Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 03:38:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/10_2023/6nqd_0485.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12645 2.51 5 N 3273 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 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: "X" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Z" 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "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: 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: "h" 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: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 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: "s" 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.06, per 1000 atoms: 0.55 Number of scatterers: 20175 At special positions: 0 Unit cell: (150, 145, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4143 8.00 N 3273 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.11 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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 M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN X 8 " - " MAN X 9 " " MAN Y 4 " - " MAN Y 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 10 " " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 10 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA j 3 " - " MAN j 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 8 " " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 619 " - " ASN A 160 " " NAG A 620 " - " ASN A 241 " " NAG A 623 " - " ASN A 295 " " NAG A 624 " - " ASN A 301 " " NAG A 627 " - " ASN A 355 " " NAG A 632 " - " ASN A 448 " " NAG B 705 " - " ASN B 611 " " NAG B 706 " - " ASN B 616 " " NAG B 707 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 619 " - " ASN E 160 " " NAG E 620 " - " ASN E 241 " " NAG E 623 " - " ASN E 295 " " NAG E 624 " - " ASN E 301 " " NAG E 627 " - " ASN E 355 " " NAG E 632 " - " ASN E 448 " " NAG F 705 " - " ASN F 611 " " NAG F 706 " - " ASN F 616 " " NAG F 707 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 619 " - " ASN I 160 " " NAG I 620 " - " ASN I 241 " " NAG I 623 " - " ASN I 295 " " NAG I 624 " - " ASN I 301 " " NAG I 627 " - " ASN I 355 " " NAG I 632 " - " ASN I 448 " " NAG J 705 " - " ASN J 611 " " NAG J 706 " - " ASN J 616 " " NAG J 707 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 392 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 289 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 392 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 130 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG k 1 " - " ASN I 156 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 11.16 Conformation dependent library (CDL) restraints added in 2.8 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 16.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 114 Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.042A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN A 170 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 496 removed outlier: 4.453A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN E 170 " --> pdb=" O MET E 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 312 removed outlier: 6.632A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 393 through 395 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 5.086A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 46 Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN I 170 " --> pdb=" O MET I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER I 334 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS I 374 " --> pdb=" O CYS I 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 393 through 395 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AE8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 11.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6141 1.35 - 1.48: 5862 1.48 - 1.61: 8430 1.61 - 1.74: 0 1.74 - 1.87: 150 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 NAG o 1 " pdb=" O5 NAG o 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 NAG J 706 " pdb=" O5 NAG J 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.68: 331 104.68 - 112.13: 10706 112.13 - 119.57: 7456 119.57 - 127.02: 9195 127.02 - 134.46: 317 Bond angle restraints: 28005 Sorted by residual: angle pdb=" N GLY B 516 " pdb=" CA GLY B 516 " pdb=" C GLY B 516 " ideal model delta sigma weight residual 112.51 124.41 -11.90 1.53e+00 4.27e-01 6.04e+01 angle pdb=" N GLY J 516 " pdb=" CA GLY J 516 " pdb=" C GLY J 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" N GLY F 516 " pdb=" CA GLY F 516 " pdb=" C GLY F 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" C ALA F 517 " pdb=" N MET F 518 " pdb=" CA MET F 518 " ideal model delta sigma weight residual 122.07 110.71 11.36 1.71e+00 3.42e-01 4.41e+01 angle pdb=" C ALA J 517 " pdb=" N MET J 518 " pdb=" CA MET J 518 " ideal model delta sigma weight residual 122.07 110.72 11.35 1.71e+00 3.42e-01 4.40e+01 ... (remaining 28000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 9920 15.78 - 31.56: 796 31.56 - 47.34: 291 47.34 - 63.12: 69 63.12 - 78.90: 12 Dihedral angle restraints: 11088 sinusoidal: 4221 harmonic: 6867 Sorted by residual: dihedral pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " pdb=" SG CYS J 605 " pdb=" CB CYS J 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 11085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3479 0.177 - 0.354: 106 0.354 - 0.531: 9 0.531 - 0.708: 6 0.708 - 0.885: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN E 289 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN I 289 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 ... (remaining 3600 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO E 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 123 " 0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 124 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.049 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3185 2.75 - 3.29: 18917 3.29 - 3.83: 34025 3.83 - 4.36: 37626 4.36 - 4.90: 64547 Nonbonded interactions: 158300 Sorted by model distance: nonbonded pdb=" O ASN E 67 " pdb=" OG1 THR E 71 " model vdw 2.213 2.440 nonbonded pdb=" O ASN A 67 " pdb=" OG1 THR A 71 " model vdw 2.213 2.440 nonbonded pdb=" O ASN I 67 " pdb=" OG1 THR I 71 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR E 283 " pdb=" O GLY E 472 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR I 283 " pdb=" O GLY I 472 " model vdw 2.285 2.440 ... (remaining 158295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'h' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.970 Check model and map are aligned: 0.280 Set scattering table: 0.200 Process input model: 57.470 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.410 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.012 0.114 20583 Z= 0.787 Angle : 1.404 11.895 28005 Z= 0.738 Chirality : 0.085 0.885 3603 Planarity : 0.008 0.083 3342 Dihedral : 13.921 78.896 6555 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.88 % Favored : 88.35 % Rotamer: Outliers : 8.15 % Allowed : 8.05 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.15), residues: 2343 helix: -3.03 (0.18), residues: 378 sheet: -1.65 (0.22), residues: 555 loop : -2.74 (0.15), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 545 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 160 outliers final: 49 residues processed: 654 average time/residue: 0.3042 time to fit residues: 302.8791 Evaluate side-chains 467 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 418 time to evaluate : 2.287 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 3 residues processed: 49 average time/residue: 0.2314 time to fit residues: 22.0854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 249 HIS A 308 HIS A 354 ASN A 375 HIS B 590 GLN C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 249 HIS E 308 HIS E 354 ASN E 375 HIS E 478 ASN F 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN H 27 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 249 HIS I 308 HIS I 354 ASN I 375 HIS I 478 ASN J 590 GLN K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20583 Z= 0.250 Angle : 0.848 13.426 28005 Z= 0.414 Chirality : 0.055 0.508 3603 Planarity : 0.006 0.056 3342 Dihedral : 6.987 28.109 2529 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.20 % Allowed : 14.48 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.16), residues: 2343 helix: -1.65 (0.22), residues: 390 sheet: -1.16 (0.23), residues: 549 loop : -2.31 (0.16), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 495 time to evaluate : 2.163 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: 102 outliers final: 52 residues processed: 554 average time/residue: 0.3076 time to fit residues: 263.0554 Evaluate side-chains 480 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 428 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.1848 time to fit residues: 21.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35AASN ** C 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN K 43 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20583 Z= 0.238 Angle : 0.799 12.781 28005 Z= 0.384 Chirality : 0.053 0.574 3603 Planarity : 0.005 0.047 3342 Dihedral : 6.283 28.352 2529 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.62 % Allowed : 19.06 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.17), residues: 2343 helix: -0.40 (0.25), residues: 378 sheet: -1.03 (0.23), residues: 549 loop : -2.26 (0.16), residues: 1416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 482 time to evaluate : 2.031 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: 71 outliers final: 46 residues processed: 519 average time/residue: 0.3032 time to fit residues: 245.1266 Evaluate side-chains 473 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 427 time to evaluate : 2.160 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 3 residues processed: 46 average time/residue: 0.1814 time to fit residues: 18.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 4.9990 chunk 160 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 354 ASN ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 HIS ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20583 Z= 0.274 Angle : 0.804 13.209 28005 Z= 0.386 Chirality : 0.052 0.380 3603 Planarity : 0.005 0.047 3342 Dihedral : 6.022 33.716 2529 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.13 % Allowed : 20.44 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % 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: -2.16 (0.17), residues: 2343 helix: 0.00 (0.26), residues: 375 sheet: -1.06 (0.22), residues: 612 loop : -2.11 (0.17), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 463 time to evaluate : 2.441 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: 81 outliers final: 42 residues processed: 514 average time/residue: 0.2982 time to fit residues: 239.3861 Evaluate side-chains 472 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 430 time to evaluate : 1.992 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 4 residues processed: 42 average time/residue: 0.1802 time to fit residues: 16.7298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN E 478 ASN ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20583 Z= 0.467 Angle : 0.926 12.990 28005 Z= 0.450 Chirality : 0.057 0.389 3603 Planarity : 0.005 0.062 3342 Dihedral : 6.418 27.614 2529 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 5.86 % Allowed : 19.72 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.17), residues: 2343 helix: -0.57 (0.25), residues: 399 sheet: -1.22 (0.21), residues: 642 loop : -2.18 (0.17), residues: 1302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 478 time to evaluate : 2.279 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: 115 outliers final: 65 residues processed: 537 average time/residue: 0.3031 time to fit residues: 254.1519 Evaluate side-chains 496 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 431 time to evaluate : 2.172 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 5 residues processed: 65 average time/residue: 0.1907 time to fit residues: 26.0503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 375 HIS C 100EHIS ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 375 HIS ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** K 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.049 20583 Z= 0.241 Angle : 0.806 13.621 28005 Z= 0.387 Chirality : 0.053 0.355 3603 Planarity : 0.005 0.051 3342 Dihedral : 6.058 25.756 2529 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.41 % Allowed : 21.56 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 2343 helix: -0.19 (0.25), residues: 396 sheet: -1.10 (0.22), residues: 570 loop : -2.01 (0.17), residues: 1377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 467 time to evaluate : 2.297 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: 67 outliers final: 35 residues processed: 506 average time/residue: 0.2954 time to fit residues: 235.9749 Evaluate side-chains 463 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 428 time to evaluate : 2.053 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 4 residues processed: 35 average time/residue: 0.1936 time to fit residues: 15.4746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 0.0870 chunk 165 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 225 optimal weight: 0.1980 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 92 ASN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 ASN K 39 GLN K 100EHIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20583 Z= 0.211 Angle : 0.765 13.511 28005 Z= 0.366 Chirality : 0.051 0.341 3603 Planarity : 0.004 0.051 3342 Dihedral : 5.847 24.803 2529 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.40 % Allowed : 24.26 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.18), residues: 2343 helix: -0.09 (0.26), residues: 408 sheet: -1.06 (0.22), residues: 576 loop : -1.89 (0.17), residues: 1359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 453 time to evaluate : 2.332 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 outliers start: 47 outliers final: 29 residues processed: 474 average time/residue: 0.3192 time to fit residues: 237.0124 Evaluate side-chains 450 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 421 time to evaluate : 2.300 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 4 residues processed: 29 average time/residue: 0.1912 time to fit residues: 13.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 43 optimal weight: 0.0870 chunk 143 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 624 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20583 Z= 0.220 Angle : 0.796 15.388 28005 Z= 0.381 Chirality : 0.052 0.354 3603 Planarity : 0.005 0.055 3342 Dihedral : 5.810 36.384 2529 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.38 % Allowed : 25.69 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.83 (0.18), residues: 2343 helix: 0.18 (0.26), residues: 399 sheet: -0.94 (0.22), residues: 576 loop : -1.82 (0.17), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 442 time to evaluate : 2.232 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 outliers start: 27 outliers final: 18 residues processed: 453 average time/residue: 0.3102 time to fit residues: 219.2487 Evaluate side-chains 431 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 413 time to evaluate : 2.038 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.2183 time to fit residues: 9.6674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20583 Z= 0.252 Angle : 0.781 13.621 28005 Z= 0.375 Chirality : 0.052 0.352 3603 Planarity : 0.005 0.050 3342 Dihedral : 5.733 34.470 2529 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 1.02 % Allowed : 26.50 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % 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: -1.70 (0.18), residues: 2343 helix: 0.22 (0.26), residues: 399 sheet: -0.79 (0.22), residues: 618 loop : -1.76 (0.18), residues: 1326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 424 time to evaluate : 2.212 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 outliers start: 20 outliers final: 12 residues processed: 435 average time/residue: 0.3098 time to fit residues: 211.4901 Evaluate side-chains 421 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 409 time to evaluate : 2.225 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 12 average time/residue: 0.2188 time to fit residues: 7.7528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 105 optimal weight: 0.0770 chunk 154 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20583 Z= 0.332 Angle : 0.827 13.753 28005 Z= 0.400 Chirality : 0.053 0.367 3603 Planarity : 0.005 0.051 3342 Dihedral : 5.817 28.258 2529 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.07 % Allowed : 26.66 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2343 helix: 0.04 (0.25), residues: 399 sheet: -0.77 (0.22), residues: 642 loop : -1.77 (0.18), residues: 1302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 427 time to evaluate : 2.203 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 outliers start: 21 outliers final: 16 residues processed: 433 average time/residue: 0.3076 time to fit residues: 208.3274 Evaluate side-chains 422 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 406 time to evaluate : 2.141 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 16 average time/residue: 0.1904 time to fit residues: 8.5692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.1980 chunk 56 optimal weight: 0.2980 chunk 171 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.173049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.146595 restraints weight = 31315.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.150575 restraints weight = 19744.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.152547 restraints weight = 13003.964| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20583 Z= 0.238 Angle : 0.786 14.110 28005 Z= 0.379 Chirality : 0.051 0.339 3603 Planarity : 0.005 0.051 3342 Dihedral : 5.768 27.181 2529 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.92 % Allowed : 26.86 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2343 helix: 0.18 (0.26), residues: 399 sheet: -0.81 (0.22), residues: 648 loop : -1.73 (0.18), residues: 1296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4685.17 seconds wall clock time: 86 minutes 6.73 seconds (5166.73 seconds total)