Starting phenix.real_space_refine on Fri Nov 17 08:34:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/11_2023/8g3o_29706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/11_2023/8g3o_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_29706/11_2023/8g3o_29706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/11_2023/8g3o_29706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/11_2023/8g3o_29706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3o_29706/11_2023/8g3o_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 9.70, per 1000 atoms: 0.52 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: 8.84 Conformation dependent library (CDL) restraints added in 3.5 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: 2.23 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: 7.51 Time building geometry restraints manager: 9.43 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 - 18.00: 9952 18.00 - 35.99: 475 35.99 - 53.99: 108 53.99 - 71.99: 38 71.99 - 89.98: 26 Dihedral angle restraints: 10599 sinusoidal: 4148 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 10596 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: 4.810 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: 0.010 Extract box with map and model: 19.410 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 53.640 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.320 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.930 ------------------------------------------------------------------------------- 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 : 12.942 89.983 6365 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 *********************** 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 : 2.081 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 outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.4070 time to fit residues: 170.3383 Evaluate side-chains 177 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.152 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9997 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8180 ------------------------------------------------------------------------------- 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 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** I 6 GLN G 274 HIS G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18875 Z= 0.202 Angle : 0.669 11.425 25617 Z= 0.353 Chirality : 0.047 0.325 3016 Planarity : 0.004 0.034 3198 Dihedral : 5.845 24.757 2466 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.02 % Favored : 96.80 % Rotamer: Outliers : 1.03 % Allowed : 6.34 % Favored : 92.63 % 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: -0.21 (0.17), residues: 2252 helix: -0.30 (0.86), residues: 24 sheet: 0.03 (0.16), residues: 948 loop : -0.16 (0.17), residues: 1280 *********************** 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 229 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 223 average time/residue: 0.3911 time to fit residues: 125.4503 Evaluate side-chains 185 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 2.055 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2211 time to fit residues: 6.7840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 79 GLN D 92 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 347 HIS G 468 HIS H 347 HIS B 274 HIS B 347 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18875 Z= 0.367 Angle : 0.686 11.022 25617 Z= 0.355 Chirality : 0.048 0.305 3016 Planarity : 0.004 0.046 3198 Dihedral : 5.599 25.171 2466 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 1.03 % Allowed : 9.39 % Favored : 89.58 % 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: -0.20 (0.17), residues: 2252 helix: 0.47 (0.92), residues: 24 sheet: -0.03 (0.16), residues: 914 loop : -0.12 (0.17), residues: 1314 *********************** 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 202 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 196 average time/residue: 0.4138 time to fit residues: 116.2490 Evaluate side-chains 177 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 2.100 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1717 time to fit residues: 6.3734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 D 42 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8925 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18875 Z= 0.236 Angle : 0.613 10.398 25617 Z= 0.313 Chirality : 0.045 0.274 3016 Planarity : 0.003 0.031 3198 Dihedral : 5.270 21.559 2466 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.71 % Favored : 97.11 % Rotamer: Outliers : 0.57 % Allowed : 10.68 % Favored : 88.76 % 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: -0.46 (0.88), residues: 28 sheet: -0.07 (0.16), residues: 918 loop : -0.03 (0.17), residues: 1306 *********************** 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 188 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 186 average time/residue: 0.4118 time to fit residues: 108.4338 Evaluate side-chains 167 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 2.082 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1641 time to fit residues: 4.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 37 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: 0.8990 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 18875 Z= 0.545 Angle : 0.723 10.606 25617 Z= 0.369 Chirality : 0.049 0.283 3016 Planarity : 0.004 0.042 3198 Dihedral : 5.597 22.723 2466 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 1.13 % Allowed : 11.55 % Favored : 87.31 % 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: -0.52 (0.17), residues: 2252 helix: 0.36 (0.93), residues: 24 sheet: -0.30 (0.16), residues: 946 loop : -0.30 (0.17), residues: 1282 *********************** 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 189 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 185 average time/residue: 0.4249 time to fit residues: 112.1231 Evaluate side-chains 175 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 2.246 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.1798 time to fit residues: 6.7846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS B 358 ASN J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18875 Z= 0.201 Angle : 0.609 10.909 25617 Z= 0.310 Chirality : 0.044 0.292 3016 Planarity : 0.003 0.032 3198 Dihedral : 5.208 27.267 2466 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.84 % Favored : 96.98 % Rotamer: Outliers : 0.57 % Allowed : 11.86 % Favored : 87.57 % 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: -0.57 (0.90), residues: 28 sheet: -0.11 (0.16), residues: 932 loop : -0.19 (0.17), residues: 1292 *********************** 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 183 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 178 average time/residue: 0.4354 time to fit residues: 109.1054 Evaluate side-chains 165 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 2.109 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.1613 time to fit residues: 4.3628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN G 468 HIS J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18875 Z= 0.305 Angle : 0.631 16.610 25617 Z= 0.317 Chirality : 0.045 0.267 3016 Planarity : 0.003 0.036 3198 Dihedral : 5.182 25.228 2466 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.86 % Favored : 95.96 % Rotamer: Outliers : 0.77 % Allowed : 12.74 % 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: -0.38 (0.17), residues: 2252 helix: -0.40 (0.92), residues: 28 sheet: -0.12 (0.16), residues: 946 loop : -0.25 (0.17), residues: 1278 *********************** 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 183 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 178 average time/residue: 0.4205 time to fit residues: 106.3445 Evaluate side-chains 165 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 2.248 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.1863 time to fit residues: 5.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS J 147 ASN J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18875 Z= 0.423 Angle : 0.680 13.643 25617 Z= 0.340 Chirality : 0.047 0.268 3016 Planarity : 0.004 0.036 3198 Dihedral : 5.351 29.093 2466 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.95 % Favored : 95.87 % Rotamer: Outliers : 0.88 % Allowed : 12.84 % Favored : 86.28 % 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: -0.46 (0.17), residues: 2252 helix: 0.47 (0.96), residues: 24 sheet: -0.29 (0.16), residues: 935 loop : -0.22 (0.17), residues: 1293 *********************** 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 182 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 175 average time/residue: 0.4178 time to fit residues: 103.7570 Evaluate side-chains 165 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 2.289 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.3211 time to fit residues: 4.8194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN D 79 GLN G 468 HIS J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18875 Z= 0.185 Angle : 0.631 17.936 25617 Z= 0.310 Chirality : 0.044 0.271 3016 Planarity : 0.003 0.034 3198 Dihedral : 5.061 23.588 2466 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 0.36 % Allowed : 13.41 % Favored : 86.23 % 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: -0.28 (0.17), residues: 2252 helix: -0.45 (0.92), residues: 28 sheet: -0.04 (0.16), residues: 926 loop : -0.19 (0.17), residues: 1298 *********************** 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 182 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 178 average time/residue: 0.4019 time to fit residues: 100.8733 Evaluate side-chains 171 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 166 time to evaluate : 2.022 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.1699 time to fit residues: 4.1550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 129 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 223 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.3618 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= 0.218 Angle : 0.636 23.548 25617 Z= 0.308 Chirality : 0.044 0.258 3016 Planarity : 0.003 0.037 3198 Dihedral : 5.008 22.619 2466 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 0.26 % Allowed : 13.92 % Favored : 85.82 % 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: -0.29 (0.18), residues: 2252 helix: -0.30 (0.93), residues: 28 sheet: -0.04 (0.16), residues: 946 loop : -0.20 (0.18), residues: 1278 ********************** 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 177 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 2.022 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 outliers start: 5 outliers final: 4 residues processed: 176 average time/residue: 0.4210 time to fit residues: 104.8140 Evaluate side-chains 168 residues out of total 1939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 2.045 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.1788 time to fit residues: 4.0798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.058753 restraints weight = 43820.799| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.71 r_work: 0.2813 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18875 Z= 0.303 Angle : 0.652 20.098 25617 Z= 0.320 Chirality : 0.045 0.251 3016 Planarity : 0.003 0.037 3198 Dihedral : 5.109 24.460 2466 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.23 % Rotamer: Outliers : 0.26 % Allowed : 14.29 % Favored : 85.46 % 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: -0.35 (0.17), residues: 2252 helix: -0.26 (0.92), residues: 28 sheet: -0.11 (0.16), residues: 949 loop : -0.23 (0.18), residues: 1275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3996.18 seconds wall clock time: 75 minutes 27.57 seconds (4527.57 seconds total)