Starting phenix.real_space_refine on Sat Feb 17 11:36:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/02_2024/8g3o_29706.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11416 2.51 5 N 3132 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 24": "NH1" <-> "NH2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 107": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 283": "NH1" <-> "NH2" Residue "G ARG 288": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "G ARG 300": "NH1" <-> "NH2" Residue "G ARG 327": "NH1" <-> "NH2" Residue "G ARG 364": "NH1" <-> "NH2" Residue "G ARG 371": "NH1" <-> "NH2" Residue "G ARG 394": "NH1" <-> "NH2" Residue "G ARG 400": "NH1" <-> "NH2" Residue "G ARG 403": "NH1" <-> "NH2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ARG 430": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 210": "NH1" <-> "NH2" Residue "H ARG 224": "NH1" <-> "NH2" Residue "H TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 283": "NH1" <-> "NH2" Residue "H ARG 288": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "H ARG 300": "NH1" <-> "NH2" Residue "H ARG 327": "NH1" <-> "NH2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 371": "NH1" <-> "NH2" Residue "H ARG 394": "NH1" <-> "NH2" Residue "H ARG 400": "NH1" <-> "NH2" Residue "H ARG 403": "NH1" <-> "NH2" Residue "H ARG 420": "NH1" <-> "NH2" Residue "H PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ARG 430": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B ARG 292": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "J PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J ARG 152": "NH1" <-> "NH2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 210": "NH1" <-> "NH2" Residue "J ARG 224": "NH1" <-> "NH2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 283": "NH1" <-> "NH2" Residue "J ARG 288": "NH1" <-> "NH2" Residue "J ARG 292": "NH1" <-> "NH2" Residue "J ARG 300": "NH1" <-> "NH2" Residue "J ARG 327": "NH1" <-> "NH2" Residue "J ARG 364": "NH1" <-> "NH2" Residue "J ARG 371": "NH1" <-> "NH2" Residue "J ARG 394": "NH1" <-> "NH2" Residue "J ARG 400": "NH1" <-> "NH2" Residue "J ARG 403": "NH1" <-> "NH2" Residue "J ARG 420": "NH1" <-> "NH2" Residue "J PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "J ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18487 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "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: "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: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" 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: "2" 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: "4" 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: "5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.19, per 1000 atoms: 0.55 Number of scatterers: 18487 At special positions: 0 Unit cell: (112.88, 140.27, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3825 8.00 N 3132 7.00 C 11416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.07 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.06 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.08 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.06 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.07 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.05 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.02 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.09 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.07 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.08 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.12 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.06 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.06 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.08 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.13 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.09 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.06 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.08 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.05 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.12 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 ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG 5 1 " - " FUC 5 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG e 1 " - " FUC e 3 " " NAG m 1 " - " FUC m 3 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG 1 1 " - " ASN J 86 " " NAG 2 1 " - " ASN J 146 " " NAG 3 1 " - " ASN J 200 " " NAG 4 1 " - " ASN J 234 " " NAG 5 1 " - " ASN J 245 " " NAG 7 1 " - " ASN J 367 " " NAG a 1 " - " ASN G 86 " " NAG b 1 " - " ASN G 146 " " NAG c 1 " - " ASN G 200 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 245 " " NAG g 1 " - " ASN G 367 " " NAG i 1 " - " ASN H 86 " " NAG j 1 " - " ASN H 146 " " NAG k 1 " - " ASN H 200 " " NAG l 1 " - " ASN H 234 " " NAG m 1 " - " ASN H 245 " " NAG o 1 " - " ASN H 367 " " NAG q 1 " - " ASN B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 9.98 Conformation dependent library (CDL) restraints added in 7.6 seconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 4.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.792A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.780A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.785A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.736A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.740A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.731A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.629A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.632A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.595A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.631A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.573A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.470A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.802A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.447A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.414A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.485A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.764A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.782A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.778A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.427A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.404A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.461A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.543A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.750A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.346A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.479A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.772A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.123A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.429A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.494A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.815A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.373A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.796A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.117A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.435A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.458A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.789A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.357A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1518 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: 7.34 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3171 1.32 - 1.45: 5346 1.45 - 1.58: 10224 1.58 - 1.71: 0 1.71 - 1.85: 134 Bond restraints: 18875 Sorted by residual: bond pdb=" C SER J 404 " pdb=" O SER J 404 " ideal model delta sigma weight residual 1.235 1.298 -0.062 1.26e-02 6.30e+03 2.45e+01 bond pdb=" C LYS G 350 " pdb=" O LYS G 350 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.20e-02 6.94e+03 1.97e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" N GLY G 286 " pdb=" CA GLY G 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" C PRO H 90 " pdb=" O PRO H 90 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.73e+01 ... (remaining 18870 not shown) Histogram of bond angle deviations from ideal: 96.99 - 104.66: 269 104.66 - 112.33: 8784 112.33 - 120.01: 8847 120.01 - 127.68: 7487 127.68 - 135.35: 230 Bond angle restraints: 25617 Sorted by residual: angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.53e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" CA ASP H 125 " pdb=" CB ASP H 125 " pdb=" CG ASP H 125 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.00e+00 1.00e+00 3.38e+01 ... (remaining 25612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 11476 19.75 - 39.50: 466 39.50 - 59.25: 107 59.25 - 79.00: 55 79.00 - 98.75: 27 Dihedral angle restraints: 12131 sinusoidal: 5680 harmonic: 6451 Sorted by residual: dihedral pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N ASN J 245 " pdb=" CA ASN J 245 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP J 127 " pdb=" C ASP J 127 " pdb=" N LYS J 128 " pdb=" CA LYS J 128 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLY J 297 " pdb=" C GLY J 297 " pdb=" N SER J 298 " pdb=" CA SER J 298 " ideal model delta harmonic sigma weight residual 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 12128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2423 0.120 - 0.240: 576 0.240 - 0.361: 11 0.361 - 0.481: 5 0.481 - 0.601: 1 Chirality restraints: 3016 Sorted by residual: chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.21e+01 chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.96e+01 chirality pdb=" C1 MAN 3 4 " pdb=" O3 BMA 3 3 " pdb=" C2 MAN 3 4 " pdb=" O5 MAN 3 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 3013 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.076 2.00e-02 2.50e+03 6.44e-02 5.18e+01 pdb=" C7 NAG c 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.098 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 1 " -0.074 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG r 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG r 1 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG r 1 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG r 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 281 " -0.084 2.00e-02 2.50e+03 4.45e-02 3.97e+01 pdb=" CG TYR J 281 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR J 281 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR J 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR J 281 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 281 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR J 281 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR J 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1410 2.75 - 3.29: 18460 3.29 - 3.83: 30748 3.83 - 4.36: 42465 4.36 - 4.90: 67681 Nonbonded interactions: 160764 Sorted by model distance: nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.218 2.510 nonbonded pdb=" OD2 ASP B 324 " pdb="CA CA B2000 " model vdw 2.239 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.252 2.510 nonbonded pdb=" OD2 ASP H 324 " pdb="CA CA H2000 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 160759 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 '1' selection = chain '2' selection = chain '4' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '5' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'G' and (resid 82 through 469 or resid 501)) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.990 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: 0.000 Extract box with map and model: 18.900 Check model and map are aligned: 0.340 Set scattering table: 0.180 Process input model: 64.140 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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 : 0.015 0.064 18875 Z= 0.978 Angle : 1.708 11.045 25617 Z= 1.112 Chirality : 0.094 0.601 3016 Planarity : 0.010 0.064 3198 Dihedral : 13.443 98.749 7897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.77 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2252 helix: -1.12 (0.70), residues: 24 sheet: 0.04 (0.16), residues: 925 loop : -0.70 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.013 TRP B 458 HIS 0.046 0.007 HIS H 168 PHE 0.057 0.013 PHE G 205 TYR 0.084 0.013 TYR J 281 ARG 0.030 0.003 ARG H 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.7815 (m-30) cc_final: 0.6939 (m-30) REVERT: F 11 LEU cc_start: 0.8017 (tp) cc_final: 0.7664 (tt) REVERT: F 75 ILE cc_start: 0.9128 (mt) cc_final: 0.8911 (mp) REVERT: F 79 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7050 (mp10) REVERT: A 43 GLN cc_start: 0.8830 (tt0) cc_final: 0.8480 (mt0) REVERT: A 65 GLN cc_start: 0.8812 (tt0) cc_final: 0.8611 (tp-100) REVERT: D 42 GLN cc_start: 0.8890 (mt0) cc_final: 0.8662 (mt0) REVERT: D 75 ILE cc_start: 0.9472 (mt) cc_final: 0.9241 (tt) REVERT: C 23 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8999 (tttp) REVERT: C 36 TRP cc_start: 0.9275 (m100) cc_final: 0.8952 (m100) REVERT: C 64 PHE cc_start: 0.8594 (m-80) cc_final: 0.8256 (m-10) REVERT: C 81 MET cc_start: 0.8256 (tmm) cc_final: 0.8035 (tmm) REVERT: C 90 ASP cc_start: 0.7477 (m-30) cc_final: 0.6935 (m-30) REVERT: C 93 VAL cc_start: 0.9147 (t) cc_final: 0.8892 (p) REVERT: C 102 ASP cc_start: 0.9066 (p0) cc_final: 0.8703 (p0) REVERT: I 4 MET cc_start: 0.8606 (mmm) cc_final: 0.7799 (mmm) REVERT: I 6 GLN cc_start: 0.8277 (tt0) cc_final: 0.7883 (tt0) REVERT: I 42 GLN cc_start: 0.7786 (mt0) cc_final: 0.7228 (mp10) REVERT: I 82 ASP cc_start: 0.7994 (m-30) cc_final: 0.7645 (m-30) REVERT: I 109 ARG cc_start: 0.6332 (ptm160) cc_final: 0.5263 (pmt-80) REVERT: H 141 ASN cc_start: 0.9366 (t0) cc_final: 0.8904 (p0) REVERT: B 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8671 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3983 time to fit residues: 165.7537 Evaluate side-chains 182 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 65 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 HIS G 468 HIS B 274 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18875 Z= 0.205 Angle : 0.664 10.698 25617 Z= 0.352 Chirality : 0.047 0.335 3016 Planarity : 0.004 0.033 3198 Dihedral : 8.485 73.312 3998 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 1.03 % Allowed : 6.19 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.18 (0.17), residues: 2252 helix: -0.36 (0.87), residues: 24 sheet: 0.04 (0.16), residues: 948 loop : -0.14 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 178 HIS 0.007 0.001 HIS J 468 PHE 0.016 0.002 PHE B 410 TYR 0.014 0.002 TYR F 49 ARG 0.005 0.001 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 11 LEU cc_start: 0.7908 (tp) cc_final: 0.7656 (tt) REVERT: F 79 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6838 (mp10) REVERT: D 42 GLN cc_start: 0.8833 (mt0) cc_final: 0.8595 (mt0) REVERT: C 12 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8106 (mmtm) REVERT: C 23 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8888 (tttm) REVERT: C 31 ASN cc_start: 0.8853 (t0) cc_final: 0.8620 (t0) REVERT: C 94 TYR cc_start: 0.8298 (m-10) cc_final: 0.8088 (m-10) REVERT: C 102 ASP cc_start: 0.9219 (p0) cc_final: 0.8750 (p0) REVERT: I 4 MET cc_start: 0.8488 (mmm) cc_final: 0.7856 (mmm) REVERT: I 11 LEU cc_start: 0.8708 (tp) cc_final: 0.8446 (tt) REVERT: I 42 GLN cc_start: 0.7767 (mt0) cc_final: 0.7367 (mt0) REVERT: I 101 GLN cc_start: 0.9294 (mm110) cc_final: 0.8820 (pm20) REVERT: I 109 ARG cc_start: 0.6144 (ptm160) cc_final: 0.4979 (pmt-80) REVERT: B 400 ARG cc_start: 0.8925 (ptm-80) cc_final: 0.8697 (ptp-110) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 0.3803 time to fit residues: 122.0320 Evaluate side-chains 190 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 381 GLU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 330 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.0070 chunk 63 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN A 65 GLN D 92 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18875 Z= 0.202 Angle : 0.621 10.687 25617 Z= 0.322 Chirality : 0.046 0.301 3016 Planarity : 0.003 0.039 3198 Dihedral : 7.613 63.975 3998 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.11 % Favored : 96.71 % Rotamer: Outliers : 1.24 % Allowed : 8.77 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.07 (0.17), residues: 2252 helix: 0.29 (0.90), residues: 24 sheet: 0.02 (0.16), residues: 930 loop : 0.02 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 178 HIS 0.006 0.001 HIS J 468 PHE 0.022 0.002 PHE C 64 TYR 0.017 0.001 TYR H 121 ARG 0.006 0.000 ARG I 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 87 ARG cc_start: 0.6412 (mpp80) cc_final: 0.6013 (mmm160) REVERT: F 79 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6903 (mp10) REVERT: A 43 GLN cc_start: 0.8612 (mt0) cc_final: 0.8388 (mt0) REVERT: A 77 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8326 (p) REVERT: D 42 GLN cc_start: 0.8844 (mt0) cc_final: 0.8556 (mt0) REVERT: D 45 ARG cc_start: 0.8886 (ttm-80) cc_final: 0.8485 (ttp80) REVERT: C 12 LYS cc_start: 0.8472 (mmtm) cc_final: 0.8241 (mmtm) REVERT: C 23 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8815 (tttm) REVERT: C 65 GLN cc_start: 0.8605 (tp40) cc_final: 0.8221 (tm-30) REVERT: C 94 TYR cc_start: 0.8273 (m-10) cc_final: 0.8012 (m-10) REVERT: C 102 ASP cc_start: 0.9218 (p0) cc_final: 0.8791 (p0) REVERT: I 4 MET cc_start: 0.8416 (mmm) cc_final: 0.7945 (mmm) REVERT: I 42 GLN cc_start: 0.7904 (mt0) cc_final: 0.7513 (mt0) REVERT: I 109 ARG cc_start: 0.6196 (ptm160) cc_final: 0.5003 (pmt-80) REVERT: B 400 ARG cc_start: 0.8962 (ptm-80) cc_final: 0.8733 (ptp-110) outliers start: 24 outliers final: 17 residues processed: 208 average time/residue: 0.3947 time to fit residues: 115.7885 Evaluate side-chains 193 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 ASN F 92 ASN A 65 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 HIS G 468 HIS H 468 HIS B 347 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18875 Z= 0.241 Angle : 0.602 9.932 25617 Z= 0.310 Chirality : 0.046 0.278 3016 Planarity : 0.003 0.045 3198 Dihedral : 6.990 56.672 3998 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.89 % Favored : 96.94 % Rotamer: Outliers : 1.50 % Allowed : 9.49 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.02 (0.17), residues: 2252 helix: -0.38 (0.90), residues: 28 sheet: 0.00 (0.16), residues: 944 loop : 0.11 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 178 HIS 0.011 0.001 HIS H 468 PHE 0.015 0.002 PHE H 410 TYR 0.016 0.001 TYR F 49 ARG 0.007 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8622 (mp0) REVERT: E 12 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7636 (mmtt) REVERT: E 87 ARG cc_start: 0.6490 (mpp80) cc_final: 0.6165 (mmm160) REVERT: F 13 LEU cc_start: 0.8444 (mt) cc_final: 0.8197 (mt) REVERT: F 17 GLU cc_start: 0.8815 (pt0) cc_final: 0.8597 (pm20) REVERT: F 74 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7870 (t) REVERT: F 79 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6749 (mp10) REVERT: A 12 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7560 (mmmt) REVERT: A 43 GLN cc_start: 0.8669 (mt0) cc_final: 0.8445 (mt0) REVERT: A 77 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8408 (p) REVERT: D 42 GLN cc_start: 0.8801 (mt0) cc_final: 0.8436 (mt0) REVERT: D 45 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8413 (ttp80) REVERT: C 12 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8286 (mmtm) REVERT: C 23 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8808 (tttm) REVERT: C 65 GLN cc_start: 0.8608 (tp40) cc_final: 0.8147 (tm-30) REVERT: C 94 TYR cc_start: 0.8239 (m-10) cc_final: 0.7961 (m-10) REVERT: C 102 ASP cc_start: 0.9246 (p0) cc_final: 0.8826 (p0) REVERT: C 107 ASP cc_start: 0.8892 (t0) cc_final: 0.8622 (t0) REVERT: I 4 MET cc_start: 0.8428 (mmm) cc_final: 0.7999 (mmm) REVERT: I 42 GLN cc_start: 0.7930 (mt0) cc_final: 0.7555 (mt0) REVERT: I 101 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8873 (pm20) REVERT: I 109 ARG cc_start: 0.6243 (ptm160) cc_final: 0.5046 (pmt-80) REVERT: B 400 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8826 (ptp-110) outliers start: 29 outliers final: 21 residues processed: 206 average time/residue: 0.3967 time to fit residues: 115.2628 Evaluate side-chains 199 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 468 HIS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN D 79 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 18875 Z= 0.491 Angle : 0.696 10.118 25617 Z= 0.356 Chirality : 0.049 0.288 3016 Planarity : 0.004 0.034 3198 Dihedral : 7.438 59.843 3998 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.23 % Rotamer: Outliers : 1.65 % Allowed : 10.16 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.33 (0.17), residues: 2252 helix: 0.46 (0.94), residues: 24 sheet: -0.19 (0.16), residues: 952 loop : -0.14 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 178 HIS 0.034 0.002 HIS H 468 PHE 0.019 0.002 PHE J 410 TYR 0.020 0.002 TYR H 121 ARG 0.007 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 61 ARG cc_start: 0.7423 (ptm-80) cc_final: 0.6631 (ptm-80) REVERT: F 74 THR cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 12 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7607 (mmmt) REVERT: D 42 GLN cc_start: 0.8715 (mt0) cc_final: 0.8286 (mt0) REVERT: D 45 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.8427 (ttp80) REVERT: C 23 LYS cc_start: 0.9073 (ttmt) cc_final: 0.8816 (tttp) REVERT: C 65 GLN cc_start: 0.8725 (tp40) cc_final: 0.8153 (tm-30) REVERT: C 94 TYR cc_start: 0.8284 (m-10) cc_final: 0.7973 (m-10) REVERT: C 102 ASP cc_start: 0.9324 (p0) cc_final: 0.8987 (p0) REVERT: C 107 ASP cc_start: 0.8859 (t0) cc_final: 0.8565 (t0) REVERT: I 4 MET cc_start: 0.8483 (mmm) cc_final: 0.7991 (mmm) REVERT: I 42 GLN cc_start: 0.8056 (mt0) cc_final: 0.7671 (mt0) REVERT: I 47 LEU cc_start: 0.9038 (tp) cc_final: 0.8561 (tt) REVERT: I 54 ARG cc_start: 0.8924 (ttp-110) cc_final: 0.8509 (ttp-110) REVERT: I 101 GLN cc_start: 0.9346 (mm-40) cc_final: 0.8879 (pm20) REVERT: I 109 ARG cc_start: 0.6081 (ptm160) cc_final: 0.4814 (pmt-80) REVERT: B 400 ARG cc_start: 0.9178 (ptm-80) cc_final: 0.8963 (ptp-110) outliers start: 32 outliers final: 22 residues processed: 199 average time/residue: 0.4220 time to fit residues: 117.3677 Evaluate side-chains 192 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS H 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18875 Z= 0.202 Angle : 0.599 10.833 25617 Z= 0.304 Chirality : 0.045 0.259 3016 Planarity : 0.003 0.045 3198 Dihedral : 6.711 49.805 3998 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.02 % Favored : 96.80 % Rotamer: Outliers : 1.39 % Allowed : 10.88 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.17 (0.17), residues: 2252 helix: -0.45 (0.91), residues: 28 sheet: -0.08 (0.16), residues: 914 loop : -0.01 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 178 HIS 0.011 0.001 HIS H 468 PHE 0.014 0.001 PHE H 410 TYR 0.016 0.001 TYR F 49 ARG 0.007 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 182 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8547 (mp0) REVERT: E 12 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7701 (mmtt) REVERT: F 17 GLU cc_start: 0.8594 (pt0) cc_final: 0.8275 (pm20) REVERT: F 61 ARG cc_start: 0.7124 (ptm-80) cc_final: 0.6627 (ptm-80) REVERT: A 12 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7654 (mmmt) REVERT: A 46 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8328 (pt0) REVERT: D 45 ARG cc_start: 0.8837 (ttm-80) cc_final: 0.8426 (ttp80) REVERT: C 23 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8796 (tttp) REVERT: C 65 GLN cc_start: 0.8707 (tp40) cc_final: 0.8137 (tm-30) REVERT: C 94 TYR cc_start: 0.8142 (m-10) cc_final: 0.7896 (m-10) REVERT: C 102 ASP cc_start: 0.9276 (p0) cc_final: 0.8875 (p0) REVERT: I 4 MET cc_start: 0.8419 (mmm) cc_final: 0.8012 (mmm) REVERT: I 11 LEU cc_start: 0.8684 (tp) cc_final: 0.8382 (tt) REVERT: I 42 GLN cc_start: 0.8030 (mt0) cc_final: 0.7656 (mt0) REVERT: I 54 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8601 (ttp-110) REVERT: I 101 GLN cc_start: 0.9349 (mm-40) cc_final: 0.8882 (pm20) REVERT: I 109 ARG cc_start: 0.6063 (ptm160) cc_final: 0.4840 (pmt-80) REVERT: B 400 ARG cc_start: 0.9116 (ptm-80) cc_final: 0.8911 (ptp-110) outliers start: 27 outliers final: 19 residues processed: 199 average time/residue: 0.4192 time to fit residues: 116.6145 Evaluate side-chains 195 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18875 Z= 0.302 Angle : 0.620 13.110 25617 Z= 0.313 Chirality : 0.046 0.262 3016 Planarity : 0.003 0.034 3198 Dihedral : 6.728 49.524 3998 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.23 (0.17), residues: 2252 helix: -0.32 (0.92), residues: 28 sheet: -0.12 (0.16), residues: 914 loop : -0.06 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 PHE 0.016 0.002 PHE H 410 TYR 0.017 0.001 TYR F 49 ARG 0.007 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8505 (mp0) REVERT: E 12 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7564 (mmtt) REVERT: F 17 GLU cc_start: 0.8536 (pt0) cc_final: 0.8118 (pm20) REVERT: F 61 ARG cc_start: 0.7245 (ptm-80) cc_final: 0.6657 (ptm-80) REVERT: A 12 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7561 (mmmt) REVERT: A 46 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8353 (pt0) REVERT: D 45 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8502 (ttp80) REVERT: C 23 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8791 (tttp) REVERT: C 65 GLN cc_start: 0.8737 (tp40) cc_final: 0.8180 (tm-30) REVERT: C 94 TYR cc_start: 0.8161 (m-10) cc_final: 0.7843 (m-10) REVERT: C 102 ASP cc_start: 0.9256 (p0) cc_final: 0.8900 (p0) REVERT: I 4 MET cc_start: 0.8448 (mmm) cc_final: 0.8022 (mmm) REVERT: I 11 LEU cc_start: 0.8661 (tp) cc_final: 0.8350 (tt) REVERT: I 42 GLN cc_start: 0.8042 (mt0) cc_final: 0.7649 (mt0) REVERT: I 47 LEU cc_start: 0.9037 (tp) cc_final: 0.8545 (tt) REVERT: I 54 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8637 (ttp80) REVERT: I 101 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8889 (pm20) REVERT: I 109 ARG cc_start: 0.6169 (ptm160) cc_final: 0.5024 (pmt-80) REVERT: G 103 ASP cc_start: 0.8813 (p0) cc_final: 0.8472 (m-30) REVERT: B 400 ARG cc_start: 0.9160 (ptm-80) cc_final: 0.8951 (ptp-110) outliers start: 35 outliers final: 24 residues processed: 201 average time/residue: 0.3984 time to fit residues: 113.5179 Evaluate side-chains 195 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN C 65 GLN G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18875 Z= 0.290 Angle : 0.625 11.880 25617 Z= 0.313 Chirality : 0.046 0.262 3016 Planarity : 0.003 0.035 3198 Dihedral : 6.664 47.261 3998 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.75 % Allowed : 11.60 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.23 (0.17), residues: 2252 helix: -0.41 (0.92), residues: 28 sheet: -0.12 (0.16), residues: 914 loop : -0.05 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 PHE 0.015 0.002 PHE H 410 TYR 0.018 0.001 TYR F 49 ARG 0.007 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8523 (mp0) REVERT: E 12 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7573 (mmtt) REVERT: E 81 MET cc_start: 0.8344 (tmm) cc_final: 0.7911 (ttt) REVERT: F 61 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6674 (ptm-80) REVERT: A 12 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7611 (mmmt) REVERT: A 46 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8388 (pt0) REVERT: A 111 GLU cc_start: 0.8811 (tt0) cc_final: 0.8468 (pm20) REVERT: D 45 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8406 (ttp80) REVERT: C 23 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8770 (tttp) REVERT: C 65 GLN cc_start: 0.8800 (tp-100) cc_final: 0.8258 (tm-30) REVERT: C 94 TYR cc_start: 0.8136 (m-10) cc_final: 0.7865 (m-10) REVERT: C 102 ASP cc_start: 0.9242 (p0) cc_final: 0.8881 (p0) REVERT: I 4 MET cc_start: 0.8446 (mmm) cc_final: 0.8013 (mmm) REVERT: I 42 GLN cc_start: 0.8075 (mt0) cc_final: 0.7691 (mt0) REVERT: I 47 LEU cc_start: 0.9041 (tp) cc_final: 0.8569 (tt) REVERT: I 54 ARG cc_start: 0.8999 (ttp-110) cc_final: 0.8595 (ttp-110) REVERT: I 101 GLN cc_start: 0.9321 (mm-40) cc_final: 0.8891 (pm20) REVERT: I 109 ARG cc_start: 0.6331 (ptm160) cc_final: 0.5215 (pmt-80) REVERT: G 103 ASP cc_start: 0.8826 (p0) cc_final: 0.8454 (m-30) outliers start: 34 outliers final: 27 residues processed: 203 average time/residue: 0.4030 time to fit residues: 115.8946 Evaluate side-chains 198 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 120 GLN I 6 GLN G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18875 Z= 0.188 Angle : 0.597 12.037 25617 Z= 0.297 Chirality : 0.045 0.256 3016 Planarity : 0.003 0.034 3198 Dihedral : 6.243 43.245 3998 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.37 % Favored : 96.45 % Rotamer: Outliers : 1.50 % Allowed : 12.02 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2252 helix: -0.40 (0.90), residues: 28 sheet: 0.02 (0.16), residues: 908 loop : -0.03 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.012 0.001 PHE E 29 TYR 0.017 0.001 TYR F 49 ARG 0.008 0.000 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 181 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8551 (mp0) REVERT: E 12 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7624 (mmtt) REVERT: E 29 PHE cc_start: 0.5793 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: E 81 MET cc_start: 0.8352 (tmm) cc_final: 0.7921 (ttt) REVERT: F 17 GLU cc_start: 0.8590 (pt0) cc_final: 0.8333 (pm20) REVERT: F 61 ARG cc_start: 0.7299 (ptm-80) cc_final: 0.6726 (ptm-80) REVERT: A 10 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7492 (mp0) REVERT: A 46 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8346 (pt0) REVERT: A 111 GLU cc_start: 0.8790 (tt0) cc_final: 0.8447 (pm20) REVERT: D 45 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8511 (ttp80) REVERT: C 23 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8780 (tttp) REVERT: C 65 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8259 (tm-30) REVERT: C 81 MET cc_start: 0.8427 (tmm) cc_final: 0.7751 (tpp) REVERT: C 93 VAL cc_start: 0.9059 (t) cc_final: 0.8839 (p) REVERT: C 94 TYR cc_start: 0.8091 (m-10) cc_final: 0.7796 (m-10) REVERT: C 102 ASP cc_start: 0.9207 (p0) cc_final: 0.8789 (p0) REVERT: I 4 MET cc_start: 0.8418 (mmm) cc_final: 0.8040 (mmm) REVERT: I 42 GLN cc_start: 0.8088 (mt0) cc_final: 0.7717 (mt0) REVERT: I 54 ARG cc_start: 0.9015 (ttp-110) cc_final: 0.8639 (ttp-110) REVERT: I 101 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8928 (pm20) REVERT: I 109 ARG cc_start: 0.6229 (ptm160) cc_final: 0.5198 (pmt-80) REVERT: G 103 ASP cc_start: 0.8782 (p0) cc_final: 0.8384 (m-30) REVERT: B 358 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (t0) outliers start: 29 outliers final: 24 residues processed: 200 average time/residue: 0.4085 time to fit residues: 115.2435 Evaluate side-chains 202 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 176 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 147 optimal weight: 0.3980 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN D 79 GLN G 441 ASN G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18875 Z= 0.177 Angle : 0.598 12.002 25617 Z= 0.296 Chirality : 0.045 0.245 3016 Planarity : 0.003 0.037 3198 Dihedral : 6.148 43.446 3998 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.20 % Favored : 96.63 % Rotamer: Outliers : 1.60 % Allowed : 12.07 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.07 (0.18), residues: 2252 helix: -0.32 (0.91), residues: 28 sheet: 0.06 (0.16), residues: 908 loop : -0.00 (0.18), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.012 0.001 PHE J 410 TYR 0.018 0.001 TYR F 49 ARG 0.009 0.000 ARG F 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8565 (mp0) REVERT: E 12 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7645 (mmtt) REVERT: E 29 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.5226 (m-80) REVERT: E 81 MET cc_start: 0.8348 (tmm) cc_final: 0.7931 (ttt) REVERT: F 17 GLU cc_start: 0.8587 (pt0) cc_final: 0.8336 (pm20) REVERT: F 61 ARG cc_start: 0.7312 (ptm-80) cc_final: 0.6785 (ptm-80) REVERT: A 46 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8346 (pt0) REVERT: A 111 GLU cc_start: 0.8799 (tt0) cc_final: 0.8459 (pm20) REVERT: D 45 ARG cc_start: 0.8765 (ttm-80) cc_final: 0.8518 (ttp80) REVERT: C 23 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8782 (tttp) REVERT: C 65 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8290 (tm-30) REVERT: C 93 VAL cc_start: 0.9055 (t) cc_final: 0.8833 (p) REVERT: C 94 TYR cc_start: 0.8083 (m-10) cc_final: 0.7779 (m-10) REVERT: C 102 ASP cc_start: 0.9203 (p0) cc_final: 0.8787 (p0) REVERT: I 42 GLN cc_start: 0.8108 (mt0) cc_final: 0.7745 (mt0) REVERT: I 47 LEU cc_start: 0.9036 (tp) cc_final: 0.8550 (tt) REVERT: I 54 ARG cc_start: 0.9005 (ttp-110) cc_final: 0.8647 (ttp-110) REVERT: I 101 GLN cc_start: 0.9284 (mm-40) cc_final: 0.8917 (pm20) REVERT: I 109 ARG cc_start: 0.6230 (ptm160) cc_final: 0.5223 (pmt-80) outliers start: 31 outliers final: 24 residues processed: 202 average time/residue: 0.3938 time to fit residues: 111.9917 Evaluate side-chains 203 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 359 ASP Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN G 441 ASN G 468 HIS B 441 ASN J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.079492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058271 restraints weight = 43695.022| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.69 r_work: 0.2788 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18875 Z= 0.362 Angle : 0.650 11.865 25617 Z= 0.323 Chirality : 0.047 0.249 3016 Planarity : 0.003 0.036 3198 Dihedral : 6.577 44.221 3998 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 1.70 % Allowed : 12.33 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % 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: -0.26 (0.17), residues: 2252 helix: -0.19 (0.95), residues: 28 sheet: -0.09 (0.16), residues: 931 loop : -0.13 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 178 HIS 0.009 0.001 HIS J 468 PHE 0.017 0.002 PHE C 29 TYR 0.020 0.002 TYR I 87 ARG 0.010 0.001 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3998.06 seconds wall clock time: 74 minutes 51.56 seconds (4491.56 seconds total)