Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 03:08:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/07_2023/8g30_29686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/07_2023/8g30_29686.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/8g30_29686/07_2023/8g30_29686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/07_2023/8g30_29686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/07_2023/8g30_29686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g30_29686/07_2023/8g30_29686.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.053 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 116 5.16 5 C 12715 2.51 5 N 3422 2.21 5 O 4191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 87": "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 ARG 109": "NH1" <-> "NH2" Residue "M ARG 85": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 152": "NH1" <-> "NH2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M ARG 210": "NH1" <-> "NH2" Residue "M ARG 224": "NH1" <-> "NH2" Residue "M ARG 283": "NH1" <-> "NH2" Residue "M ARG 288": "NH1" <-> "NH2" Residue "M ARG 292": "NH1" <-> "NH2" Residue "M ARG 300": "NH1" <-> "NH2" Residue "M ARG 327": "NH1" <-> "NH2" Residue "M ARG 364": "NH1" <-> "NH2" Residue "M ARG 371": "NH1" <-> "NH2" Residue "M ARG 394": "NH1" <-> "NH2" Residue "M ARG 400": "NH1" <-> "NH2" Residue "M ARG 403": "NH1" <-> "NH2" Residue "M ARG 420": "NH1" <-> "NH2" Residue "M PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 428": "NH1" <-> "NH2" Residue "M ARG 430": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 67": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "G 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 ARG 109": "NH1" <-> "NH2" Residue "N ARG 85": "NH1" <-> "NH2" Residue "N ARG 107": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "N PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 150": "NH1" <-> "NH2" Residue "N ARG 152": "NH1" <-> "NH2" Residue "N ARG 156": "NH1" <-> "NH2" Residue "N ARG 210": "NH1" <-> "NH2" Residue "N ARG 224": "NH1" <-> "NH2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 288": "NH1" <-> "NH2" Residue "N ARG 292": "NH1" <-> "NH2" Residue "N ARG 300": "NH1" <-> "NH2" Residue "N ARG 327": "NH1" <-> "NH2" Residue "N ARG 364": "NH1" <-> "NH2" Residue "N ARG 371": "NH1" <-> "NH2" Residue "N ARG 394": "NH1" <-> "NH2" Residue "N ARG 400": "NH1" <-> "NH2" Residue "N ARG 403": "NH1" <-> "NH2" Residue "N ARG 420": "NH1" <-> "NH2" Residue "N ARG 428": "NH1" <-> "NH2" Residue "N ARG 430": "NH1" <-> "NH2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "O ARG 85": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "O PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "O ARG 152": "NH1" <-> "NH2" Residue "O ARG 156": "NH1" <-> "NH2" Residue "O ARG 210": "NH1" <-> "NH2" Residue "O ARG 224": "NH1" <-> "NH2" Residue "O ARG 283": "NH1" <-> "NH2" Residue "O ARG 288": "NH1" <-> "NH2" Residue "O ARG 292": "NH1" <-> "NH2" Residue "O ARG 300": "NH1" <-> "NH2" Residue "O ARG 327": "NH1" <-> "NH2" Residue "O ARG 364": "NH1" <-> "NH2" Residue "O ARG 371": "NH1" <-> "NH2" Residue "O ARG 394": "NH1" <-> "NH2" Residue "O ARG 400": "NH1" <-> "NH2" Residue "O ARG 403": "NH1" <-> "NH2" Residue "O ARG 420": "NH1" <-> "NH2" Residue "O ARG 428": "NH1" <-> "NH2" Residue "O ARG 430": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 19": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "J ARG 106": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "P ARG 85": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "P PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "P ARG 152": "NH1" <-> "NH2" Residue "P ARG 156": "NH1" <-> "NH2" Residue "P ARG 210": "NH1" <-> "NH2" Residue "P ARG 224": "NH1" <-> "NH2" Residue "P ARG 283": "NH1" <-> "NH2" Residue "P ARG 288": "NH1" <-> "NH2" Residue "P ARG 292": "NH1" <-> "NH2" Residue "P ARG 300": "NH1" <-> "NH2" Residue "P ARG 327": "NH1" <-> "NH2" Residue "P ARG 364": "NH1" <-> "NH2" Residue "P ARG 371": "NH1" <-> "NH2" Residue "P ARG 394": "NH1" <-> "NH2" Residue "P ARG 400": "NH1" <-> "NH2" Residue "P ARG 403": "NH1" <-> "NH2" Residue "P ARG 420": "NH1" <-> "NH2" Residue "P ARG 428": "NH1" <-> "NH2" Residue "P ARG 430": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20449 Number of models: 1 Model: "" Number of chains: 40 Chain: "E" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "F" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2972 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 367} Chain breaks: 1 Chain: "G" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "I" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "O" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "K" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "P" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3002 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 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: "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: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "4" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "6" 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: "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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "P" 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: 9.89, per 1000 atoms: 0.48 Number of scatterers: 20449 At special positions: 0 Unit cell: (165.933, 165.933, 105.678, 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 116 16.00 O 4191 8.00 N 3422 7.00 C 12715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.06 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS M 92 " - pdb=" SG CYS M 417 " distance=2.06 Simple disulfide: pdb=" SG CYS M 124 " - pdb=" SG CYS M 129 " distance=2.07 Simple disulfide: pdb=" SG CYS M 175 " - pdb=" SG CYS M 193 " distance=2.01 Simple disulfide: pdb=" SG CYS M 183 " - pdb=" SG CYS M 230 " distance=2.08 Simple disulfide: pdb=" SG CYS M 232 " - pdb=" SG CYS M 237 " distance=2.07 Simple disulfide: pdb=" SG CYS M 278 " - pdb=" SG CYS M 291 " distance=2.01 Simple disulfide: pdb=" SG CYS M 280 " - pdb=" SG CYS M 289 " distance=2.08 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.07 Simple disulfide: pdb=" SG CYS M 421 " - pdb=" SG CYS M 447 " distance=2.09 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.06 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.02 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 417 " distance=2.05 Simple disulfide: pdb=" SG CYS N 124 " - pdb=" SG CYS N 129 " distance=2.07 Simple disulfide: pdb=" SG CYS N 175 " - pdb=" SG CYS N 193 " distance=2.01 Simple disulfide: pdb=" SG CYS N 183 " - pdb=" SG CYS N 230 " distance=2.08 Simple disulfide: pdb=" SG CYS N 232 " - pdb=" SG CYS N 237 " distance=2.07 Simple disulfide: pdb=" SG CYS N 278 " - pdb=" SG CYS N 291 " distance=2.01 Simple disulfide: pdb=" SG CYS N 280 " - pdb=" SG CYS N 289 " distance=2.08 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.06 Simple disulfide: pdb=" SG CYS N 421 " - pdb=" SG CYS N 447 " distance=2.09 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.06 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS O 92 " - pdb=" SG CYS O 417 " distance=2.05 Simple disulfide: pdb=" SG CYS O 124 " - pdb=" SG CYS O 129 " distance=2.07 Simple disulfide: pdb=" SG CYS O 175 " - pdb=" SG CYS O 193 " distance=2.01 Simple disulfide: pdb=" SG CYS O 183 " - pdb=" SG CYS O 230 " distance=2.07 Simple disulfide: pdb=" SG CYS O 232 " - pdb=" SG CYS O 237 " distance=2.07 Simple disulfide: pdb=" SG CYS O 278 " - pdb=" SG CYS O 291 " distance=2.01 Simple disulfide: pdb=" SG CYS O 280 " - pdb=" SG CYS O 289 " distance=2.08 Simple disulfide: pdb=" SG CYS O 318 " - pdb=" SG CYS O 337 " distance=2.06 Simple disulfide: pdb=" SG CYS O 421 " - pdb=" SG CYS O 447 " distance=2.09 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.06 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS P 92 " - pdb=" SG CYS P 417 " distance=2.05 Simple disulfide: pdb=" SG CYS P 124 " - pdb=" SG CYS P 129 " distance=2.07 Simple disulfide: pdb=" SG CYS P 175 " - pdb=" SG CYS P 193 " distance=2.01 Simple disulfide: pdb=" SG CYS P 183 " - pdb=" SG CYS P 230 " distance=2.07 Simple disulfide: pdb=" SG CYS P 232 " - pdb=" SG CYS P 237 " distance=2.07 Simple disulfide: pdb=" SG CYS P 278 " - pdb=" SG CYS P 291 " distance=2.01 Simple disulfide: pdb=" SG CYS P 280 " - pdb=" SG CYS P 289 " distance=2.08 Simple disulfide: pdb=" SG CYS P 318 " - pdb=" SG CYS P 337 " distance=2.06 Simple disulfide: pdb=" SG CYS P 421 " - pdb=" SG CYS P 447 " distance=2.09 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 b 3 " - " MAN b 4 " " 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 r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " NAG-ASN " NAG 1 1 " - " ASN P 86 " " NAG 2 1 " - " ASN P 146 " " NAG 3 1 " - " ASN P 200 " " NAG 4 1 " - " ASN P 234 " " NAG 6 1 " - " ASN P 329 " " NAG 7 1 " - " ASN P 367 " " NAG a 1 " - " ASN M 86 " " NAG b 1 " - " ASN M 146 " " NAG c 1 " - " ASN M 200 " " NAG d 1 " - " ASN M 234 " " NAG f 1 " - " ASN M 329 " " NAG g 1 " - " ASN M 367 " " NAG i 1 " - " ASN N 86 " " NAG j 1 " - " ASN N 146 " " NAG k 1 " - " ASN N 200 " " NAG l 1 " - " ASN N 234 " " NAG n 1 " - " ASN N 329 " " NAG o 1 " - " ASN N 367 " " NAG q 1 " - " ASN O 86 " " NAG r 1 " - " ASN O 146 " " NAG s 1 " - " ASN O 200 " " NAG t 1 " - " ASN O 234 " " NAG v 1 " - " ASN O 329 " " NAG w 1 " - " ASN O 367 " Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 3.0 seconds 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 48 sheets defined 5.0% alpha, 38.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.828A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.553A pdb=" N ALA M 110 " --> pdb=" O ILE M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.629A pdb=" N SER M 145 " --> pdb=" O ASN M 142 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN M 146 " --> pdb=" O VAL M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 142 through 146' Processing helix chain 'M' and resid 197 through 200 Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER N 145 " --> pdb=" O ASN N 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN N 146 " --> pdb=" O VAL N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 142 through 146' Processing helix chain 'N' and resid 197 through 200 Processing helix chain 'H' and resid 27 through 31 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.787A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 110 removed outlier: 3.551A pdb=" N ALA O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.584A pdb=" N SER O 145 " --> pdb=" O ASN O 142 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN O 146 " --> pdb=" O VAL O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 146' Processing helix chain 'O' and resid 197 through 200 Processing helix chain 'J' and resid 27 through 31 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.788A pdb=" N PHE K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 110 removed outlier: 3.552A pdb=" N ALA P 110 " --> pdb=" O ILE P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.583A pdb=" N SER P 145 " --> pdb=" O ASN P 142 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN P 146 " --> pdb=" O VAL P 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 197 through 200 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: 6.414A pdb=" N LEU E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.868A pdb=" N GLN F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU F 33 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 97 through 102 removed outlier: 5.336A pdb=" N CYS M 447 " --> pdb=" O PRO M 99 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG M 420 " --> pdb=" O GLY M 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP M 115 " --> pdb=" O THR M 138 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR M 138 " --> pdb=" O TRP M 115 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR M 117 " --> pdb=" O GLN M 136 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN M 136 " --> pdb=" O THR M 117 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU M 119 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU M 134 " --> pdb=" O GLU M 119 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU M 158 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS M 172 " --> pdb=" O MET M 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 179 through 184 removed outlier: 3.537A pdb=" N SER M 179 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR M 207 " --> pdb=" O LEU M 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU M 211 " --> pdb=" O TYR M 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 224 through 225 removed outlier: 3.501A pdb=" N VAL M 231 " --> pdb=" O THR M 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU M 258 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 276 through 283 removed outlier: 5.416A pdb=" N GLU M 277 " --> pdb=" O ARG M 292 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG M 292 " --> pdb=" O GLU M 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 352 through 356 removed outlier: 4.441A pdb=" N TRP M 352 " --> pdb=" O GLY M 363 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY M 363 " --> pdb=" O TRP M 352 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU M 372 " --> pdb=" O VAL M 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL M 398 " --> pdb=" O LEU M 372 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N TYR M 374 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N VAL M 396 " --> pdb=" O TYR M 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR M 376 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG M 394 " --> pdb=" O THR M 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.412A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 104 through 105 Processing sheet with id=AB7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.870A pdb=" N GLN I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU I 33 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 97 through 102 removed outlier: 5.347A pdb=" N CYS N 447 " --> pdb=" O PRO N 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG N 420 " --> pdb=" O GLY N 448 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP N 115 " --> pdb=" O THR N 138 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR N 138 " --> pdb=" O TRP N 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR N 117 " --> pdb=" O GLN N 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN N 136 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU N 119 " --> pdb=" O LEU N 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU N 134 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU N 158 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 172 " --> pdb=" O MET N 160 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 179 through 184 removed outlier: 3.551A pdb=" N SER N 179 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR N 207 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU N 211 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 224 through 225 Processing sheet with id=AC4, first strand: chain 'N' and resid 224 through 225 removed outlier: 6.443A pdb=" N GLU N 258 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU N 277 " --> pdb=" O ARG N 292 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG N 292 " --> pdb=" O GLU N 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 352 through 356 removed outlier: 4.442A pdb=" N TRP N 352 " --> pdb=" O GLY N 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY N 363 " --> pdb=" O TRP N 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU N 372 " --> pdb=" O VAL N 398 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL N 398 " --> pdb=" O LEU N 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR N 374 " --> pdb=" O VAL N 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL N 396 " --> pdb=" O TYR N 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR N 376 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 394 " --> pdb=" O THR N 376 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.411A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.866A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.441A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS O 447 " --> pdb=" O PRO O 99 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG O 420 " --> pdb=" O GLY O 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP O 115 " --> pdb=" O THR O 138 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR O 138 " --> pdb=" O TRP O 115 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR O 117 " --> pdb=" O GLN O 136 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN O 136 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU O 119 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU O 134 " --> pdb=" O GLU O 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU O 158 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS O 172 " --> pdb=" O MET O 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER O 179 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR O 207 " --> pdb=" O LEU O 211 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU O 211 " --> pdb=" O TYR O 207 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 224 through 225 Processing sheet with id=AD7, first strand: chain 'O' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU O 258 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE O 262 " --> pdb=" O GLU O 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'O' and resid 276 through 283 removed outlier: 5.427A pdb=" N GLU O 277 " --> pdb=" O ARG O 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG O 292 " --> pdb=" O GLU O 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 352 through 356 removed outlier: 4.443A pdb=" N TRP O 352 " --> pdb=" O GLY O 363 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY O 363 " --> pdb=" O TRP O 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU O 372 " --> pdb=" O VAL O 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL O 398 " --> pdb=" O LEU O 372 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR O 374 " --> pdb=" O VAL O 396 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL O 396 " --> pdb=" O TYR O 374 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR O 376 " --> pdb=" O ARG O 394 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG O 394 " --> pdb=" O THR O 376 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.414A pdb=" N LEU J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AE4, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.865A pdb=" N GLN K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.442A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU K 33 " --> pdb=" O PHE K 49 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 97 through 102 removed outlier: 5.346A pdb=" N CYS P 447 " --> pdb=" O PRO P 99 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG P 420 " --> pdb=" O GLY P 448 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 115 through 124 removed outlier: 4.692A pdb=" N TRP P 115 " --> pdb=" O THR P 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR P 138 " --> pdb=" O TRP P 115 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR P 117 " --> pdb=" O GLN P 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLN P 136 " --> pdb=" O THR P 117 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU P 119 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU P 134 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU P 158 " --> pdb=" O VAL P 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS P 172 " --> pdb=" O MET P 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER P 179 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR P 207 " --> pdb=" O LEU P 211 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU P 211 " --> pdb=" O TYR P 207 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 224 through 225 Processing sheet with id=AF1, first strand: chain 'P' and resid 224 through 225 removed outlier: 6.444A pdb=" N GLU P 258 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE P 262 " --> pdb=" O GLU P 258 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 276 through 283 removed outlier: 5.428A pdb=" N GLU P 277 " --> pdb=" O ARG P 292 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG P 292 " --> pdb=" O GLU P 277 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 352 through 356 removed outlier: 4.439A pdb=" N TRP P 352 " --> pdb=" O GLY P 363 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY P 363 " --> pdb=" O TRP P 352 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU P 372 " --> pdb=" O VAL P 398 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL P 398 " --> pdb=" O LEU P 372 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TYR P 374 " --> pdb=" O VAL P 396 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL P 396 " --> pdb=" O TYR P 374 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR P 376 " --> pdb=" O ARG P 394 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG P 394 " --> pdb=" O THR P 376 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1632 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: 6.74 Time building geometry restraints manager: 9.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3376 1.31 - 1.44: 5850 1.44 - 1.58: 11529 1.58 - 1.71: 0 1.71 - 1.85: 144 Bond restraints: 20899 Sorted by residual: bond pdb=" C PRO N 301 " pdb=" O PRO N 301 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.08e-02 8.57e+03 3.60e+01 bond pdb=" C PRO P 301 " pdb=" O PRO P 301 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.08e-02 8.57e+03 3.60e+01 bond pdb=" C PRO O 301 " pdb=" O PRO O 301 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.08e-02 8.57e+03 3.56e+01 bond pdb=" C PRO M 301 " pdb=" O PRO M 301 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.08e-02 8.57e+03 3.25e+01 bond pdb=" C PRO P 90 " pdb=" O PRO P 90 " ideal model delta sigma weight residual 1.233 1.171 0.062 1.18e-02 7.18e+03 2.74e+01 ... (remaining 20894 not shown) Histogram of bond angle deviations from ideal: 79.48 - 96.55: 2 96.55 - 113.63: 11898 113.63 - 130.70: 16370 130.70 - 147.77: 117 147.77 - 164.84: 1 Bond angle restraints: 28388 Sorted by residual: angle pdb=" OE1 GLN I 70 " pdb=" CD GLN I 70 " pdb=" NE2 GLN I 70 " ideal model delta sigma weight residual 122.60 79.48 43.12 1.00e+00 1.00e+00 1.86e+03 angle pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " pdb=" NE2 GLN I 70 " ideal model delta sigma weight residual 116.40 164.84 -48.44 1.50e+00 4.44e-01 1.04e+03 angle pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " pdb=" OE1 GLN I 70 " ideal model delta sigma weight residual 120.80 86.77 34.03 2.00e+00 2.50e-01 2.90e+02 angle pdb=" CB GLN I 70 " pdb=" CG GLN I 70 " pdb=" CD GLN I 70 " ideal model delta sigma weight residual 112.60 124.86 -12.26 1.70e+00 3.46e-01 5.20e+01 angle pdb=" N ILE M 397 " pdb=" CA ILE M 397 " pdb=" C ILE M 397 " ideal model delta sigma weight residual 111.90 107.13 4.77 8.10e-01 1.52e+00 3.47e+01 ... (remaining 28383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 10864 17.63 - 35.26: 688 35.26 - 52.89: 124 52.89 - 70.52: 40 70.52 - 88.15: 20 Dihedral angle restraints: 11736 sinusoidal: 4606 harmonic: 7130 Sorted by residual: dihedral pdb=" CA GLU M 276 " pdb=" C GLU M 276 " pdb=" N GLU M 277 " pdb=" CA GLU M 277 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N TYR E 103 " pdb=" CA TYR E 103 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CB CYS P 318 " pdb=" SG CYS P 318 " pdb=" SG CYS P 337 " pdb=" CB CYS P 337 " ideal model delta sinusoidal sigma weight residual 93.00 137.43 -44.43 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 11733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1650 0.065 - 0.130: 1109 0.130 - 0.195: 461 0.195 - 0.259: 119 0.259 - 0.324: 15 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 NAG t 2 " pdb=" O4 NAG t 1 " pdb=" C2 NAG t 2 " pdb=" O5 NAG t 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.31e+01 chirality pdb=" C1 BMA c 3 " pdb=" O4 NAG c 2 " pdb=" C2 BMA c 3 " pdb=" O5 BMA c 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.77e+01 chirality pdb=" C1 BMA s 3 " pdb=" O4 NAG s 2 " pdb=" C2 BMA s 3 " pdb=" O5 BMA s 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.67e+01 ... (remaining 3351 not shown) Planarity restraints: 3550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 121 " -0.116 2.00e-02 2.50e+03 6.06e-02 7.34e+01 pdb=" CG TYR N 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR N 121 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR N 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR N 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR N 121 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR N 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR N 121 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 121 " 0.116 2.00e-02 2.50e+03 6.05e-02 7.32e+01 pdb=" CG TYR O 121 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR O 121 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR O 121 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR O 121 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR O 121 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR O 121 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR O 121 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 121 " -0.116 2.00e-02 2.50e+03 6.04e-02 7.30e+01 pdb=" CG TYR P 121 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR P 121 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TYR P 121 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR P 121 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR P 121 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR P 121 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR P 121 " -0.081 2.00e-02 2.50e+03 ... (remaining 3547 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1956 2.75 - 3.29: 20789 3.29 - 3.83: 34655 3.83 - 4.36: 47087 4.36 - 4.90: 76572 Nonbonded interactions: 181059 Sorted by model distance: nonbonded pdb=" O GLY N 345 " pdb="CA CA N2000 " model vdw 2.213 2.510 nonbonded pdb=" O GLY P 345 " pdb="CA CA P2000 " model vdw 2.214 2.510 nonbonded pdb=" O GLY O 345 " pdb="CA CA O2000 " model vdw 2.214 2.510 nonbonded pdb=" O HIS M 347 " pdb="CA CA M 501 " model vdw 2.236 2.510 nonbonded pdb=" O HIS O 347 " pdb="CA CA O2000 " model vdw 2.237 2.510 ... (remaining 181054 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 'a' selection = chain 'd' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'q' selection = chain 'v' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '6' selection = chain '7' selection = chain 'f' selection = chain 'g' selection = chain 'n' selection = chain 'o' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 82 through 469 or resid 501)) selection = (chain 'N' and (resid 82 through 244 or resid 250 through 469 or resid 2000)) selection = (chain 'O' and (resid 82 through 244 or resid 250 through 469 or resid 2000)) selection = (chain 'P' and (resid 82 through 244 or resid 250 through 469 or resid 2000)) } ncs_group { reference = chain 'b' selection = chain 'r' } 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: 1.390 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: 8.560 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 51.770 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.016 0.075 20899 Z= 1.035 Angle : 1.867 48.443 28388 Z= 1.223 Chirality : 0.095 0.324 3354 Planarity : 0.012 0.073 3526 Dihedral : 13.157 88.150 7060 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.22 % Favored : 93.46 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2477 helix: -3.10 (0.72), residues: 28 sheet: -0.77 (0.16), residues: 918 loop : -1.56 (0.14), residues: 1531 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 448 time to evaluate : 2.111 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 456 average time/residue: 0.3863 time to fit residues: 254.2828 Evaluate side-chains 342 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 334 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2319 time to fit residues: 6.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 ASN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 147 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 20899 Z= 0.283 Angle : 0.752 8.564 28388 Z= 0.391 Chirality : 0.047 0.177 3354 Planarity : 0.004 0.037 3526 Dihedral : 6.408 30.061 2726 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.20 % Favored : 95.64 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.17), residues: 2477 helix: -2.15 (0.77), residues: 28 sheet: -0.09 (0.18), residues: 861 loop : -0.78 (0.15), residues: 1588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 369 time to evaluate : 2.445 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: symmetry clash outliers start: 17 outliers final: 15 residues processed: 380 average time/residue: 0.3676 time to fit residues: 207.6910 Evaluate side-chains 341 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 326 time to evaluate : 2.352 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 0.1953 time to fit residues: 8.6277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 GLN M 347 HIS N 347 HIS H 65 GLN O 347 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 20899 Z= 0.501 Angle : 0.754 9.775 28388 Z= 0.384 Chirality : 0.046 0.158 3354 Planarity : 0.005 0.038 3526 Dihedral : 6.009 22.564 2726 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.33 % Favored : 94.51 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.82 (0.17), residues: 2477 helix: -1.55 (0.93), residues: 28 sheet: -0.17 (0.17), residues: 930 loop : -0.74 (0.16), residues: 1519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 334 time to evaluate : 2.173 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: symmetry clash 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: 33 outliers final: 25 residues processed: 354 average time/residue: 0.3715 time to fit residues: 194.2224 Evaluate side-chains 325 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 2.282 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 4 residues processed: 25 average time/residue: 0.2171 time to fit residues: 12.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 274 HIS G 3 GLN I 70 GLN H 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20899 Z= 0.200 Angle : 0.639 9.635 28388 Z= 0.326 Chirality : 0.044 0.158 3354 Planarity : 0.004 0.038 3526 Dihedral : 5.462 21.606 2726 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.08 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: 2477 helix: -1.25 (0.90), residues: 25 sheet: -0.00 (0.17), residues: 938 loop : -0.44 (0.16), residues: 1514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 356 time to evaluate : 2.309 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 371 average time/residue: 0.3689 time to fit residues: 202.7688 Evaluate side-chains 331 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 2.319 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.1892 time to fit residues: 8.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN G 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 20899 Z= 0.265 Angle : 0.644 9.556 28388 Z= 0.325 Chirality : 0.044 0.160 3354 Planarity : 0.004 0.039 3526 Dihedral : 5.308 21.024 2726 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.04 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.45 (0.17), residues: 2477 helix: -1.73 (0.78), residues: 28 sheet: -0.07 (0.17), residues: 962 loop : -0.35 (0.16), residues: 1487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 330 time to evaluate : 2.586 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 343 average time/residue: 0.3642 time to fit residues: 188.4481 Evaluate side-chains 329 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 313 time to evaluate : 2.283 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 16 average time/residue: 0.1866 time to fit residues: 8.5253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 chunk 123 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN G 62 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 20899 Z= 0.365 Angle : 0.663 8.882 28388 Z= 0.336 Chirality : 0.044 0.157 3354 Planarity : 0.004 0.061 3526 Dihedral : 5.288 20.766 2726 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.92 % Favored : 95.92 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.49 (0.17), residues: 2477 helix: -1.29 (0.87), residues: 28 sheet: -0.08 (0.17), residues: 961 loop : -0.41 (0.16), residues: 1488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 319 time to evaluate : 2.222 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 337 average time/residue: 0.3444 time to fit residues: 176.1641 Evaluate side-chains 322 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 305 time to evaluate : 2.192 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 17 average time/residue: 0.1863 time to fit residues: 8.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 20899 Z= 0.322 Angle : 0.655 8.389 28388 Z= 0.332 Chirality : 0.043 0.158 3354 Planarity : 0.004 0.047 3526 Dihedral : 5.301 24.095 2726 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.50 (0.17), residues: 2477 helix: -1.14 (0.91), residues: 28 sheet: -0.02 (0.17), residues: 955 loop : -0.47 (0.16), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 311 time to evaluate : 2.316 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 324 average time/residue: 0.3528 time to fit residues: 173.5275 Evaluate side-chains 309 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 295 time to evaluate : 2.277 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 14 average time/residue: 0.2065 time to fit residues: 8.4584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0060 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN M 226 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 20899 Z= 0.360 Angle : 0.674 7.935 28388 Z= 0.342 Chirality : 0.044 0.171 3354 Planarity : 0.004 0.049 3526 Dihedral : 5.373 31.959 2726 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2477 helix: -0.87 (0.97), residues: 28 sheet: -0.04 (0.17), residues: 952 loop : -0.54 (0.16), residues: 1497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 305 time to evaluate : 2.463 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: symmetry clash outliers start: 24 outliers final: 15 residues processed: 317 average time/residue: 0.3589 time to fit residues: 172.6599 Evaluate side-chains 309 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 294 time to evaluate : 2.834 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 15 average time/residue: 0.3032 time to fit residues: 13.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 172 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 198 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 226 GLN L 37 GLN K 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20899 Z= 0.287 Angle : 0.667 8.645 28388 Z= 0.338 Chirality : 0.044 0.194 3354 Planarity : 0.004 0.056 3526 Dihedral : 5.323 28.215 2726 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.48 (0.17), residues: 2477 helix: -0.83 (0.97), residues: 28 sheet: 0.05 (0.18), residues: 909 loop : -0.49 (0.16), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 313 time to evaluate : 2.467 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: 13 outliers final: 8 residues processed: 322 average time/residue: 0.3528 time to fit residues: 171.4642 Evaluate side-chains 312 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 304 time to evaluate : 2.329 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 8 average time/residue: 0.1931 time to fit residues: 5.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN M 226 GLN G 65 GLN I 37 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 20899 Z= 0.381 Angle : 0.704 8.562 28388 Z= 0.357 Chirality : 0.045 0.197 3354 Planarity : 0.004 0.062 3526 Dihedral : 5.467 27.385 2726 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: -0.53 (0.17), residues: 2477 helix: -0.57 (1.03), residues: 28 sheet: 0.08 (0.18), residues: 903 loop : -0.59 (0.16), residues: 1546 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4954 Ramachandran restraints generated. 2477 Oldfield, 0 Emsley, 2477 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 297 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 304 average time/residue: 0.3675 time to fit residues: 166.9315 Evaluate side-chains 304 residues out of total 2129 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 2.400 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 14 average time/residue: 0.1934 time to fit residues: 8.0077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN M 226 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.048569 restraints weight = 62251.933| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.85 r_work: 0.2670 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 20899 Z= 0.300 Angle : 0.670 8.386 28388 Z= 0.341 Chirality : 0.044 0.199 3354 Planarity : 0.004 0.051 3526 Dihedral : 5.379 25.126 2726 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.16 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.17 % 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: 2477 helix: -0.62 (1.02), residues: 28 sheet: -0.02 (0.17), residues: 948 loop : -0.44 (0.16), residues: 1501 =============================================================================== Job complete usr+sys time: 4452.85 seconds wall clock time: 82 minutes 21.34 seconds (4941.34 seconds total)