Starting phenix.real_space_refine on Wed Mar 20 06:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7enf_31209/03_2024/7enf_31209.pdb" } resolution = 2.76 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 16921 2.51 5 N 4353 2.21 5 O 5229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 138": "OD1" <-> "OD2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 148": "NH1" <-> "NH2" Residue "O GLU 193": "OE1" <-> "OE2" Residue "O PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ASP 54": "OD1" <-> "OD2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P ASP 90": "OD1" <-> "OD2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 98": "NH1" <-> "NH2" Residue "P ASP 111": "OD1" <-> "OD2" Residue "P TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 158": "OE1" <-> "OE2" Residue "P PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 218": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26619 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7393 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 52, 'TRANS': 915} Chain breaks: 11 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 120 Chain: "B" Number of atoms: 7746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7746 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 7355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7355 Classifications: {'peptide': 976} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 923} Chain breaks: 12 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 5, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 205 Chain: "O" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.90, per 1000 atoms: 0.52 Number of scatterers: 26619 At special positions: 0 Unit cell: (130.353, 137.894, 224.078, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 5229 8.00 N 4353 7.00 C 16921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.00 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 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=2.04 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=2.00 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 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=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.01 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 O 140 " - pdb=" SG CYS O 200 " distance=2.03 Simple disulfide: pdb=" SG CYS P 103 " - pdb=" SG CYS P 108 " distance=2.03 Simple disulfide: pdb=" SG CYS P 150 " - pdb=" SG CYS P 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1134 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1074 " " NAG L 1 " - " ASN C 717 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C1074 " " NAG R 1 " - " ASN C 165 " " NAG S 1 " - " ASN B 343 " Time building additional restraints: 11.05 Conformation dependent library (CDL) restraints added in 5.0 seconds 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6360 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 53 sheets defined 23.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.570A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.802A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.511A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.659A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.758A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.100A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.251A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.749A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.817A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.876A pdb=" N LYS B 814 " --> pdb=" O LYS B 811 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG B 815 " --> pdb=" O PRO B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 815' Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.676A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.549A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.514A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.836A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.103A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 removed outlier: 4.151A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.882A pdb=" N TYR C 160 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.646A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.900A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.137A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.519A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.264A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.775A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.563A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.127A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 983 removed outlier: 3.578A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.087A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.643A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 134 removed outlier: 3.948A pdb=" N LEU O 131 " --> pdb=" O ASP O 128 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS O 132 " --> pdb=" O GLU O 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY O 134 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 193 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.572A pdb=" N SER P 31 " --> pdb=" O THR P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 65 Processing helix chain 'P' and resid 195 through 199 removed outlier: 3.630A pdb=" N LEU P 199 " --> pdb=" O SER P 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.582A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.767A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.909A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 122 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.024A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.234A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.310A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.844A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.942A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.655A pdb=" N VAL A1133 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.007A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.195A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.758A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.894A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.356A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.177A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.549A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.508A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.103A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.043A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.701A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.980A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.518A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.275A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.872A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.985A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.792A 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: 4.533A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'O' and resid 12 through 13 Processing sheet with id=AF1, first strand: chain 'O' and resid 59 through 60 removed outlier: 6.433A pdb=" N TRP O 41 " --> pdb=" O LEU O 53 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N TYR O 55 " --> pdb=" O LEU O 39 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU O 39 " --> pdb=" O TYR O 55 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 122 through 124 removed outlier: 6.141A pdb=" N TYR O 179 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 151 through 156 Processing sheet with id=AF4, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AF5, first strand: chain 'P' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'P' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET P 34 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS P 96 " --> pdb=" O GLY P 114 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR P 112 " --> pdb=" O ARG P 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 132 through 134 Processing sheet with id=AF8, first strand: chain 'P' and resid 162 through 164 removed outlier: 3.647A pdb=" N SER P 163 " --> pdb=" O ASN P 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN P 207 " --> pdb=" O SER P 163 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR P 204 " --> pdb=" O VAL P 221 " (cutoff:3.500A) 1103 hydrogen bonds defined for protein. 2988 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: 13.23 Time building geometry restraints manager: 11.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4328 1.31 - 1.44: 7350 1.44 - 1.57: 15376 1.57 - 1.70: 0 1.70 - 1.83: 143 Bond restraints: 27197 Sorted by residual: bond pdb=" C7 NAG I 2 " pdb=" N2 NAG I 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C7 NAG A1306 " pdb=" N2 NAG A1306 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG I 1 " pdb=" N2 NAG I 1 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C7 NAG B1305 " pdb=" N2 NAG B1305 " ideal model delta sigma weight residual 1.346 1.458 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 27192 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.91: 670 105.91 - 112.98: 14826 112.98 - 120.05: 9270 120.05 - 127.11: 12072 127.11 - 134.18: 231 Bond angle restraints: 37069 Sorted by residual: angle pdb=" C CYS C 743 " pdb=" CA CYS C 743 " pdb=" CB CYS C 743 " ideal model delta sigma weight residual 111.85 99.62 12.23 1.47e+00 4.63e-01 6.93e+01 angle pdb=" N LEU B 517 " pdb=" CA LEU B 517 " pdb=" C LEU B 517 " ideal model delta sigma weight residual 113.21 105.35 7.86 1.15e+00 7.56e-01 4.67e+01 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 112.17 121.11 -8.94 1.40e+00 5.10e-01 4.08e+01 angle pdb=" N SER O 33 " pdb=" CA SER O 33 " pdb=" C SER O 33 " ideal model delta sigma weight residual 111.28 105.03 6.25 1.09e+00 8.42e-01 3.29e+01 angle pdb=" N ASP A 138 " pdb=" CA ASP A 138 " pdb=" C ASP A 138 " ideal model delta sigma weight residual 108.75 99.35 9.40 1.70e+00 3.46e-01 3.06e+01 ... (remaining 37064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 15800 25.35 - 50.70: 729 50.70 - 76.06: 186 76.06 - 101.41: 100 101.41 - 126.76: 65 Dihedral angle restraints: 16880 sinusoidal: 7022 harmonic: 9858 Sorted by residual: dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -174.06 88.06 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -6.53 -79.47 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 ... (remaining 16877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 3890 0.085 - 0.171: 489 0.171 - 0.256: 39 0.256 - 0.342: 12 0.342 - 0.427: 3 Chirality restraints: 4433 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.02e+01 chirality pdb=" CA TYR O 31 " pdb=" N TYR O 31 " pdb=" C TYR O 31 " pdb=" CB TYR O 31 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA CYS C 743 " pdb=" N CYS C 743 " pdb=" C CYS C 743 " pdb=" CB CYS C 743 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 4430 not shown) Planarity restraints: 4760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.332 2.00e-02 2.50e+03 2.89e-01 1.04e+03 pdb=" C7 NAG R 2 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 741 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C TYR C 741 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR C 741 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 742 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 31 " -0.031 2.00e-02 2.50e+03 2.01e-02 8.10e+00 pdb=" CG TYR O 31 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR O 31 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR O 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR O 31 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR O 31 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 31 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR O 31 " -0.005 2.00e-02 2.50e+03 ... (remaining 4757 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2044 2.73 - 3.28: 26337 3.28 - 3.82: 42561 3.82 - 4.36: 51571 4.36 - 4.90: 89517 Nonbonded interactions: 212030 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.192 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.197 2.440 nonbonded pdb=" O PHE P 29 " pdb=" NH2 ARG P 72 " model vdw 2.197 2.520 nonbonded pdb=" OD2 ASP C 40 " pdb=" NH1 ARG C 44 " model vdw 2.208 2.520 nonbonded pdb=" O PRO B1053 " pdb=" NE2 GLN B1054 " model vdw 2.208 2.520 ... (remaining 212025 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 27 through 66 or resid 81 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 128 or ( \ resid 129 and (name N or name CA or name C or name O or name CB )) or resid 130 \ through 140 or (resid 157 through 160 and (name N or name CA or name C or name O \ or name CB )) or resid 161 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA \ or name C or name O or name CB )) or resid 191 through 194 or (resid 195 throug \ h 198 and (name N or name CA or name C or name O or name CB )) or resid 199 thro \ ugh 209 or resid 217 through 236 or (resid 237 and (name N or name CA or name C \ or name O or name CB )) or resid 238 or (resid 239 and (name N or name CA or nam \ e C or name O or name CB )) or resid 240 through 243 or resid 264 through 331 or \ (resid 332 through 335 and (name N or name CA or name C or name O or name CB )) \ or resid 336 through 350 or (resid 351 through 352 and (name N or name CA or na \ me C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 368 or (resid \ 369 and (name N or name CA or name C or name O or name CB )) or resid 370 throug \ h 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or \ resid 375 through 407 or (resid 408 and (name N or name CA or name C or name O o \ r name CB )) or resid 409 through 441 or (resid 442 and (name N or name CA or na \ me C or name O or name CB )) or resid 443 or (resid 449 and (name N or name CA o \ r name C or name O or name CB )) or resid 450 through 496 or (resid 497 through \ 498 and (name N or name CA or name C or name O or name CB )) or resid 503 throug \ h 508 or (resid 509 and (name N or name CA or name C or name O or name CB )) or \ resid 510 through 620 or resid 641 through 1146 or resid 1301 through 1307)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 195 or (resid 196 through 19 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 199 through \ 236 or (resid 237 and (name N or name CA or name C or name O or name CB )) or re \ sid 238 or (resid 239 and (name N or name CA or name C or name O or name CB )) o \ r resid 240 through 289 or (resid 290 and (name N or name CA or name C or name O \ or name CB )) or resid 291 through 332 or (resid 333 through 335 and (name N or \ name CA or name C or name O or name CB )) or resid 336 through 339 or (resid 34 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 341 through \ 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or re \ sid 347 through 348 or (resid 349 and (name N or name CA or name C or name O or \ name CB )) or resid 350 or (resid 351 through 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 through 363 or (resid 364 and (name N or \ name CA or name C or name O or name CB )) or resid 365 through 368 or (resid 36 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 373 or (resid 374 and (name N or name CA or name C or name O or name CB )) or re \ sid 375 through 397 or (resid 398 and (name N or name CA or name C or name O or \ name CB )) or resid 399 through 402 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 or (resid 405 through 408 and (name N or \ name CA or name C or name O or name CB )) or resid 409 through 413 or (resid 41 \ 4 through 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or re \ sid 418 through 419 or (resid 420 and (name N or name CA or name C or name O or \ name CB )) or resid 421 through 423 or (resid 424 and (name N or name CA or name \ C or name O or name CB )) or resid 425 through 426 or (resid 427 through 428 an \ d (name N or name CA or name C or name O or name CB )) or resid 429 through 440 \ or (resid 441 through 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 or (resid 449 and (name N or name CA or name C or name O or name \ CB )) or resid 450 through 453 or (resid 454 and (name N or name CA or name C o \ r name O or name CB )) or resid 491 or (resid 492 through 493 and (name N or nam \ e CA or name C or name O or name CB )) or resid 494 through 496 or (resid 497 th \ rough 498 and (name N or name CA or name C or name O or name CB )) or resid 503 \ through 508 or (resid 509 and (name N or name CA or name C or name O or name CB \ )) or resid 510 through 515 or (resid 516 and (name N or name CA or name C or na \ me O or name CB )) or resid 517 through 518 or (resid 519 through 520 and (name \ N or name CA or name C or name O or name CB )) or resid 521 through 527 or (resi \ d 528 through 529 and (name N or name CA or name C or name O or name CB )) or re \ sid 530 through 620 or resid 641 through 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 27 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or resid 81 through 187 or (res \ id 188 and (name N or name CA or name C or name O or name CB )) or resid 189 thr \ ough 209 or resid 217 through 243 or resid 264 through 280 or (resid 281 and (na \ me N or name CA or name C or name O or name CB )) or resid 282 through 454 or re \ sid 491 through 1146 or resid 1301 through 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.410 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 75.290 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.270 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.010 0.117 27197 Z= 0.641 Angle : 0.955 12.233 37069 Z= 0.514 Chirality : 0.058 0.427 4433 Planarity : 0.007 0.289 4720 Dihedral : 19.135 126.759 10403 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.53 % Allowed : 0.63 % Favored : 98.84 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.23 % 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: -1.36 (0.14), residues: 3318 helix: 0.64 (0.21), residues: 667 sheet: -0.33 (0.17), residues: 838 loop : -1.85 (0.13), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 886 HIS 0.006 0.001 HIS O 204 PHE 0.041 0.002 PHE B 906 TYR 0.047 0.002 TYR O 31 ARG 0.009 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6346 (p90) cc_final: 0.5962 (p-80) REVERT: A 168 PHE cc_start: 0.7286 (t80) cc_final: 0.6905 (t80) REVERT: A 170 TYR cc_start: 0.8240 (t80) cc_final: 0.7891 (t80) REVERT: A 574 ASP cc_start: 0.7826 (t70) cc_final: 0.7593 (t0) REVERT: A 869 MET cc_start: 0.8826 (mtt) cc_final: 0.8456 (mtt) REVERT: B 118 LEU cc_start: 0.7743 (mm) cc_final: 0.7517 (mm) REVERT: B 129 LYS cc_start: 0.8666 (mppt) cc_final: 0.8416 (mppt) REVERT: B 342 PHE cc_start: 0.8828 (m-80) cc_final: 0.8625 (m-10) REVERT: B 358 ILE cc_start: 0.8531 (pt) cc_final: 0.8219 (pp) REVERT: B 408 ARG cc_start: 0.8039 (ppt170) cc_final: 0.7637 (ppt170) REVERT: B 458 LYS cc_start: 0.8042 (pttp) cc_final: 0.7768 (tttt) REVERT: C 100 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7571 (mp) REVERT: C 133 PHE cc_start: 0.8592 (m-10) cc_final: 0.8212 (m-80) REVERT: C 174 PRO cc_start: 0.7294 (Cg_endo) cc_final: 0.6904 (Cg_exo) REVERT: O 95 HIS cc_start: 0.6500 (t70) cc_final: 0.5577 (t-90) REVERT: P 90 ASP cc_start: 0.3174 (OUTLIER) cc_final: 0.2544 (t70) outliers start: 15 outliers final: 4 residues processed: 217 average time/residue: 1.1148 time to fit residues: 291.1755 Evaluate side-chains 148 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain O residue 115 THR Chi-restraints excluded: chain P residue 90 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A1010 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 703 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN O 35 ASN P 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27197 Z= 0.244 Angle : 0.722 11.714 37069 Z= 0.348 Chirality : 0.050 0.304 4433 Planarity : 0.005 0.062 4720 Dihedral : 15.936 113.247 4714 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.88 % Allowed : 7.44 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.99 (0.14), residues: 3318 helix: 1.11 (0.21), residues: 681 sheet: -0.16 (0.17), residues: 855 loop : -1.67 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 164 HIS 0.004 0.001 HIS O 204 PHE 0.026 0.002 PHE B 906 TYR 0.027 0.002 TYR C 904 ARG 0.007 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 2.974 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6400 (p90) cc_final: 0.5991 (p-80) REVERT: A 84 LEU cc_start: 0.6778 (mt) cc_final: 0.6489 (mt) REVERT: A 168 PHE cc_start: 0.7295 (t80) cc_final: 0.6683 (t80) REVERT: A 170 TYR cc_start: 0.8240 (t80) cc_final: 0.7844 (t80) REVERT: A 574 ASP cc_start: 0.7775 (t70) cc_final: 0.7490 (OUTLIER) REVERT: A 869 MET cc_start: 0.8851 (mtt) cc_final: 0.8451 (mtt) REVERT: B 118 LEU cc_start: 0.7880 (mm) cc_final: 0.7583 (mt) REVERT: B 129 LYS cc_start: 0.8675 (mppt) cc_final: 0.8462 (mppt) REVERT: B 200 TYR cc_start: 0.8448 (m-80) cc_final: 0.8200 (m-80) REVERT: B 342 PHE cc_start: 0.8851 (m-80) cc_final: 0.8646 (m-10) REVERT: B 458 LYS cc_start: 0.8024 (pttp) cc_final: 0.7675 (mmmt) REVERT: B 740 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8517 (ttp) REVERT: C 133 PHE cc_start: 0.8487 (m-10) cc_final: 0.8171 (m-80) REVERT: C 174 PRO cc_start: 0.7228 (Cg_endo) cc_final: 0.6805 (Cg_exo) REVERT: C 357 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8175 (mmm-85) REVERT: C 740 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7370 (ttp) REVERT: O 95 HIS cc_start: 0.6474 (t70) cc_final: 0.5995 (t70) outliers start: 25 outliers final: 9 residues processed: 186 average time/residue: 1.1028 time to fit residues: 249.6897 Evaluate side-chains 155 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 388 ASN B 394 ASN B 703 ASN C 52 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27197 Z= 0.340 Angle : 0.711 11.590 37069 Z= 0.345 Chirality : 0.050 0.292 4433 Planarity : 0.005 0.063 4720 Dihedral : 12.147 114.146 4711 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.94 % Allowed : 10.61 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.87 (0.14), residues: 3318 helix: 1.20 (0.21), residues: 678 sheet: 0.02 (0.17), residues: 857 loop : -1.65 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 47 HIS 0.014 0.001 HIS B 207 PHE 0.027 0.002 PHE B 906 TYR 0.032 0.002 TYR C 904 ARG 0.006 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 163 time to evaluate : 3.365 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6297 (p90) cc_final: 0.5895 (p-80) REVERT: A 84 LEU cc_start: 0.6597 (mt) cc_final: 0.6299 (mt) REVERT: A 168 PHE cc_start: 0.7191 (t80) cc_final: 0.6845 (t80) REVERT: A 170 TYR cc_start: 0.8261 (t80) cc_final: 0.7940 (t80) REVERT: A 574 ASP cc_start: 0.7811 (t70) cc_final: 0.7540 (OUTLIER) REVERT: A 869 MET cc_start: 0.8834 (mtt) cc_final: 0.8481 (mtt) REVERT: B 129 LYS cc_start: 0.8683 (mppt) cc_final: 0.8439 (mppt) REVERT: B 200 TYR cc_start: 0.8490 (m-80) cc_final: 0.8233 (m-80) REVERT: B 342 PHE cc_start: 0.8877 (m-80) cc_final: 0.8639 (m-10) REVERT: B 458 LYS cc_start: 0.8063 (pttp) cc_final: 0.7696 (tttt) REVERT: B 488 CYS cc_start: 0.4344 (OUTLIER) cc_final: 0.3278 (m) REVERT: C 100 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7507 (mp) REVERT: C 133 PHE cc_start: 0.8514 (m-10) cc_final: 0.8211 (m-80) REVERT: C 174 PRO cc_start: 0.7024 (Cg_endo) cc_final: 0.6561 (Cg_exo) REVERT: C 319 ARG cc_start: 0.7999 (ttm110) cc_final: 0.7799 (ttp-170) REVERT: C 357 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8258 (mmm-85) REVERT: C 400 PHE cc_start: 0.7994 (p90) cc_final: 0.7759 (p90) REVERT: C 421 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.3648 (m-80) REVERT: C 740 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7466 (ttp) REVERT: C 794 ILE cc_start: 0.8741 (mm) cc_final: 0.8396 (pp) REVERT: O 95 HIS cc_start: 0.6635 (t70) cc_final: 0.5907 (t70) REVERT: P 90 ASP cc_start: 0.3328 (OUTLIER) cc_final: 0.2191 (t70) outliers start: 55 outliers final: 25 residues processed: 201 average time/residue: 1.0039 time to fit residues: 248.0045 Evaluate side-chains 180 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 33 optimal weight: 30.0000 chunk 145 optimal weight: 5.9990 chunk 205 optimal weight: 0.0670 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 506 GLN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN C 506 GLN C 751 ASN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27197 Z= 0.162 Angle : 0.627 12.468 37069 Z= 0.302 Chirality : 0.046 0.285 4433 Planarity : 0.004 0.061 4720 Dihedral : 10.051 110.192 4710 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.97 % Allowed : 11.64 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3318 helix: 1.59 (0.21), residues: 674 sheet: 0.19 (0.17), residues: 849 loop : -1.50 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 47 HIS 0.003 0.000 HIS P 35 PHE 0.018 0.001 PHE B 92 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 3.065 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6458 (p90) cc_final: 0.6047 (p-80) REVERT: A 84 LEU cc_start: 0.6584 (mt) cc_final: 0.6303 (mt) REVERT: A 168 PHE cc_start: 0.7403 (t80) cc_final: 0.6750 (t80) REVERT: A 170 TYR cc_start: 0.8238 (t80) cc_final: 0.7945 (t80) REVERT: A 574 ASP cc_start: 0.7778 (t70) cc_final: 0.7471 (OUTLIER) REVERT: A 869 MET cc_start: 0.8820 (mtt) cc_final: 0.8489 (mtt) REVERT: A 1040 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8882 (m) REVERT: B 118 LEU cc_start: 0.7289 (mm) cc_final: 0.6902 (mm) REVERT: B 129 LYS cc_start: 0.8699 (mppt) cc_final: 0.8449 (mppt) REVERT: B 200 TYR cc_start: 0.8379 (m-80) cc_final: 0.8113 (m-80) REVERT: B 342 PHE cc_start: 0.8903 (m-80) cc_final: 0.8650 (m-10) REVERT: B 458 LYS cc_start: 0.8087 (pttp) cc_final: 0.7652 (mmmt) REVERT: B 488 CYS cc_start: 0.4067 (OUTLIER) cc_final: 0.3069 (m) REVERT: B 490 PHE cc_start: 0.5669 (OUTLIER) cc_final: 0.5079 (t80) REVERT: B 904 TYR cc_start: 0.7262 (m-80) cc_final: 0.7059 (m-80) REVERT: C 133 PHE cc_start: 0.8569 (m-80) cc_final: 0.8284 (m-80) REVERT: C 174 PRO cc_start: 0.6956 (Cg_endo) cc_final: 0.6442 (Cg_exo) REVERT: C 226 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8461 (tt) REVERT: C 357 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8229 (mmm-85) REVERT: C 400 PHE cc_start: 0.7984 (p90) cc_final: 0.7763 (p90) REVERT: C 421 TYR cc_start: 0.4907 (OUTLIER) cc_final: 0.3637 (m-80) REVERT: C 725 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: O 95 HIS cc_start: 0.6735 (t70) cc_final: 0.6032 (t-90) outliers start: 56 outliers final: 23 residues processed: 214 average time/residue: 0.9815 time to fit residues: 261.1214 Evaluate side-chains 181 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 179 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 703 ASN C 506 GLN C 580 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27197 Z= 0.282 Angle : 0.642 12.193 37069 Z= 0.315 Chirality : 0.047 0.276 4433 Planarity : 0.004 0.062 4720 Dihedral : 9.327 109.416 4708 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.15 % Allowed : 13.50 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3318 helix: 1.52 (0.21), residues: 678 sheet: 0.20 (0.17), residues: 859 loop : -1.48 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 47 HIS 0.006 0.001 HIS B 207 PHE 0.022 0.001 PHE C 106 TYR 0.024 0.001 TYR B 904 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 155 time to evaluate : 2.773 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6382 (p90) cc_final: 0.5944 (p-80) REVERT: A 84 LEU cc_start: 0.6702 (mt) cc_final: 0.6417 (mt) REVERT: A 168 PHE cc_start: 0.7284 (t80) cc_final: 0.6729 (t80) REVERT: A 170 TYR cc_start: 0.8220 (t80) cc_final: 0.7912 (t80) REVERT: A 574 ASP cc_start: 0.7784 (t70) cc_final: 0.7477 (OUTLIER) REVERT: A 869 MET cc_start: 0.8831 (mtt) cc_final: 0.8577 (mtt) REVERT: A 990 GLU cc_start: 0.7292 (mm-30) cc_final: 0.7061 (mm-30) REVERT: A 1040 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8893 (m) REVERT: B 118 LEU cc_start: 0.7301 (mm) cc_final: 0.6985 (mm) REVERT: B 129 LYS cc_start: 0.8696 (mppt) cc_final: 0.8435 (mppt) REVERT: B 200 TYR cc_start: 0.8432 (m-80) cc_final: 0.8166 (m-80) REVERT: B 342 PHE cc_start: 0.8926 (m-80) cc_final: 0.8687 (m-10) REVERT: B 458 LYS cc_start: 0.8117 (pttp) cc_final: 0.7653 (mmmt) REVERT: B 490 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.5061 (t80) REVERT: B 904 TYR cc_start: 0.7406 (m-80) cc_final: 0.7185 (m-80) REVERT: C 133 PHE cc_start: 0.8581 (m-80) cc_final: 0.8302 (m-80) REVERT: C 174 PRO cc_start: 0.6741 (Cg_endo) cc_final: 0.6280 (Cg_exo) REVERT: C 200 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.6327 (t80) REVERT: C 226 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8482 (tt) REVERT: C 357 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8244 (mmm-85) REVERT: C 400 PHE cc_start: 0.8027 (p90) cc_final: 0.7809 (p90) REVERT: C 421 TYR cc_start: 0.4897 (OUTLIER) cc_final: 0.3413 (m-80) REVERT: C 725 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: O 95 HIS cc_start: 0.6727 (t70) cc_final: 0.6143 (t-90) REVERT: P 47 TRP cc_start: 0.7542 (t-100) cc_final: 0.6585 (t-100) REVERT: P 90 ASP cc_start: 0.3101 (OUTLIER) cc_final: 0.2292 (t70) outliers start: 61 outliers final: 35 residues processed: 201 average time/residue: 0.9157 time to fit residues: 231.1421 Evaluate side-chains 186 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 190 optimal weight: 0.0050 chunk 80 optimal weight: 0.9990 chunk 325 optimal weight: 9.9990 chunk 269 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 107 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27197 Z= 0.148 Angle : 0.588 11.512 37069 Z= 0.288 Chirality : 0.045 0.264 4433 Planarity : 0.004 0.060 4720 Dihedral : 8.438 109.628 4708 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.12 % Allowed : 14.10 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3318 helix: 1.76 (0.21), residues: 674 sheet: 0.36 (0.17), residues: 837 loop : -1.36 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 41 HIS 0.002 0.000 HIS B1064 PHE 0.015 0.001 PHE B 92 TYR 0.019 0.001 TYR B 904 ARG 0.009 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 164 time to evaluate : 2.729 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6370 (p90) cc_final: 0.5942 (p-80) REVERT: A 84 LEU cc_start: 0.6672 (mt) cc_final: 0.6396 (mt) REVERT: A 168 PHE cc_start: 0.7279 (t80) cc_final: 0.6746 (t80) REVERT: A 170 TYR cc_start: 0.8226 (t80) cc_final: 0.7887 (t80) REVERT: A 574 ASP cc_start: 0.7671 (t70) cc_final: 0.7347 (OUTLIER) REVERT: A 869 MET cc_start: 0.8821 (mtt) cc_final: 0.8495 (mtt) REVERT: A 1040 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8880 (m) REVERT: B 86 PHE cc_start: 0.5542 (t80) cc_final: 0.5101 (t80) REVERT: B 118 LEU cc_start: 0.7299 (mm) cc_final: 0.6894 (mm) REVERT: B 129 LYS cc_start: 0.8672 (mppt) cc_final: 0.8401 (mppt) REVERT: B 200 TYR cc_start: 0.8356 (m-80) cc_final: 0.8038 (m-80) REVERT: B 207 HIS cc_start: 0.6744 (m-70) cc_final: 0.6531 (m-70) REVERT: B 342 PHE cc_start: 0.8876 (m-80) cc_final: 0.8616 (m-10) REVERT: B 421 TYR cc_start: 0.7771 (m-80) cc_final: 0.7491 (m-80) REVERT: B 458 LYS cc_start: 0.8140 (pttp) cc_final: 0.7664 (tptt) REVERT: B 488 CYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3107 (m) REVERT: B 490 PHE cc_start: 0.5796 (OUTLIER) cc_final: 0.5196 (t80) REVERT: C 133 PHE cc_start: 0.8499 (m-80) cc_final: 0.8272 (m-80) REVERT: C 174 PRO cc_start: 0.6669 (Cg_endo) cc_final: 0.6241 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8906 (tttp) cc_final: 0.8640 (ttmm) REVERT: C 319 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7603 (ttp-170) REVERT: C 357 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8356 (mmm-85) REVERT: C 421 TYR cc_start: 0.5014 (OUTLIER) cc_final: 0.3543 (m-80) REVERT: C 745 ASP cc_start: 0.7443 (t0) cc_final: 0.7086 (t0) REVERT: C 1125 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7898 (p0) REVERT: O 95 HIS cc_start: 0.6905 (t70) cc_final: 0.6239 (t-90) REVERT: P 196 SER cc_start: 0.1509 (OUTLIER) cc_final: 0.1045 (m) outliers start: 60 outliers final: 31 residues processed: 212 average time/residue: 0.9321 time to fit residues: 247.5044 Evaluate side-chains 185 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 148 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 0.0060 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 323 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 13 GLN P 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 27197 Z= 0.245 Angle : 0.609 10.899 37069 Z= 0.302 Chirality : 0.046 0.333 4433 Planarity : 0.004 0.058 4720 Dihedral : 8.201 109.255 4707 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.50 % Allowed : 14.53 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.41 (0.14), residues: 3318 helix: 1.61 (0.21), residues: 686 sheet: 0.34 (0.17), residues: 832 loop : -1.38 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 353 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE C 400 TYR 0.027 0.001 TYR B 904 ARG 0.006 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 155 time to evaluate : 3.059 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6335 (p90) cc_final: 0.5907 (p-80) REVERT: A 84 LEU cc_start: 0.6700 (mt) cc_final: 0.6483 (mt) REVERT: A 168 PHE cc_start: 0.7349 (t80) cc_final: 0.6740 (t80) REVERT: A 170 TYR cc_start: 0.8272 (t80) cc_final: 0.7898 (t80) REVERT: A 196 ASN cc_start: 0.7370 (t0) cc_final: 0.6752 (m-40) REVERT: A 574 ASP cc_start: 0.7662 (t70) cc_final: 0.7338 (OUTLIER) REVERT: A 869 MET cc_start: 0.8847 (mtt) cc_final: 0.8469 (mtt) REVERT: A 1040 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8893 (m) REVERT: B 118 LEU cc_start: 0.7279 (mm) cc_final: 0.6945 (mm) REVERT: B 129 LYS cc_start: 0.8684 (mppt) cc_final: 0.8397 (mppt) REVERT: B 157 PHE cc_start: 0.7895 (p90) cc_final: 0.7674 (p90) REVERT: B 200 TYR cc_start: 0.8329 (m-80) cc_final: 0.8012 (m-80) REVERT: B 207 HIS cc_start: 0.6765 (m-70) cc_final: 0.6544 (m-70) REVERT: B 342 PHE cc_start: 0.8890 (m-80) cc_final: 0.8624 (m-10) REVERT: B 421 TYR cc_start: 0.7826 (m-80) cc_final: 0.7592 (m-80) REVERT: B 458 LYS cc_start: 0.8060 (pttp) cc_final: 0.7585 (tptt) REVERT: B 488 CYS cc_start: 0.4160 (OUTLIER) cc_final: 0.3108 (m) REVERT: B 490 PHE cc_start: 0.5832 (OUTLIER) cc_final: 0.5246 (t80) REVERT: C 42 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7811 (m) REVERT: C 133 PHE cc_start: 0.8455 (m-80) cc_final: 0.8209 (m-80) REVERT: C 174 PRO cc_start: 0.6697 (Cg_endo) cc_final: 0.6272 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8971 (tttp) cc_final: 0.8696 (ttmm) REVERT: C 319 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7709 (ttp-170) REVERT: C 357 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8376 (mmm-85) REVERT: C 421 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.3545 (m-80) REVERT: C 725 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: O 95 HIS cc_start: 0.6902 (t70) cc_final: 0.6253 (t-90) REVERT: P 90 ASP cc_start: 0.3012 (OUTLIER) cc_final: 0.2285 (t70) REVERT: P 196 SER cc_start: 0.1493 (OUTLIER) cc_final: 0.1034 (m) outliers start: 71 outliers final: 37 residues processed: 209 average time/residue: 0.9469 time to fit residues: 246.8269 Evaluate side-chains 188 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 57 ASN Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 30 optimal weight: 0.0070 chunk 254 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 955 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27197 Z= 0.193 Angle : 0.611 20.023 37069 Z= 0.300 Chirality : 0.046 0.340 4433 Planarity : 0.004 0.059 4720 Dihedral : 7.926 109.202 4707 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.36 % Allowed : 15.09 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.36 (0.14), residues: 3318 helix: 1.68 (0.21), residues: 679 sheet: 0.37 (0.17), residues: 836 loop : -1.34 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 41 HIS 0.002 0.000 HIS O 195 PHE 0.014 0.001 PHE A 643 TYR 0.024 0.001 TYR B 904 ARG 0.012 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 3.089 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6326 (p90) cc_final: 0.5902 (p-80) REVERT: A 84 LEU cc_start: 0.7014 (mt) cc_final: 0.6809 (mt) REVERT: A 168 PHE cc_start: 0.7308 (t80) cc_final: 0.6705 (t80) REVERT: A 170 TYR cc_start: 0.8232 (t80) cc_final: 0.7876 (t80) REVERT: A 574 ASP cc_start: 0.7650 (t70) cc_final: 0.7315 (OUTLIER) REVERT: A 869 MET cc_start: 0.8825 (mtt) cc_final: 0.8466 (mtt) REVERT: A 878 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 1040 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8885 (m) REVERT: B 86 PHE cc_start: 0.5599 (t80) cc_final: 0.5150 (t80) REVERT: B 118 LEU cc_start: 0.7297 (mm) cc_final: 0.6892 (mm) REVERT: B 129 LYS cc_start: 0.8622 (mppt) cc_final: 0.8352 (mppt) REVERT: B 157 PHE cc_start: 0.7997 (p90) cc_final: 0.7715 (p90) REVERT: B 200 TYR cc_start: 0.8309 (m-80) cc_final: 0.8002 (m-80) REVERT: B 342 PHE cc_start: 0.8896 (m-80) cc_final: 0.8493 (m-10) REVERT: B 421 TYR cc_start: 0.7886 (m-80) cc_final: 0.7635 (m-80) REVERT: B 458 LYS cc_start: 0.8054 (pttp) cc_final: 0.7582 (tptt) REVERT: B 488 CYS cc_start: 0.4189 (OUTLIER) cc_final: 0.3146 (m) REVERT: B 490 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.5113 (t80) REVERT: B 540 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8034 (p0) REVERT: C 171 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8385 (p) REVERT: C 174 PRO cc_start: 0.6689 (Cg_endo) cc_final: 0.6264 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8948 (tttp) cc_final: 0.8681 (ttmm) REVERT: C 357 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8406 (mmm-85) REVERT: C 421 TYR cc_start: 0.4881 (OUTLIER) cc_final: 0.3387 (m-80) REVERT: C 725 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: C 745 ASP cc_start: 0.7496 (t0) cc_final: 0.7165 (t0) REVERT: O 95 HIS cc_start: 0.6840 (t70) cc_final: 0.6271 (t-90) REVERT: P 90 ASP cc_start: 0.2676 (OUTLIER) cc_final: 0.1918 (t70) REVERT: P 196 SER cc_start: 0.1479 (OUTLIER) cc_final: 0.1021 (m) outliers start: 67 outliers final: 35 residues processed: 213 average time/residue: 0.8818 time to fit residues: 236.5588 Evaluate side-chains 197 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 30.0000 chunk 310 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 285 optimal weight: 0.5980 chunk 300 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 172 GLN ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27197 Z= 0.227 Angle : 0.612 17.780 37069 Z= 0.302 Chirality : 0.046 0.309 4433 Planarity : 0.004 0.058 4720 Dihedral : 7.782 108.951 4707 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.19 % Allowed : 15.30 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.36 (0.14), residues: 3318 helix: 1.63 (0.21), residues: 676 sheet: 0.38 (0.17), residues: 826 loop : -1.32 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 41 HIS 0.002 0.001 HIS B1048 PHE 0.023 0.001 PHE C 106 TYR 0.028 0.001 TYR B 904 ARG 0.010 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 159 time to evaluate : 3.026 Fit side-chains revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6330 (p90) cc_final: 0.5915 (p-80) REVERT: A 84 LEU cc_start: 0.7006 (mt) cc_final: 0.6765 (mt) REVERT: A 168 PHE cc_start: 0.7340 (t80) cc_final: 0.6770 (t80) REVERT: A 170 TYR cc_start: 0.8283 (t80) cc_final: 0.7866 (t80) REVERT: A 196 ASN cc_start: 0.7356 (t0) cc_final: 0.6634 (m-40) REVERT: A 574 ASP cc_start: 0.7642 (t70) cc_final: 0.7305 (OUTLIER) REVERT: A 869 MET cc_start: 0.8824 (mtt) cc_final: 0.8453 (mtt) REVERT: A 878 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 1040 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8892 (m) REVERT: B 86 PHE cc_start: 0.5578 (t80) cc_final: 0.5147 (t80) REVERT: B 118 LEU cc_start: 0.7295 (mm) cc_final: 0.6979 (mm) REVERT: B 129 LYS cc_start: 0.8632 (mppt) cc_final: 0.8347 (mppt) REVERT: B 157 PHE cc_start: 0.8013 (p90) cc_final: 0.7773 (p90) REVERT: B 200 TYR cc_start: 0.8262 (m-80) cc_final: 0.7945 (m-80) REVERT: B 342 PHE cc_start: 0.8813 (m-80) cc_final: 0.8517 (m-10) REVERT: B 408 ARG cc_start: 0.7743 (ptm-80) cc_final: 0.7531 (pmt-80) REVERT: B 421 TYR cc_start: 0.7904 (m-80) cc_final: 0.7674 (m-80) REVERT: B 458 LYS cc_start: 0.8052 (pttp) cc_final: 0.7547 (mmmt) REVERT: B 488 CYS cc_start: 0.4085 (OUTLIER) cc_final: 0.3048 (m) REVERT: B 490 PHE cc_start: 0.5704 (OUTLIER) cc_final: 0.5050 (t80) REVERT: B 540 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8025 (p0) REVERT: C 171 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8395 (p) REVERT: C 174 PRO cc_start: 0.6684 (Cg_endo) cc_final: 0.6258 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8946 (tttp) cc_final: 0.8677 (ttmm) REVERT: C 319 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7575 (ttp-170) REVERT: C 357 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8420 (mmm-85) REVERT: C 365 TYR cc_start: 0.8387 (m-80) cc_final: 0.7946 (m-80) REVERT: C 421 TYR cc_start: 0.4872 (OUTLIER) cc_final: 0.3296 (m-80) REVERT: C 725 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: C 745 ASP cc_start: 0.7504 (t0) cc_final: 0.7190 (t0) REVERT: C 1125 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7866 (p0) REVERT: O 95 HIS cc_start: 0.6826 (t70) cc_final: 0.6266 (t-90) REVERT: P 90 ASP cc_start: 0.2704 (OUTLIER) cc_final: 0.1945 (t70) REVERT: P 196 SER cc_start: 0.1672 (OUTLIER) cc_final: 0.1243 (m) outliers start: 62 outliers final: 37 residues processed: 206 average time/residue: 0.9061 time to fit residues: 233.4243 Evaluate side-chains 197 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 149 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 7.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 334 optimal weight: 40.0000 chunk 308 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 205 optimal weight: 0.0370 chunk 163 optimal weight: 0.0470 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27197 Z= 0.217 Angle : 0.611 17.275 37069 Z= 0.301 Chirality : 0.046 0.288 4433 Planarity : 0.004 0.058 4720 Dihedral : 7.668 108.795 4707 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.94 % Allowed : 15.62 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % 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: -0.30 (0.14), residues: 3318 helix: 1.73 (0.21), residues: 670 sheet: 0.37 (0.17), residues: 825 loop : -1.27 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 41 HIS 0.002 0.000 HIS O 195 PHE 0.023 0.001 PHE C 106 TYR 0.027 0.001 TYR B 904 ARG 0.014 0.000 ARG C 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6636 Ramachandran restraints generated. 3318 Oldfield, 0 Emsley, 3318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 153 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6266 (p90) cc_final: 0.5817 (p-80) REVERT: A 84 LEU cc_start: 0.7015 (mt) cc_final: 0.6771 (mt) REVERT: A 168 PHE cc_start: 0.7296 (t80) cc_final: 0.6736 (t80) REVERT: A 170 TYR cc_start: 0.8324 (t80) cc_final: 0.7919 (t80) REVERT: A 189 LEU cc_start: 0.8634 (tp) cc_final: 0.8347 (tp) REVERT: A 574 ASP cc_start: 0.7632 (t70) cc_final: 0.7289 (OUTLIER) REVERT: A 869 MET cc_start: 0.8821 (mtt) cc_final: 0.8453 (mtt) REVERT: A 878 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (mt) REVERT: A 1040 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8891 (m) REVERT: B 66 HIS cc_start: 0.4111 (OUTLIER) cc_final: 0.3769 (t-90) REVERT: B 86 PHE cc_start: 0.5573 (t80) cc_final: 0.5148 (t80) REVERT: B 118 LEU cc_start: 0.7287 (mm) cc_final: 0.6879 (mm) REVERT: B 129 LYS cc_start: 0.8656 (mppt) cc_final: 0.8375 (mppt) REVERT: B 157 PHE cc_start: 0.7997 (p90) cc_final: 0.7763 (p90) REVERT: B 200 TYR cc_start: 0.8255 (m-80) cc_final: 0.7938 (m-80) REVERT: B 342 PHE cc_start: 0.8794 (m-80) cc_final: 0.8487 (m-10) REVERT: B 408 ARG cc_start: 0.7672 (ptm-80) cc_final: 0.7400 (pmt-80) REVERT: B 421 TYR cc_start: 0.7829 (m-80) cc_final: 0.7603 (m-80) REVERT: B 458 LYS cc_start: 0.8072 (pttp) cc_final: 0.7571 (tptt) REVERT: B 488 CYS cc_start: 0.4528 (OUTLIER) cc_final: 0.3515 (m) REVERT: B 490 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4991 (t80) REVERT: B 540 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8013 (p0) REVERT: C 171 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8393 (p) REVERT: C 174 PRO cc_start: 0.6672 (Cg_endo) cc_final: 0.6262 (Cg_exo) REVERT: C 206 LYS cc_start: 0.8950 (tttp) cc_final: 0.8677 (ttmm) REVERT: C 319 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7603 (ttp-170) REVERT: C 357 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8427 (mmm-85) REVERT: C 365 TYR cc_start: 0.8422 (m-80) cc_final: 0.7987 (m-80) REVERT: C 421 TYR cc_start: 0.4917 (OUTLIER) cc_final: 0.3345 (m-80) REVERT: C 725 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: C 745 ASP cc_start: 0.7496 (t0) cc_final: 0.7195 (t0) REVERT: C 1125 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7864 (p0) REVERT: O 95 HIS cc_start: 0.6830 (t70) cc_final: 0.6288 (t-90) REVERT: P 90 ASP cc_start: 0.2723 (OUTLIER) cc_final: 0.1967 (t70) REVERT: P 196 SER cc_start: 0.1660 (OUTLIER) cc_final: 0.1231 (m) outliers start: 55 outliers final: 38 residues processed: 196 average time/residue: 0.9275 time to fit residues: 229.3818 Evaluate side-chains 202 residues out of total 2971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1125 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 VAL Chi-restraints excluded: chain P residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.7980 chunk 283 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 245 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 49 optimal weight: 5.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.157498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094086 restraints weight = 48573.673| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.67 r_work: 0.3242 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 27197 Z= 0.159 Angle : 0.584 16.672 37069 Z= 0.289 Chirality : 0.045 0.269 4433 Planarity : 0.004 0.057 4720 Dihedral : 7.407 108.588 4707 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.76 % Allowed : 15.80 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3318 helix: 1.88 (0.21), residues: 671 sheet: 0.37 (0.17), residues: 826 loop : -1.20 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 41 HIS 0.002 0.000 HIS B1064 PHE 0.014 0.001 PHE A 643 TYR 0.026 0.001 TYR C 380 ARG 0.011 0.000 ARG C 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7273.92 seconds wall clock time: 131 minutes 5.75 seconds (7865.75 seconds total)