Starting phenix.real_space_refine on Sun Mar 24 16:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x87_22089/03_2024/6x87_22089.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19656 atoms to isotropic. 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 98 5.16 5 C 14593 2.51 5 N 3856 2.21 5 O 4626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "X ASP 8": "OD1" <-> "OD2" Residue "X ASP 16": "OD1" <-> "OD2" Residue "X ASP 24": "OD1" <-> "OD2" Residue "X ASP 32": "OD1" <-> "OD2" Residue "X ASP 40": "OD1" <-> "OD2" Residue "X ASP 48": "OD1" <-> "OD2" Residue "M TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 144": "OD1" <-> "OD2" Residue "M TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "N TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 55": "OD1" <-> "OD2" Residue "N ASP 60": "OD1" <-> "OD2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 55": "OD1" <-> "OD2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H ASP 60": "OD1" <-> "OD2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "E TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F ASP 60": "OD1" <-> "OD2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 55": "OD1" <-> "OD2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23173 Number of models: 1 Model: "" Number of chains: 15 Chain: "K" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 437 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 32, 'TRANS': 28} Chain: "M" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1571 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1677 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.43, per 1000 atoms: 0.54 Number of scatterers: 23173 At special positions: 0 Unit cell: (170.66, 169.6, 179.14, 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 98 16.00 O 4626 8.00 N 3856 7.00 C 14593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 216 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 216 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 216 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 216 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS D 214 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 4.4 seconds 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 70 sheets defined 6.8% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.518A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.613A pdb=" N SER K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 189 No H-bonds generated for 'chain 'K' and resid 187 through 189' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.961A pdb=" N LEU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 182 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.519A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.649A pdb=" N SER M 87 " --> pdb=" O SER M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 189 No H-bonds generated for 'chain 'M' and resid 187 through 189' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.963A pdb=" N LEU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 182 through 187 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.523A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.678A pdb=" N SER I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 189 No H-bonds generated for 'chain 'I' and resid 187 through 189' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.953A pdb=" N LEU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 182 through 187 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.501A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.639A pdb=" N SER G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.973A pdb=" N LEU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 128 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.537A pdb=" N SER E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.646A pdb=" N SER E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 189 No H-bonds generated for 'chain 'E' and resid 187 through 189' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.966A pdb=" N LEU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.537A pdb=" N SER C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.662A pdb=" N SER C 87 " --> pdb=" O SER C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.934A pdb=" N LEU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.522A pdb=" N SER A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.627A pdb=" N SER A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.963A pdb=" N LEU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.777A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.777A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 120 through 124 removed outlier: 4.125A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 120 through 124 removed outlier: 4.125A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA K 137 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL K 184 " --> pdb=" O ALA K 137 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLY K 139 " --> pdb=" O VAL K 182 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL K 182 " --> pdb=" O GLY K 139 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU K 141 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER K 180 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS K 143 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 178 " --> pdb=" O LYS K 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.598A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.597A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AB3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.854A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.854A pdb=" N GLU M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 120 through 124 removed outlier: 4.166A pdb=" N GLY M 139 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 120 through 124 removed outlier: 4.166A pdb=" N GLY M 139 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ALA M 137 " --> pdb=" O VAL M 184 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL M 184 " --> pdb=" O ALA M 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY M 139 " --> pdb=" O VAL M 182 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL M 182 " --> pdb=" O GLY M 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU M 141 " --> pdb=" O SER M 180 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER M 180 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS M 143 " --> pdb=" O LEU M 178 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU M 178 " --> pdb=" O LYS M 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 151 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.503A pdb=" N LEU N 36 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 114 through 118 removed outlier: 3.567A pdb=" N VAL N 133 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL N 132 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 154 through 155 removed outlier: 4.593A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL N 205 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.767A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.767A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 120 through 124 removed outlier: 4.188A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA I 137 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL I 184 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY I 139 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL I 182 " --> pdb=" O GLY I 139 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER I 180 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS I 143 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU I 178 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 120 through 124 removed outlier: 4.188A pdb=" N GLY I 139 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ALA I 137 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL I 184 " --> pdb=" O ALA I 137 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLY I 139 " --> pdb=" O VAL I 182 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL I 182 " --> pdb=" O GLY I 139 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU I 141 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER I 180 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS I 143 " --> pdb=" O LEU I 178 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU I 178 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 151 through 154 Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.607A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.602A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL J 132 " --> pdb=" O LEU J 179 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 154 through 155 removed outlier: 4.653A pdb=" N TRP J 148 " --> pdb=" O GLN J 155 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL J 205 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.743A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.743A pdb=" N GLU G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.264A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 4.264A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA G 137 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL G 184 " --> pdb=" O ALA G 137 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY G 139 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL G 182 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU G 141 " --> pdb=" O SER G 180 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER G 180 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS G 143 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G 178 " --> pdb=" O LYS G 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.623A pdb=" N LEU H 36 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.658A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL H 132 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.574A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL H 205 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.782A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.782A pdb=" N GLU E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.036A pdb=" N GLY E 139 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA E 137 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 184 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY E 139 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 182 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 141 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 180 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 143 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 178 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 131 through 132 removed outlier: 5.083A pdb=" N ALA E 137 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 184 " --> pdb=" O ALA E 137 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLY E 139 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 182 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU E 141 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N SER E 180 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS E 143 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU E 178 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.527A pdb=" N LEU F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 114 through 118 removed outlier: 3.526A pdb=" N VAL F 132 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 154 through 155 removed outlier: 4.692A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL F 205 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AF7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.754A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.754A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.208A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.208A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AG3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.521A pdb=" N LEU D 36 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.581A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 132 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 154 through 155 removed outlier: 4.688A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AG8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.779A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.779A pdb=" N GLU A 10 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.183A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.183A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 151 through 154 Processing sheet with id=AH4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.656A pdb=" N LEU B 33 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.620A pdb=" N VAL B 133 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 154 through 155 removed outlier: 4.607A pdb=" N TRP B 148 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 205 " --> pdb=" O VAL B 196 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 1962 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: 7.95 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7353 1.35 - 1.46: 5721 1.46 - 1.58: 10523 1.58 - 1.70: 0 1.70 - 1.81: 126 Bond restraints: 23723 Sorted by residual: bond pdb=" C VAL J 58 " pdb=" N PRO J 59 " ideal model delta sigma weight residual 1.330 1.343 -0.013 1.19e-02 7.06e+03 1.19e+00 bond pdb=" C VAL N 58 " pdb=" N PRO N 59 " ideal model delta sigma weight residual 1.330 1.343 -0.012 1.19e-02 7.06e+03 1.08e+00 bond pdb=" C VAL D 58 " pdb=" N PRO D 59 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.19e-02 7.06e+03 9.70e-01 bond pdb=" C VAL F 58 " pdb=" N PRO F 59 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.19e-02 7.06e+03 8.51e-01 bond pdb=" CG PRO L 141 " pdb=" CD PRO L 141 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 ... (remaining 23718 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 895 106.97 - 113.73: 13246 113.73 - 120.50: 8144 120.50 - 127.26: 9744 127.26 - 134.03: 273 Bond angle restraints: 32302 Sorted by residual: angle pdb=" C LEU H 50 " pdb=" N VAL H 51 " pdb=" CA VAL H 51 " ideal model delta sigma weight residual 121.97 125.23 -3.26 1.80e+00 3.09e-01 3.27e+00 angle pdb=" C LEU J 50 " pdb=" N VAL J 51 " pdb=" CA VAL J 51 " ideal model delta sigma weight residual 121.97 125.14 -3.17 1.80e+00 3.09e-01 3.11e+00 angle pdb=" N VAL F 115 " pdb=" CA VAL F 115 " pdb=" C VAL F 115 " ideal model delta sigma weight residual 108.36 110.85 -2.49 1.43e+00 4.89e-01 3.04e+00 angle pdb=" N PRO F 141 " pdb=" CD PRO F 141 " pdb=" CG PRO F 141 " ideal model delta sigma weight residual 103.80 101.71 2.09 1.20e+00 6.94e-01 3.03e+00 angle pdb=" N VAL J 51 " pdb=" CA VAL J 51 " pdb=" C VAL J 51 " ideal model delta sigma weight residual 109.34 112.96 -3.62 2.08e+00 2.31e-01 3.02e+00 ... (remaining 32297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 13041 15.24 - 30.48: 858 30.48 - 45.71: 286 45.71 - 60.95: 42 60.95 - 76.19: 14 Dihedral angle restraints: 14241 sinusoidal: 5358 harmonic: 8883 Sorted by residual: dihedral pdb=" CB CYS K 216 " pdb=" SG CYS K 216 " pdb=" SG CYS L 214 " pdb=" CB CYS L 214 " ideal model delta sinusoidal sigma weight residual 93.00 122.52 -29.52 1 1.00e+01 1.00e-02 1.25e+01 dihedral pdb=" CB CYS G 216 " pdb=" SG CYS G 216 " pdb=" SG CYS H 214 " pdb=" CB CYS H 214 " ideal model delta sinusoidal sigma weight residual 93.00 120.63 -27.63 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CB CYS M 216 " pdb=" SG CYS M 216 " pdb=" SG CYS N 214 " pdb=" CB CYS N 214 " ideal model delta sinusoidal sigma weight residual 93.00 120.06 -27.06 1 1.00e+01 1.00e-02 1.05e+01 ... (remaining 14238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2192 0.028 - 0.056: 987 0.056 - 0.083: 230 0.083 - 0.111: 222 0.111 - 0.139: 56 Chirality restraints: 3687 Sorted by residual: chirality pdb=" CA ILE J 21 " pdb=" N ILE J 21 " pdb=" C ILE J 21 " pdb=" CB ILE J 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE H 21 " pdb=" N ILE H 21 " pdb=" C ILE H 21 " pdb=" CB ILE H 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE N 21 " pdb=" N ILE N 21 " pdb=" C ILE N 21 " pdb=" CB ILE N 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3684 not shown) Planarity restraints: 4111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO X 2 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO X 3 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO X 3 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO X 3 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 148 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 149 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 148 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 149 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.024 5.00e-02 4.00e+02 ... (remaining 4108 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5207 2.79 - 3.32: 19864 3.32 - 3.84: 36976 3.84 - 4.37: 43810 4.37 - 4.90: 76772 Nonbonded interactions: 182629 Sorted by model distance: nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.262 2.440 nonbonded pdb=" OE1 GLU B 105 " pdb=" OH TYR B 173 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR H 14 " pdb=" OE1 GLN H 17 " model vdw 2.294 2.440 nonbonded pdb=" OG1 THR F 14 " pdb=" OE1 GLN F 17 " model vdw 2.299 2.440 nonbonded pdb=" OG1 THR B 14 " pdb=" OE1 GLN B 17 " model vdw 2.311 2.440 ... (remaining 182624 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 8.170 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 61.490 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5992 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 : 0.002 0.026 23723 Z= 0.136 Angle : 0.519 5.316 32302 Z= 0.272 Chirality : 0.040 0.139 3687 Planarity : 0.005 0.078 4111 Dihedral : 11.695 76.187 8456 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % 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: -1.72 (0.14), residues: 3055 helix: -2.44 (0.68), residues: 42 sheet: -1.00 (0.13), residues: 1358 loop : -1.15 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 89 HIS 0.003 0.001 HIS H 189 PHE 0.007 0.001 PHE J 98 TYR 0.019 0.001 TYR G 50 ARG 0.004 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 532 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 LEU cc_start: 0.8485 (tp) cc_final: 0.8199 (mm) REVERT: E 155 ASN cc_start: 0.4920 (m-40) cc_final: 0.4714 (m-40) REVERT: A 72 ASP cc_start: 0.7779 (t0) cc_final: 0.7442 (t0) outliers start: 3 outliers final: 2 residues processed: 533 average time/residue: 0.3539 time to fit residues: 286.1642 Evaluate side-chains 316 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain I residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 39 GLN K 199 ASN K 204 ASN L 38 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 164 HIS N 137 ASN I 6 GLN I 39 GLN I 197 ASN J 38 GLN J 166 GLN G 6 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 43 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS F 27 GLN F 38 GLN C 35 HIS C 39 GLN D 137 ASN D 166 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 HIS A 171 GLN B 137 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 23723 Z= 0.676 Angle : 0.770 9.432 32302 Z= 0.399 Chirality : 0.050 0.251 3687 Planarity : 0.006 0.057 4111 Dihedral : 4.657 27.955 3270 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.28 % Allowed : 11.94 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % 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: -1.20 (0.15), residues: 3055 helix: -3.56 (0.33), residues: 91 sheet: -0.56 (0.14), residues: 1295 loop : -0.73 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 89 HIS 0.009 0.002 HIS I 35 PHE 0.024 0.003 PHE H 98 TYR 0.026 0.003 TYR E 50 ARG 0.008 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 327 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 7 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7648 (m-40) REVERT: X 47 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8389 (m-40) REVERT: F 36 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (pp) REVERT: C 34 MET cc_start: 0.8293 (tpp) cc_final: 0.7876 (tpt) REVERT: B 36 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8749 (pp) outliers start: 113 outliers final: 76 residues processed: 416 average time/residue: 0.3462 time to fit residues: 224.1769 Evaluate side-chains 363 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 283 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 176 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 23 ASN Chi-restraints excluded: chain X residue 47 ASN Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.1980 chunk 226 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN L 6 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN M 6 GLN M 58 ASN M 81 GLN N 137 ASN N 166 GLN J 189 HIS H 166 GLN E 6 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS A 58 ASN B 137 ASN B 138 ASN B 160 GLN B 166 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23723 Z= 0.208 Angle : 0.552 10.043 32302 Z= 0.281 Chirality : 0.043 0.187 3687 Planarity : 0.005 0.055 4111 Dihedral : 4.156 23.779 3270 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.79 % Allowed : 14.48 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 3055 helix: -3.48 (0.35), residues: 91 sheet: -0.32 (0.14), residues: 1267 loop : -0.32 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.003 0.001 HIS F 189 PHE 0.026 0.001 PHE N 118 TYR 0.014 0.001 TYR A 145 ARG 0.008 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 300 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 27 TYR cc_start: 0.8548 (t80) cc_final: 0.8152 (t80) REVERT: G 211 VAL cc_start: 0.1770 (OUTLIER) cc_final: 0.1557 (m) REVERT: C 34 MET cc_start: 0.8246 (tpp) cc_final: 0.7841 (tpt) REVERT: A 10 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: B 36 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8593 (pp) outliers start: 100 outliers final: 58 residues processed: 378 average time/residue: 0.3461 time to fit residues: 203.2747 Evaluate side-chains 320 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 259 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 166 GLN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 143 optimal weight: 30.0000 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 166 GLN J 166 GLN J 189 HIS E 43 GLN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN B 137 ASN B 138 ASN B 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 23723 Z= 0.303 Angle : 0.570 7.823 32302 Z= 0.289 Chirality : 0.043 0.217 3687 Planarity : 0.005 0.055 4111 Dihedral : 4.172 25.102 3270 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.44 % Allowed : 14.67 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3055 helix: -3.40 (0.37), residues: 91 sheet: -0.14 (0.14), residues: 1225 loop : -0.16 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 89 HIS 0.003 0.001 HIS I 35 PHE 0.013 0.001 PHE L 139 TYR 0.015 0.002 TYR K 50 ARG 0.008 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 275 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 73 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8094 (tp) REVERT: X 7 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7628 (m-40) REVERT: N 36 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (pt) REVERT: H 36 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7406 (pp) REVERT: F 28 ASP cc_start: 0.8326 (p0) cc_final: 0.8083 (p0) REVERT: C 34 MET cc_start: 0.8218 (tpp) cc_final: 0.7855 (tpt) REVERT: A 10 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: B 36 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (pp) outliers start: 117 outliers final: 83 residues processed: 371 average time/residue: 0.3406 time to fit residues: 196.3951 Evaluate side-chains 352 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 263 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 SER Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 166 GLN Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 6.9990 chunk 164 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 260 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 189 HIS M 81 GLN N 166 GLN J 166 GLN E 105 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN B 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23723 Z= 0.231 Angle : 0.536 7.661 32302 Z= 0.273 Chirality : 0.042 0.174 3687 Planarity : 0.005 0.054 4111 Dihedral : 4.046 23.987 3270 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.51 % Allowed : 15.20 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3055 helix: -3.39 (0.36), residues: 91 sheet: 0.07 (0.14), residues: 1204 loop : -0.13 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 89 HIS 0.002 0.001 HIS F 189 PHE 0.012 0.001 PHE L 139 TYR 0.016 0.001 TYR A 145 ARG 0.005 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 274 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 105 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: L 73 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8045 (tp) REVERT: X 7 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7643 (m-40) REVERT: N 36 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7880 (pt) REVERT: J 31 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8678 (t) REVERT: G 105 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6855 (pm20) REVERT: H 31 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7332 (m) REVERT: F 28 ASP cc_start: 0.8273 (p0) cc_final: 0.8016 (p0) REVERT: C 34 MET cc_start: 0.8203 (tpp) cc_final: 0.7887 (tpt) REVERT: A 10 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: B 36 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8725 (pp) outliers start: 119 outliers final: 78 residues processed: 367 average time/residue: 0.3410 time to fit residues: 197.7820 Evaluate side-chains 339 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 252 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 105 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 290 optimal weight: 0.2980 chunk 240 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** I 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 38 GLN C 39 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23723 Z= 0.172 Angle : 0.515 8.376 32302 Z= 0.260 Chirality : 0.042 0.163 3687 Planarity : 0.004 0.055 4111 Dihedral : 3.909 21.555 3270 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.02 % Allowed : 16.19 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3055 helix: -3.36 (0.35), residues: 91 sheet: -0.16 (0.14), residues: 1393 loop : 0.09 (0.17), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 89 HIS 0.003 0.000 HIS F 189 PHE 0.010 0.001 PHE F 139 TYR 0.015 0.001 TYR C 27 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 278 time to evaluate : 2.723 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: K 105 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: L 73 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (tp) REVERT: N 36 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7832 (pt) REVERT: J 31 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8703 (t) REVERT: F 28 ASP cc_start: 0.8196 (p0) cc_final: 0.7956 (p0) REVERT: C 34 MET cc_start: 0.8156 (tpp) cc_final: 0.7766 (tpt) outliers start: 106 outliers final: 73 residues processed: 364 average time/residue: 0.3442 time to fit residues: 195.9893 Evaluate side-chains 338 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 261 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 117 LYS Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.0070 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** I 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23723 Z= 0.228 Angle : 0.538 10.366 32302 Z= 0.269 Chirality : 0.042 0.179 3687 Planarity : 0.005 0.058 4111 Dihedral : 3.954 23.266 3270 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.32 % Allowed : 16.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 3055 helix: -3.33 (0.34), residues: 91 sheet: -0.01 (0.14), residues: 1351 loop : 0.15 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 89 HIS 0.002 0.001 HIS F 189 PHE 0.012 0.001 PHE L 139 TYR 0.021 0.001 TYR D 27D ARG 0.013 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 276 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 105 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: L 73 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7942 (tp) REVERT: X 7 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7678 (m-40) REVERT: N 36 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7954 (pt) REVERT: J 31 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8749 (t) REVERT: G 105 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: F 28 ASP cc_start: 0.8204 (p0) cc_final: 0.7998 (p0) REVERT: C 34 MET cc_start: 0.8171 (tpp) cc_final: 0.7799 (tpt) outliers start: 114 outliers final: 91 residues processed: 370 average time/residue: 0.3379 time to fit residues: 196.9307 Evaluate side-chains 359 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 262 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 187 GLU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 56 ASP Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 27 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.1980 chunk 115 optimal weight: 0.3980 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 196 optimal weight: 0.0000 chunk 142 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 263 optimal weight: 0.2980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN ** I 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN B 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23723 Z= 0.132 Angle : 0.505 7.976 32302 Z= 0.255 Chirality : 0.041 0.150 3687 Planarity : 0.005 0.059 4111 Dihedral : 3.752 19.163 3270 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.07 % Allowed : 17.29 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 3055 helix: -3.25 (0.35), residues: 91 sheet: 0.03 (0.14), residues: 1407 loop : 0.38 (0.17), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 89 HIS 0.004 0.001 HIS F 189 PHE 0.010 0.001 PHE I 166 TYR 0.017 0.001 TYR C 27 ARG 0.014 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 286 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 105 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7469 (pm20) REVERT: L 73 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (tp) REVERT: M 27 TYR cc_start: 0.8415 (p90) cc_final: 0.8118 (p90) REVERT: N 36 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7774 (pt) REVERT: N 187 GLU cc_start: 0.3455 (OUTLIER) cc_final: 0.3085 (pt0) REVERT: J 31 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8684 (t) REVERT: H 36 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7194 (pp) REVERT: C 34 MET cc_start: 0.8099 (tpp) cc_final: 0.7699 (tpt) outliers start: 81 outliers final: 61 residues processed: 342 average time/residue: 0.3280 time to fit residues: 176.3427 Evaluate side-chains 327 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 260 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 269 optimal weight: 8.9990 chunk 276 optimal weight: 0.1980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 211 optimal weight: 0.0870 chunk 82 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 254 optimal weight: 40.0000 chunk 268 optimal weight: 0.7980 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN M 81 GLN N 38 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23723 Z= 0.222 Angle : 0.536 8.644 32302 Z= 0.269 Chirality : 0.042 0.163 3687 Planarity : 0.005 0.063 4111 Dihedral : 3.848 21.604 3270 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.45 % Allowed : 17.29 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 3055 helix: -3.20 (0.35), residues: 91 sheet: 0.05 (0.14), residues: 1407 loop : 0.42 (0.17), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 154 HIS 0.003 0.001 HIS F 189 PHE 0.014 0.001 PHE M 59 TYR 0.021 0.001 TYR D 27D ARG 0.014 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 258 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 85 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: K 105 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: L 73 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7919 (tp) REVERT: M 80 MET cc_start: 0.7948 (ttp) cc_final: 0.7569 (tmm) REVERT: N 36 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7927 (pt) REVERT: J 31 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8747 (t) REVERT: H 47 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6297 (mm) REVERT: C 34 MET cc_start: 0.8053 (tpp) cc_final: 0.7713 (tpt) outliers start: 91 outliers final: 73 residues processed: 327 average time/residue: 0.3326 time to fit residues: 172.4143 Evaluate side-chains 331 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 252 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 173 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 275 optimal weight: 3.9990 chunk 237 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 145 optimal weight: 30.0000 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 43 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN M 81 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23723 Z= 0.242 Angle : 0.550 10.365 32302 Z= 0.274 Chirality : 0.042 0.158 3687 Planarity : 0.005 0.069 4111 Dihedral : 3.968 22.889 3270 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.41 % Allowed : 17.44 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 3055 helix: -3.13 (0.35), residues: 91 sheet: 0.09 (0.14), residues: 1393 loop : 0.35 (0.17), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 89 HIS 0.003 0.001 HIS F 189 PHE 0.014 0.001 PHE M 59 TYR 0.022 0.001 TYR D 27D ARG 0.014 0.001 ARG B 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6110 Ramachandran restraints generated. 3055 Oldfield, 0 Emsley, 3055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 260 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 85 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: K 105 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: L 73 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7924 (tp) REVERT: X 7 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7693 (m-40) REVERT: M 27 TYR cc_start: 0.8535 (p90) cc_final: 0.8223 (p90) REVERT: N 36 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7944 (pt) REVERT: J 31 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8873 (t) REVERT: G 105 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: H 47 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6220 (mm) REVERT: C 34 MET cc_start: 0.8064 (tpp) cc_final: 0.7735 (tpt) outliers start: 90 outliers final: 78 residues processed: 331 average time/residue: 0.3242 time to fit residues: 169.7773 Evaluate side-chains 342 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 256 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 33 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain K residue 138 LEU Chi-restraints excluded: chain K residue 199 ASN Chi-restraints excluded: chain L residue 36 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 33 ASN Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 180 SER Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain N residue 14 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 33 ASN Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 164 HIS Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 198 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 238 optimal weight: 40.0000 chunk 99 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 171 GLN ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN N 160 GLN J 189 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN A 58 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.214599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169455 restraints weight = 30845.243| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.90 r_work: 0.3425 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23723 Z= 0.162 Angle : 0.518 8.025 32302 Z= 0.258 Chirality : 0.041 0.154 3687 Planarity : 0.005 0.061 4111 Dihedral : 3.821 20.483 3270 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.37 % Allowed : 17.63 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.16), residues: 3055 helix: -2.28 (0.61), residues: 49 sheet: 0.20 (0.14), residues: 1435 loop : 0.62 (0.17), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 154 HIS 0.003 0.000 HIS F 189 PHE 0.011 0.001 PHE F 139 TYR 0.020 0.001 TYR D 27D ARG 0.015 0.001 ARG B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5045.45 seconds wall clock time: 92 minutes 35.89 seconds (5555.89 seconds total)