Starting phenix.real_space_refine on Wed Aug 7 01:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/08_2024/7a02_11591.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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 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 115 5.16 5 C 11776 2.51 5 N 2990 2.21 5 O 3818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 39": "OD1" <-> "OD2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "F ASP 39": "OD1" <-> "OD2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G GLU 107": "OE1" <-> "OE2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I ASP 39": "OD1" <-> "OD2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "J ASP 39": "OD1" <-> "OD2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 75": "OE1" <-> "OE2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K ARG 91": "NH1" <-> "NH2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 75": "OE1" <-> "OE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "M ASP 39": "OD1" <-> "OD2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 75": "OE1" <-> "OE2" Residue "N ARG 91": "NH1" <-> "NH2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "O ASP 39": "OD1" <-> "OD2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 75": "OE1" <-> "OE2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O GLU 107": "OE1" <-> "OE2" Residue "P ASP 39": "OD1" <-> "OD2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P ARG 91": "NH1" <-> "NH2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q GLU 107": "OE1" <-> "OE2" Residue "R ASP 39": "OD1" <-> "OD2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 75": "OE1" <-> "OE2" Residue "R ARG 91": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "S ASP 39": "OD1" <-> "OD2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S ARG 91": "NH1" <-> "NH2" Residue "S GLU 107": "OE1" <-> "OE2" Residue "T ASP 39": "OD1" <-> "OD2" Residue "T TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 75": "OE1" <-> "OE2" Residue "T ARG 91": "NH1" <-> "NH2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U ARG 91": "NH1" <-> "NH2" Residue "U GLU 107": "OE1" <-> "OE2" Residue "V ASP 39": "OD1" <-> "OD2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 75": "OE1" <-> "OE2" Residue "V ARG 91": "NH1" <-> "NH2" Residue "V GLU 107": "OE1" <-> "OE2" Residue "W ASP 39": "OD1" <-> "OD2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 75": "OE1" <-> "OE2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "W GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18699 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 813 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 9.56, per 1000 atoms: 0.51 Number of scatterers: 18699 At special positions: 0 Unit cell: (108.976, 108.976, 141.904, 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 115 16.00 O 3818 8.00 N 2990 7.00 C 11776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS J 109 " distance=2.06 Simple disulfide: pdb=" SG CYS A 11 " - pdb=" SG CYS K 24 " distance=2.12 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS K 109 " distance=2.52 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS L 24 " distance=1.77 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS L 109 " distance=2.12 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS M 24 " distance=1.97 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS M 109 " distance=2.07 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS N 24 " distance=2.17 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS N 109 " distance=1.97 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS O 24 " distance=2.08 Simple disulfide: pdb=" SG CYS F 10 " - pdb=" SG CYS O 109 " distance=2.20 Simple disulfide: pdb=" SG CYS F 11 " - pdb=" SG CYS P 24 " distance=2.22 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS P 109 " distance=1.61 Simple disulfide: pdb=" SG CYS G 11 " - pdb=" SG CYS Q 24 " distance=2.17 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS Q 109 " distance=1.93 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS R 24 " distance=2.06 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS R 109 " distance=1.93 Simple disulfide: pdb=" SG CYS I 11 " - pdb=" SG CYS S 24 " distance=1.85 Simple disulfide: pdb=" SG CYS J 10 " - pdb=" SG CYS S 109 " distance=1.91 Simple disulfide: pdb=" SG CYS J 11 " - pdb=" SG CYS W 24 " distance=1.94 Simple disulfide: pdb=" SG CYS K 10 " - pdb=" SG CYS W 109 " distance=1.94 Simple disulfide: pdb=" SG CYS K 11 " - pdb=" SG CYS T 24 " distance=2.08 Simple disulfide: pdb=" SG CYS L 10 " - pdb=" SG CYS T 109 " distance=2.06 Simple disulfide: pdb=" SG CYS L 11 " - pdb=" SG CYS V 24 " distance=2.07 Simple disulfide: pdb=" SG CYS M 10 " - pdb=" SG CYS V 109 " distance=2.26 Simple disulfide: pdb=" SG CYS M 11 " - pdb=" SG CYS U 24 " distance=2.03 Simple disulfide: pdb=" SG CYS N 10 " - pdb=" SG CYS U 109 " distance=1.96 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: 6.70 Conformation dependent library (CDL) restraints added in 3.3 seconds 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4692 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 3.685A pdb=" N CYS A 10 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS K 24 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 104 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR K 105 " --> pdb=" O ASP K 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS K 52 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N SER K 84 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE L 36 " --> pdb=" O SER K 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA L 38 " --> pdb=" O SER K 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR K 88 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL L 95 " --> pdb=" O ILE L 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU L 75 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER L 66 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU A 104 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 105 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 52 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N SER A 84 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 36 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 38 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 88 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 95 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 38 removed outlier: 6.562A pdb=" N VAL A 95 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 66 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.740A pdb=" N GLU L 104 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR L 105 " --> pdb=" O ASP L 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS L 52 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N SER L 84 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE M 36 " --> pdb=" O SER L 84 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA M 38 " --> pdb=" O SER L 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 88 " --> pdb=" O ALA M 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL M 95 " --> pdb=" O ILE M 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 75 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER M 66 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA M 73 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU B 104 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR B 105 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 52 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 9.814A pdb=" N SER B 84 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE C 36 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C 38 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 88 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL C 95 " --> pdb=" O ILE C 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER C 66 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.690A pdb=" N CYS C 10 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS M 24 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M 104 " --> pdb=" O ALA M 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR M 105 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 52 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N SER M 84 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE N 36 " --> pdb=" O SER M 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA N 38 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR M 88 " --> pdb=" O ALA N 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL N 95 " --> pdb=" O ILE N 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU N 75 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER N 66 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA N 73 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU C 104 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 105 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 52 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 9.515A pdb=" N SER C 84 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE D 36 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL D 95 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER D 66 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.734A pdb=" N CYS D 10 " --> pdb=" O LYS N 22 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS N 24 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU N 104 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR N 105 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS N 52 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N SER N 84 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE O 36 " --> pdb=" O SER N 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL O 95 " --> pdb=" O ILE O 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU O 75 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER O 66 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA O 73 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU D 104 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR D 105 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 52 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N SER D 84 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE E 36 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 95 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER E 66 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.746A pdb=" N CYS E 10 " --> pdb=" O LYS O 22 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS O 24 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU O 104 " --> pdb=" O ALA O 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR O 105 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS O 52 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N SER O 84 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE P 36 " --> pdb=" O SER O 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER O 86 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA P 38 " --> pdb=" O SER O 86 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR O 88 " --> pdb=" O ALA P 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL P 95 " --> pdb=" O ILE P 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU P 75 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER P 66 " --> pdb=" O ALA P 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA P 73 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU E 104 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR E 105 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS E 52 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N SER E 84 " --> pdb=" O ALA F 34 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE F 36 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 38 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 95 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU F 75 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER F 66 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA F 73 " --> pdb=" O SER F 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.795A pdb=" N CYS F 10 " --> pdb=" O LYS P 22 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS P 24 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU P 104 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR P 105 " --> pdb=" O ASP P 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS P 52 " --> pdb=" O GLU P 107 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER P 84 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE Q 36 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL Q 95 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU Q 75 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER Q 66 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA Q 73 " --> pdb=" O SER Q 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU F 104 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR F 105 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS F 52 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N SER F 84 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE G 36 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL G 95 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 75 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER G 66 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA G 73 " --> pdb=" O SER G 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.896A pdb=" N CYS G 10 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS Q 24 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Q 104 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR Q 105 " --> pdb=" O ASP Q 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Q 52 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N SER Q 84 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE R 36 " --> pdb=" O SER Q 84 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA R 38 " --> pdb=" O SER Q 86 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL R 95 " --> pdb=" O ILE R 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU R 75 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER R 66 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA R 73 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU G 104 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR G 105 " --> pdb=" O ASP G 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 52 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N SER G 84 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE H 36 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 95 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU H 75 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER H 66 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA H 73 " --> pdb=" O SER H 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.754A pdb=" N CYS H 10 " --> pdb=" O LYS R 22 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS R 24 " --> pdb=" O CYS H 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU R 104 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR R 105 " --> pdb=" O ASP R 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS R 52 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N SER R 84 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE S 36 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL S 95 " --> pdb=" O ILE S 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU S 75 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER S 66 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA S 73 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU H 104 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR H 105 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS H 52 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N SER H 84 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE I 36 " --> pdb=" O SER H 84 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 95 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU I 75 " --> pdb=" O PHE I 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER I 66 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA I 73 " --> pdb=" O SER I 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.689A pdb=" N CYS S 24 " --> pdb=" O CYS I 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU S 104 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR S 105 " --> pdb=" O ASP S 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 52 " --> pdb=" O GLU S 107 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N SER S 84 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE W 36 " --> pdb=" O SER S 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL W 95 " --> pdb=" O ILE W 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU W 75 " --> pdb=" O PHE W 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER W 66 " --> pdb=" O ALA W 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA W 73 " --> pdb=" O SER W 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 29 removed outlier: 3.739A pdb=" N GLU I 104 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR I 105 " --> pdb=" O ASP I 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS I 52 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N SER I 84 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE J 36 " --> pdb=" O SER I 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL J 95 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU J 75 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER J 66 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA J 73 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.610A pdb=" N CYS J 10 " --> pdb=" O LYS W 22 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS W 24 " --> pdb=" O CYS J 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU W 104 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR W 105 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS W 52 " --> pdb=" O GLU W 107 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N ALA T 34 " --> pdb=" O SER W 84 " (cutoff:3.500A) removed outlier: 9.474A pdb=" N SER W 86 " --> pdb=" O ALA T 34 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE T 36 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR W 88 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA T 38 " --> pdb=" O THR W 88 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ARG W 90 " --> pdb=" O ALA T 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL T 95 " --> pdb=" O ILE T 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU T 75 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER T 66 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA T 73 " --> pdb=" O SER T 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 19 through 29 removed outlier: 3.740A pdb=" N GLU J 104 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR J 105 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS J 52 " --> pdb=" O GLU J 107 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N SER J 84 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE K 36 " --> pdb=" O SER J 84 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL K 95 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU K 75 " --> pdb=" O PHE K 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER K 66 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA K 73 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.737A pdb=" N CYS K 10 " --> pdb=" O LYS T 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS T 24 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU T 104 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR T 105 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS T 52 " --> pdb=" O GLU T 107 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N SER T 84 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE V 36 " --> pdb=" O SER T 84 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR T 88 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL V 95 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU V 75 " --> pdb=" O PHE V 64 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER V 66 " --> pdb=" O ALA V 73 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA V 73 " --> pdb=" O SER V 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 11 removed outlier: 3.696A pdb=" N CYS L 10 " --> pdb=" O LYS V 22 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS V 24 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU V 104 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR V 105 " --> pdb=" O ASP V 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS V 52 " --> pdb=" O GLU V 107 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N ALA U 34 " --> pdb=" O SER V 84 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N SER V 86 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE U 36 " --> pdb=" O SER V 86 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR V 88 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA U 38 " --> pdb=" O THR V 88 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ARG V 90 " --> pdb=" O ALA U 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL U 95 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU U 75 " --> pdb=" O PHE U 64 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER U 66 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA U 73 " --> pdb=" O SER U 66 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 3.635A pdb=" N CYS M 10 " --> pdb=" O LYS U 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS U 24 " --> pdb=" O CYS M 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU U 104 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR U 105 " --> pdb=" O ASP U 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 52 " --> pdb=" O GLU U 107 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2481 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: 5.99 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5980 1.34 - 1.46: 4830 1.46 - 1.59: 8004 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 18952 Sorted by residual: bond pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.63e+00 bond pdb=" CB CYS C 24 " pdb=" SG CYS C 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.62e+00 bond pdb=" CB CYS Q 24 " pdb=" SG CYS Q 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.61e+00 bond pdb=" CB CYS M 24 " pdb=" SG CYS M 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB CYS H 24 " pdb=" SG CYS H 24 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 18947 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.99: 211 106.99 - 113.76: 11402 113.76 - 120.52: 6356 120.52 - 127.29: 7860 127.29 - 134.06: 69 Bond angle restraints: 25898 Sorted by residual: angle pdb=" CG ARG D 91 " pdb=" CD ARG D 91 " pdb=" NE ARG D 91 " ideal model delta sigma weight residual 112.00 117.16 -5.16 2.20e+00 2.07e-01 5.51e+00 angle pdb=" CG ARG S 91 " pdb=" CD ARG S 91 " pdb=" NE ARG S 91 " ideal model delta sigma weight residual 112.00 117.15 -5.15 2.20e+00 2.07e-01 5.48e+00 angle pdb=" CG ARG B 91 " pdb=" CD ARG B 91 " pdb=" NE ARG B 91 " ideal model delta sigma weight residual 112.00 117.15 -5.15 2.20e+00 2.07e-01 5.48e+00 angle pdb=" CG ARG K 91 " pdb=" CD ARG K 91 " pdb=" NE ARG K 91 " ideal model delta sigma weight residual 112.00 117.14 -5.14 2.20e+00 2.07e-01 5.47e+00 angle pdb=" CG ARG A 91 " pdb=" CD ARG A 91 " pdb=" NE ARG A 91 " ideal model delta sigma weight residual 112.00 117.14 -5.14 2.20e+00 2.07e-01 5.46e+00 ... (remaining 25893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 10298 17.02 - 34.04: 579 34.04 - 51.07: 92 51.07 - 68.09: 0 68.09 - 85.11: 60 Dihedral angle restraints: 11029 sinusoidal: 3669 harmonic: 7360 Sorted by residual: dihedral pdb=" CB CYS M 10 " pdb=" SG CYS M 10 " pdb=" SG CYS V 109 " pdb=" CB CYS V 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.11 -85.11 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS B 10 " pdb=" SG CYS B 10 " pdb=" SG CYS K 109 " pdb=" CB CYS K 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.06 -85.06 1 1.00e+01 1.00e-02 8.77e+01 dihedral pdb=" CB CYS D 10 " pdb=" SG CYS D 10 " pdb=" SG CYS M 109 " pdb=" CB CYS M 109 " ideal model delta sinusoidal sigma weight residual 93.00 178.04 -85.04 1 1.00e+01 1.00e-02 8.77e+01 ... (remaining 11026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1752 0.032 - 0.065: 954 0.065 - 0.097: 299 0.097 - 0.130: 284 0.130 - 0.162: 46 Chirality restraints: 3335 Sorted by residual: chirality pdb=" CA CYS H 24 " pdb=" N CYS H 24 " pdb=" C CYS H 24 " pdb=" CB CYS H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA CYS J 24 " pdb=" N CYS J 24 " pdb=" C CYS J 24 " pdb=" CB CYS J 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA CYS S 24 " pdb=" N CYS S 24 " pdb=" C CYS S 24 " pdb=" CB CYS S 24 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 3332 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 36 " -0.005 2.00e-02 2.50e+03 9.03e-03 8.16e-01 pdb=" C ILE P 36 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE P 36 " -0.006 2.00e-02 2.50e+03 pdb=" N TYR P 37 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 36 " 0.005 2.00e-02 2.50e+03 8.99e-03 8.08e-01 pdb=" C ILE H 36 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE H 36 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR H 37 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 36 " 0.005 2.00e-02 2.50e+03 8.99e-03 8.08e-01 pdb=" C ILE T 36 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE T 36 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR T 37 " 0.005 2.00e-02 2.50e+03 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6732 2.84 - 3.35: 15398 3.35 - 3.87: 28208 3.87 - 4.38: 33474 4.38 - 4.90: 63111 Nonbonded interactions: 146923 Sorted by model distance: nonbonded pdb=" O SER C 117 " pdb=" OG SER C 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER U 117 " pdb=" OG SER U 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER H 117 " pdb=" OG SER H 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER D 117 " pdb=" OG SER D 117 " model vdw 2.323 3.040 nonbonded pdb=" O SER M 117 " pdb=" OG SER M 117 " model vdw 2.324 3.040 ... (remaining 146918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 49.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.120 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:15.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.008 0.042 18952 Z= 0.509 Angle : 0.740 5.164 25898 Z= 0.434 Chirality : 0.052 0.162 3335 Planarity : 0.002 0.009 3197 Dihedral : 12.609 83.656 6256 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.94 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: -0.20 (0.13), residues: 1357 loop : -2.69 (0.15), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP P 27 PHE 0.009 0.002 PHE U 108 TYR 0.009 0.002 TYR B 114 ARG 0.009 0.003 ARG J 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7259 (mtm180) REVERT: D 35 ILE cc_start: 0.8790 (mm) cc_final: 0.8559 (tp) REVERT: D 65 TYR cc_start: 0.8531 (m-80) cc_final: 0.8138 (m-80) REVERT: L 93 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (t0) REVERT: M 52 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8105 (tptp) REVERT: O 50 TYR cc_start: 0.8945 (p90) cc_final: 0.8626 (p90) REVERT: O 93 ASP cc_start: 0.7682 (t0) cc_final: 0.7481 (t0) REVERT: Q 93 ASP cc_start: 0.8112 (t0) cc_final: 0.7900 (t0) REVERT: R 22 LYS cc_start: 0.8541 (tttt) cc_final: 0.8284 (tttp) REVERT: W 52 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7992 (ttpp) REVERT: W 54 ASP cc_start: 0.8014 (t70) cc_final: 0.7646 (t70) REVERT: W 69 VAL cc_start: 0.9025 (p) cc_final: 0.8709 (t) outliers start: 0 outliers final: 1 residues processed: 665 average time/residue: 0.8563 time to fit residues: 673.0774 Evaluate side-chains 539 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 97 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18952 Z= 0.232 Angle : 0.597 11.182 25898 Z= 0.343 Chirality : 0.048 0.229 3335 Planarity : 0.003 0.030 3197 Dihedral : 4.697 19.094 2739 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.40 % Allowed : 14.54 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.16), residues: 2530 helix: None (None), residues: 0 sheet: 0.48 (0.13), residues: 1426 loop : -2.81 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 27 PHE 0.014 0.001 PHE V 92 TYR 0.021 0.002 TYR D 50 ARG 0.009 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 606 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8765 (t) cc_final: 0.8550 (m) REVERT: B 100 THR cc_start: 0.8152 (m) cc_final: 0.7789 (p) REVERT: C 84 SER cc_start: 0.9089 (OUTLIER) cc_final: 0.8868 (p) REVERT: G 21 ASP cc_start: 0.8155 (m-30) cc_final: 0.7946 (m-30) REVERT: H 46 TYR cc_start: 0.8381 (m-80) cc_final: 0.8026 (m-80) REVERT: P 52 LYS cc_start: 0.9119 (ptmm) cc_final: 0.8784 (ptmm) REVERT: Q 24 CYS cc_start: 0.7093 (m) cc_final: 0.6698 (m) REVERT: R 22 LYS cc_start: 0.8954 (tttt) cc_final: 0.8436 (tttp) REVERT: U 90 ARG cc_start: 0.8753 (ptt180) cc_final: 0.6969 (ptt-90) REVERT: W 10 CYS cc_start: 0.8324 (p) cc_final: 0.7480 (t) REVERT: W 69 VAL cc_start: 0.9005 (p) cc_final: 0.8705 (t) outliers start: 88 outliers final: 54 residues processed: 639 average time/residue: 0.8556 time to fit residues: 642.4585 Evaluate side-chains 603 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 548 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 127 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 230 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 228 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18952 Z= 0.321 Angle : 0.613 10.518 25898 Z= 0.351 Chirality : 0.048 0.202 3335 Planarity : 0.003 0.044 3197 Dihedral : 4.847 20.321 2737 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 6.25 % Allowed : 19.69 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.58 (0.13), residues: 1426 loop : -2.88 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 27 PHE 0.018 0.002 PHE V 92 TYR 0.023 0.002 TYR D 37 ARG 0.011 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 556 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 THR cc_start: 0.8386 (m) cc_final: 0.8178 (p) REVERT: C 84 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8930 (p) REVERT: G 52 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8430 (ttpt) REVERT: I 90 ARG cc_start: 0.9233 (ptt180) cc_final: 0.8972 (ptt180) REVERT: I 91 ARG cc_start: 0.8476 (mtm110) cc_final: 0.8073 (mtm180) REVERT: P 52 LYS cc_start: 0.9114 (ptmm) cc_final: 0.8783 (ptmm) REVERT: R 22 LYS cc_start: 0.8980 (tttt) cc_final: 0.8435 (tttp) REVERT: R 42 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8517 (t) REVERT: S 91 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7995 (mtm-85) REVERT: W 10 CYS cc_start: 0.8207 (p) cc_final: 0.7534 (t) outliers start: 125 outliers final: 85 residues processed: 607 average time/residue: 0.8695 time to fit residues: 619.8300 Evaluate side-chains 608 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 521 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 54 ASP Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 227 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 18952 Z= 0.364 Angle : 0.626 10.416 25898 Z= 0.358 Chirality : 0.048 0.229 3335 Planarity : 0.003 0.038 3197 Dihedral : 4.992 21.338 2737 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 7.45 % Allowed : 21.34 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.59 (0.13), residues: 1426 loop : -2.95 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 27 PHE 0.021 0.002 PHE T 64 TYR 0.023 0.002 TYR P 50 ARG 0.010 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5060 Ramachandran restraints generated. 2530 Oldfield, 0 Emsley, 2530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 540 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 88 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8082 (p) REVERT: F 105 THR cc_start: 0.8647 (t) cc_final: 0.8414 (p) REVERT: I 18 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8499 (pt) REVERT: L 90 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7756 (ptt90) REVERT: O 66 SER cc_start: 0.9226 (p) cc_final: 0.8995 (p) REVERT: P 52 LYS cc_start: 0.9120 (ptmm) cc_final: 0.8815 (ptmm) REVERT: P 91 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7800 (mtp85) REVERT: T 90 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8742 (ptt180) REVERT: W 10 CYS cc_start: 0.7979 (p) cc_final: 0.7642 (t) outliers start: 149 outliers final: 105 residues processed: 601 average time/residue: 0.8540 time to fit residues: 605.3968 Evaluate side-chains 630 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 519 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain J residue 24 CYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 48 SER Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain M residue 26 ASP Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain P residue 10 CYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 54 ASP Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 45 ILE Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 96 THR Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 48 SER Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 86 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 90 ARG Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 48 SER Chi-restraints excluded: chain U residue 84 SER Chi-restraints excluded: chain U residue 97 ILE Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 90 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 203 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 3 optimal weight: 0.0020 chunk 182 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 219 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 overall best weight: 6.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3424 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: