - pdb=" NE2 HIS F 378 " pdb="ZN ZN F 704 " - pdb=" NE2 HIS F 374 " 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9276 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 49 sheets defined 38.7% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 386 through 390 removed outlier: 4.133A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.765A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.658A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.760A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.668A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.505A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.128A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.569A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.976A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.668A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.548A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.580A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.025A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.848A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 826 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.390A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.616A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.796A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.540A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.969A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.639A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.218A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.674A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.942A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.730A 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: 3.704A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.692A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.541A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 79 removed outlier: 4.231A pdb=" N SER D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.751A pdb=" N GLU D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 88 " --> pdb=" O LEU D 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 84 through 88' Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.102A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.771A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.652A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 232 removed outlier: 4.436A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.988A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.889A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.646A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.670A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.523A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 removed outlier: 4.268A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 444 removed outlier: 4.053A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.865A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.720A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.836A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.511A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 598 Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.368A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 59 through 80 removed outlier: 3.526A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.509A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.846A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 157 through 194 removed outlier: 4.235A pdb=" N ALA E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.621A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 231 removed outlier: 4.316A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 252 removed outlier: 3.612A pdb=" N TYR E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 306 through 319 removed outlier: 4.610A pdb=" N GLU E 312 " --> pdb=" O PHE E 308 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.627A pdb=" N SER E 331 " --> pdb=" O PHE E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.516A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 removed outlier: 3.962A pdb=" N ARG E 393 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 408 removed outlier: 3.645A pdb=" N VAL E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 433 through 447 removed outlier: 4.113A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 473 through 484 removed outlier: 3.639A pdb=" N TRP E 477 " --> pdb=" O TRP E 473 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 532 removed outlier: 4.102A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN E 526 " --> pdb=" O GLN E 522 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA E 528 " --> pdb=" O GLN E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.728A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.829A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 80 removed outlier: 4.941A pdb=" N SER F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.734A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.174A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 157 through 195 removed outlier: 4.752A pdb=" N ALA F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N TRP F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU F 166 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.799A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 231 removed outlier: 4.406A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 4.115A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 removed outlier: 3.744A pdb=" N LEU F 266 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU F 267 " --> pdb=" O ALA F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 263 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.531A pdb=" N MET F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.875A pdb=" N ILE F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 329 removed outlier: 3.680A pdb=" N GLU F 329 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 385 removed outlier: 3.560A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.529A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.714A pdb=" N ILE F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 410 " --> pdb=" O GLU F 406 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 411 " --> pdb=" O ILE F 407 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 412 " --> pdb=" O MET F 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 412' Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 434 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.563A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 3.917A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN F 526 " --> pdb=" O GLN F 522 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU F 527 " --> pdb=" O PHE F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 549 through 561 removed outlier: 3.636A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 564 No H-bonds generated for 'chain 'F' and resid 562 through 564' Processing helix chain 'F' and resid 565 through 575 removed outlier: 3.766A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 removed outlier: 4.161A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.123A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.834A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.238A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.127A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.543A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.531A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.180A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.766A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.857A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.882A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.652A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 7.878A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.032A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.874A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.319A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.343A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC7, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.492A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.199A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.782A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.929A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.426A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.701A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.958A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.051A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.181A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.887A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.702A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.508A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.333A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'F' and resid 347 through 350 1664 hydrogen bonds defined for protein. 4626 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: 12.70 Time building geometry restraints manager: 13.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7141 1.33 - 1.45: 11313 1.45 - 1.58: 22226 1.58 - 1.71: 0 1.71 - 1.83: 291 Bond restraints: 40971 Sorted by residual: bond pdb=" CA SER B 816 " pdb=" CB SER B 816 " ideal model delta sigma weight residual 1.536 1.473 0.062 1.25e-02 6.40e+03 2.49e+01 bond pdb=" CA SER C 816 " pdb=" CB SER C 816 " ideal model delta sigma weight residual 1.536 1.476 0.060 1.25e-02 6.40e+03 2.31e+01 bond pdb=" CA SER A 816 " pdb=" CB SER A 816 " ideal model delta sigma weight residual 1.532 1.477 0.055 1.58e-02 4.01e+03 1.21e+01 bond pdb=" N ILE A 818 " pdb=" CA ILE A 818 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ILE B 818 " pdb=" CA ILE B 818 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.28e-02 6.10e+03 9.52e+00 ... (remaining 40966 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.50: 816 105.50 - 112.63: 21282 112.63 - 119.76: 13351 119.76 - 126.89: 19729 126.89 - 134.02: 526 Bond angle restraints: 55704 Sorted by residual: angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.31 110.28 -6.97 8.90e-01 1.26e+00 6.14e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.33 110.53 -7.20 9.30e-01 1.16e+00 5.99e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.34 110.43 -7.09 9.30e-01 1.16e+00 5.81e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 103.20 110.09 -6.89 9.50e-01 1.11e+00 5.27e+01 angle pdb=" N TYR D 196 " pdb=" CA TYR D 196 " pdb=" C TYR D 196 " ideal model delta sigma weight residual 113.55 104.87 8.68 1.26e+00 6.30e-01 4.75e+01 ... (remaining 55699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 22621 17.81 - 35.62: 2023 35.62 - 53.44: 424 53.44 - 71.25: 98 71.25 - 89.06: 28 Dihedral angle restraints: 25194 sinusoidal: 10803 harmonic: 14391 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 163.16 -70.16 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual -86.00 -24.36 -61.64 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -27.07 -58.93 1 1.00e+01 1.00e-02 4.64e+01 ... (remaining 25191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 5732 0.081 - 0.161: 559 0.161 - 0.242: 18 0.242 - 0.323: 7 0.323 - 0.403: 2 Chirality restraints: 6318 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C1 NAG E 705 " pdb=" ND2 ASN E 432 " pdb=" C2 NAG E 705 " pdb=" O5 NAG E 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA TYR D 196 " pdb=" N TYR D 196 " pdb=" C TYR D 196 " pdb=" CB TYR D 196 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 6315 not shown) Planarity restraints: 7164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 675 " 0.025 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C GLN B 675 " -0.087 2.00e-02 2.50e+03 pdb=" O GLN B 675 " 0.033 2.00e-02 2.50e+03 pdb=" N THR B 676 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1134 " 0.035 2.00e-02 2.50e+03 3.14e-02 1.23e+01 pdb=" CG ASN A1134 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1134 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A1134 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 288 " -0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO D 289 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " -0.046 5.00e-02 4.00e+02 ... (remaining 7161 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 344 2.58 - 3.16: 32455 3.16 - 3.74: 59225 3.74 - 4.32: 80760 4.32 - 4.90: 135207 Nonbonded interactions: 307991 Sorted by model distance: nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 704 " model vdw 2.001 2.230 nonbonded pdb=" OE2 GLU E 402 " pdb="ZN ZN E 704 " model vdw 2.007 2.230 nonbonded pdb=" OE2 GLU F 402 " pdb="ZN ZN F 704 " model vdw 2.009 2.230 nonbonded pdb=" OH TYR D 237 " pdb=" O VAL D 485 " model vdw 2.197 2.440 nonbonded pdb=" O PHE E 327 " pdb=" OG SER E 331 " model vdw 2.201 2.440 ... (remaining 307986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 527 or (resid 528 through 529 a \ nd (name N or name CA or name C or name O or name CB )) or resid 530 through 114 \ 7 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 827 or resid 848 through 1147 o \ r resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 528 or (resid 529 and (name N or name CA or nam \ e C or name O or name CB )) or resid 530 through 1147 or resid 1301 through 1306 \ )) } ncs_group { reference = (chain 'D' and (resid 19 through 227 or resid 229 through 614 or resid 701 throu \ gh 706)) selection = (chain 'E' and (resid 19 through 227 or resid 229 through 614 or resid 701 throu \ gh 706)) selection = (chain 'F' and (resid 19 through 227 or resid 229 through 614 or resid 701 throu \ gh 706)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.030 Extract box with map and model: 42.060 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 90.530 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.430 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40971 Z= 0.220 Angle : 0.681 10.876 55704 Z= 0.395 Chirality : 0.046 0.403 6318 Planarity : 0.005 0.084 7116 Dihedral : 14.041 89.059 15765 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4860 helix: 0.61 (0.13), residues: 1680 sheet: 0.47 (0.19), residues: 704 loop : -1.59 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 203 HIS 0.008 0.001 HIS E 373 PHE 0.025 0.001 PHE E 327 TYR 0.017 0.001 TYR A 453 ARG 0.014 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8489 (mtt) cc_final: 0.8264 (mtt) REVERT: E 376 MET cc_start: 0.0851 (ptp) cc_final: 0.0344 (tpt) outliers start: 8 outliers final: 5 residues processed: 244 average time/residue: 0.3910 time to fit residues: 164.5933 Evaluate side-chains 183 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain F residue 197 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 412 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 205 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN C 66 HIS C 658 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 194 ASN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 522 GLN ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 40971 Z= 0.393 Angle : 0.689 17.359 55704 Z= 0.350 Chirality : 0.047 0.384 6318 Planarity : 0.005 0.074 7116 Dihedral : 7.720 59.754 6614 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 0.53 % Allowed : 6.67 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.82 (0.12), residues: 4860 helix: 0.51 (0.13), residues: 1731 sheet: 0.39 (0.18), residues: 756 loop : -1.71 (0.12), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 353 HIS 0.011 0.001 HIS E 493 PHE 0.026 0.002 PHE A 906 TYR 0.029 0.002 TYR A 265 ARG 0.006 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 18 residues processed: 195 average time/residue: 0.4369 time to fit residues: 148.1738 Evaluate side-chains 179 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 369 optimal weight: 9.9990 chunk 302 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 444 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 396 optimal weight: 20.0000 chunk 441 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1106 GLN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 250 ASN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 40971 Z= 0.466 Angle : 0.723 12.870 55704 Z= 0.368 Chirality : 0.049 0.372 6318 Planarity : 0.005 0.075 7116 Dihedral : 7.629 59.276 6610 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.96 % Favored : 92.94 % Rotamer: Outliers : 1.11 % Allowed : 10.40 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 4860 helix: 0.41 (0.13), residues: 1708 sheet: 0.24 (0.19), residues: 740 loop : -1.82 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 610 HIS 0.011 0.001 HIS E 493 PHE 0.022 0.002 PHE A 906 TYR 0.024 0.002 TYR B1067 ARG 0.007 0.001 ARG F 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.8848 (mmm) cc_final: 0.8362 (tmm) outliers start: 48 outliers final: 35 residues processed: 213 average time/residue: 0.3702 time to fit residues: 137.3911 Evaluate side-chains 189 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 439 optimal weight: 5.9990 chunk 334 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 446 optimal weight: 9.9990 chunk 472 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 423 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN D 300 GLN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40971 Z= 0.208 Angle : 0.597 15.078 55704 Z= 0.302 Chirality : 0.044 0.352 6318 Planarity : 0.005 0.063 7116 Dihedral : 6.980 58.649 6610 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 1.04 % Allowed : 11.79 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.12), residues: 4860 helix: 0.79 (0.13), residues: 1702 sheet: 0.41 (0.19), residues: 695 loop : -1.71 (0.12), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP F 610 HIS 0.012 0.001 HIS E 493 PHE 0.015 0.001 PHE F 555 TYR 0.022 0.001 TYR A 265 ARG 0.004 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 553 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8056 (p) REVERT: C 740 MET cc_start: 0.8739 (mmm) cc_final: 0.8215 (tmm) REVERT: F 452 PHE cc_start: -0.0622 (m-10) cc_final: -0.0829 (m-10) outliers start: 45 outliers final: 25 residues processed: 216 average time/residue: 0.3884 time to fit residues: 146.7573 Evaluate side-chains 179 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain D residue 197 GLU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 393 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 351 optimal weight: 7.9990 chunk 195 optimal weight: 0.8980 chunk 403 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 424 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 165 ASN ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 40971 Z= 0.363 Angle : 0.655 15.642 55704 Z= 0.330 Chirality : 0.046 0.354 6318 Planarity : 0.005 0.071 7116 Dihedral : 7.047 59.558 6610 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.88 % Favored : 93.02 % Rotamer: Outliers : 1.62 % Allowed : 12.51 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4860 helix: 0.68 (0.13), residues: 1719 sheet: 0.22 (0.19), residues: 725 loop : -1.77 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP F 610 HIS 0.011 0.001 HIS E 493 PHE 0.021 0.002 PHE E 369 TYR 0.024 0.002 TYR A 265 ARG 0.004 0.000 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 165 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 553 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8086 (p) REVERT: C 33 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7906 (t) REVERT: C 740 MET cc_start: 0.8810 (mmm) cc_final: 0.8302 (tmm) REVERT: E 376 MET cc_start: -0.0106 (ptp) cc_final: -0.0472 (tpt) outliers start: 70 outliers final: 50 residues processed: 228 average time/residue: 0.3750 time to fit residues: 151.0955 Evaluate side-chains 207 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 159 optimal weight: 1.9990 chunk 425 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 277 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 473 optimal weight: 20.0000 chunk 392 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40971 Z= 0.237 Angle : 0.600 14.405 55704 Z= 0.302 Chirality : 0.045 0.424 6318 Planarity : 0.005 0.076 7116 Dihedral : 6.624 59.544 6607 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 1.25 % Allowed : 13.69 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4860 helix: 0.82 (0.13), residues: 1727 sheet: 0.34 (0.19), residues: 701 loop : -1.68 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP F 610 HIS 0.012 0.001 HIS E 493 PHE 0.013 0.001 PHE F 555 TYR 0.024 0.001 TYR A 265 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 553 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8077 (p) REVERT: C 33 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7852 (t) REVERT: C 740 MET cc_start: 0.8742 (mmm) cc_final: 0.8230 (tmm) REVERT: E 376 MET cc_start: -0.0058 (ptp) cc_final: -0.0310 (tpt) outliers start: 54 outliers final: 34 residues processed: 214 average time/residue: 0.4036 time to fit residues: 152.2834 Evaluate side-chains 189 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 456 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 269 optimal weight: 4.9990 chunk 345 optimal weight: 9.9990 chunk 267 optimal weight: 0.9990 chunk 398 optimal weight: 0.0770 chunk 264 optimal weight: 4.9990 chunk 471 optimal weight: 8.9990 chunk 294 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40971 Z= 0.288 Angle : 0.626 13.956 55704 Z= 0.315 Chirality : 0.045 0.354 6318 Planarity : 0.005 0.074 7116 Dihedral : 6.539 59.467 6604 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.10 % Rotamer: Outliers : 1.46 % Allowed : 13.78 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.70 (0.12), residues: 4860 helix: 0.84 (0.13), residues: 1709 sheet: 0.30 (0.19), residues: 719 loop : -1.72 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP F 610 HIS 0.012 0.001 HIS E 493 PHE 0.017 0.001 PHE A 392 TYR 0.026 0.001 TYR A 265 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 167 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2670 (pp) REVERT: B 553 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 33 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7823 (t) REVERT: C 740 MET cc_start: 0.8769 (mmm) cc_final: 0.8257 (tmm) REVERT: E 376 MET cc_start: -0.0250 (ptp) cc_final: -0.0523 (tpt) outliers start: 63 outliers final: 51 residues processed: 223 average time/residue: 0.3604 time to fit residues: 141.5350 Evaluate side-chains 212 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 291 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 233 optimal weight: 0.3980 chunk 43 optimal weight: 0.2980 chunk 370 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 66 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS F 586 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40971 Z= 0.151 Angle : 0.564 12.480 55704 Z= 0.283 Chirality : 0.043 0.344 6318 Planarity : 0.004 0.073 7116 Dihedral : 6.012 59.316 6604 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 0.88 % Allowed : 14.45 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.45 (0.12), residues: 4860 helix: 1.10 (0.13), residues: 1706 sheet: 0.44 (0.19), residues: 696 loop : -1.60 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP F 610 HIS 0.011 0.001 HIS E 493 PHE 0.014 0.001 PHE C1121 TYR 0.026 0.001 TYR A 265 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.2989 (OUTLIER) cc_final: 0.2773 (pp) REVERT: C 33 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7846 (t) REVERT: E 376 MET cc_start: -0.0018 (ptp) cc_final: -0.0334 (tpt) outliers start: 38 outliers final: 27 residues processed: 199 average time/residue: 0.3833 time to fit residues: 132.9808 Evaluate side-chains 187 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 428 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 411 optimal weight: 10.0000 chunk 439 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 396 optimal weight: 8.9990 chunk 415 optimal weight: 5.9990 chunk 437 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 40971 Z= 0.404 Angle : 0.690 13.798 55704 Z= 0.347 Chirality : 0.047 0.408 6318 Planarity : 0.005 0.088 7116 Dihedral : 6.502 59.493 6603 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.33 % Favored : 92.57 % Rotamer: Outliers : 1.32 % Allowed : 14.38 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.72 (0.12), residues: 4860 helix: 0.82 (0.13), residues: 1709 sheet: 0.29 (0.19), residues: 714 loop : -1.73 (0.12), residues: 2437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP F 610 HIS 0.010 0.001 HIS E 493 PHE 0.018 0.002 PHE A 400 TYR 0.029 0.002 TYR A 265 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.2912 (OUTLIER) cc_final: 0.2694 (pp) REVERT: B 553 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8068 (p) REVERT: C 33 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.7808 (t) REVERT: E 376 MET cc_start: -0.0215 (ptp) cc_final: -0.0496 (tpt) outliers start: 57 outliers final: 46 residues processed: 212 average time/residue: 0.3881 time to fit residues: 144.6966 Evaluate side-chains 205 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 156 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 981 PHE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 516 TYR Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 288 optimal weight: 0.1980 chunk 464 optimal weight: 0.3980 chunk 283 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 487 optimal weight: 9.9990 chunk 448 optimal weight: 8.9990 chunk 387 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 299 optimal weight: 0.9990 chunk 237 optimal weight: 0.3980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 66 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 40971 Z= 0.198 Angle : 0.598 12.749 55704 Z= 0.301 Chirality : 0.044 0.331 6318 Planarity : 0.004 0.077 7116 Dihedral : 6.156 59.753 6603 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 1.09 % Allowed : 14.85 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.56 (0.12), residues: 4860 helix: 1.00 (0.13), residues: 1709 sheet: 0.38 (0.19), residues: 691 loop : -1.66 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP F 610 HIS 0.010 0.001 HIS E 493 PHE 0.013 0.001 PHE C1121 TYR 0.028 0.001 TYR A 265 ARG 0.003 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9720 Ramachandran restraints generated. 4860 Oldfield, 0 Emsley, 4860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2673 (pp) REVERT: B 553 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 33 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7822 (t) REVERT: C 740 MET cc_start: 0.8706 (mmm) cc_final: 0.8148 (tmm) REVERT: E 376 MET cc_start: -0.0163 (ptp) cc_final: -0.0462 (tpt) outliers start: 47 outliers final: 41 residues processed: 201 average time/residue: 0.3785 time to fit residues: 134.3661 Evaluate side-chains 203 residues out of total 4324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 159 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 978 ASN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain E residue 493 HIS Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 364 VAL Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 574 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 308 optimal weight: 0.7980 chunk 413 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 162 optimal weight: 0.0170 chunk 398 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.158368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.133311 restraints weight = 188800.788| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 5.00 r_work: 0.3479 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40971 Z= 0.179 Angle : 0.577 15.245 55704 Z= 0.289 Chirality : 0.043 0.330 6318 Planarity : 0.004 0.076 7116 Dihedral : 5.856 59.223 6603 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 1.11 % Allowed : 14.96 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % 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: -0.42 (0.12), residues: 4860 helix: 1.07 (0.13), residues: 1724 sheet: 0.51 (0.19), residues: 682 loop : -1.56 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.001 TRP F 610 HIS 0.015 0.001 HIS E 493 PHE 0.012 0.001 PHE C1121 TYR 0.029 0.001 TYR A 265 ARG 0.015 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8419.63 seconds wall clock time: 149 minutes 22.93 seconds (8962.93 seconds total)