Starting phenix.real_space_refine on Sat Feb 17 12:57:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/02_2024/7a02_11591.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/02_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_11591/02_2024/7a02_11591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/02_2024/7a02_11591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/02_2024/7a02_11591.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a02_11591/02_2024/7a02_11591.pdb" } 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-5238/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: 9.55, 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: 6.84 Conformation dependent library (CDL) restraints added in 3.8 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: 2.33 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: 6.13 Time building geometry restraints manager: 7.50 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 2.440 nonbonded pdb=" O SER U 117 " pdb=" OG SER U 117 " model vdw 2.323 2.440 nonbonded pdb=" O SER H 117 " pdb=" OG SER H 117 " model vdw 2.323 2.440 nonbonded pdb=" O SER D 117 " pdb=" OG SER D 117 " model vdw 2.323 2.440 nonbonded pdb=" O SER M 117 " pdb=" OG SER M 117 " model vdw 2.324 2.440 ... (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 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: 0.200 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: 2.010 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 50.280 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.210 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:14.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.170 ------------------------------------------------------------------------------- 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 : 2.086 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: 0.8367 time to fit residues: 658.7933 Evaluate side-chains 539 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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: 7.9990 chunk 191 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.8337 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18952 Z= 0.266 Angle : 0.604 11.349 25898 Z= 0.347 Chirality : 0.048 0.224 3335 Planarity : 0.003 0.033 3197 Dihedral : 4.834 20.221 2739 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.10 % Allowed : 15.14 % Favored : 79.76 % 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: -1.31 (0.16), residues: 2530 helix: None (None), residues: 0 sheet: 0.45 (0.13), residues: 1426 loop : -2.82 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 27 PHE 0.015 0.002 PHE V 92 TYR 0.021 0.002 TYR D 50 ARG 0.008 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 686 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 584 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8782 (t) cc_final: 0.8567 (m) REVERT: B 100 THR cc_start: 0.8127 (m) cc_final: 0.7784 (p) REVERT: H 46 TYR cc_start: 0.8422 (m-80) cc_final: 0.8107 (m-80) REVERT: I 91 ARG cc_start: 0.8255 (mtm110) cc_final: 0.8044 (mpp-170) REVERT: P 52 LYS cc_start: 0.9157 (ptmm) cc_final: 0.8828 (ptmm) REVERT: P 54 ASP cc_start: 0.7917 (t0) cc_final: 0.7705 (t0) REVERT: Q 24 CYS cc_start: 0.7138 (m) cc_final: 0.6739 (m) REVERT: R 22 LYS cc_start: 0.8978 (tttt) cc_final: 0.8463 (tttp) REVERT: U 90 ARG cc_start: 0.8768 (ptt180) cc_final: 0.6960 (ptt-90) REVERT: W 10 CYS cc_start: 0.8294 (p) cc_final: 0.7557 (t) REVERT: W 69 VAL cc_start: 0.9009 (p) cc_final: 0.8652 (t) outliers start: 102 outliers final: 69 residues processed: 622 average time/residue: 0.8606 time to fit residues: 628.8166 Evaluate side-chains 599 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 530 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 C residue 115 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 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 57 THR 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 48 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 26 ASP Chi-restraints excluded: chain L residue 75 GLU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 115 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 Q residue 97 ILE Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 69 VAL 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 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE 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 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: 0.9980 chunk 156 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 228 optimal weight: 0.0050 chunk 78 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 overall best weight: 4.4000 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18952 Z= 0.221 Angle : 0.556 10.045 25898 Z= 0.320 Chirality : 0.046 0.196 3335 Planarity : 0.003 0.039 3197 Dihedral : 4.553 19.002 2737 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.90 % Allowed : 20.59 % Favored : 73.51 % 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: -1.19 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.63 (0.13), residues: 1426 loop : -2.89 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 27 PHE 0.017 0.001 PHE V 92 TYR 0.022 0.002 TYR D 37 ARG 0.009 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 677 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 559 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 SER cc_start: 0.8839 (t) cc_final: 0.8597 (m) REVERT: B 100 THR cc_start: 0.8211 (m) cc_final: 0.7956 (p) REVERT: C 84 SER cc_start: 0.9141 (OUTLIER) cc_final: 0.8926 (p) REVERT: J 11 CYS cc_start: 0.6536 (t) cc_final: 0.6270 (t) REVERT: P 52 LYS cc_start: 0.9124 (ptmm) cc_final: 0.8811 (ptmm) REVERT: R 21 ASP cc_start: 0.8551 (m-30) cc_final: 0.8237 (m-30) REVERT: R 22 LYS cc_start: 0.8973 (tttt) cc_final: 0.8473 (tttp) REVERT: U 90 ARG cc_start: 0.8787 (ptt180) cc_final: 0.6919 (ptt-90) REVERT: W 10 CYS cc_start: 0.8251 (p) cc_final: 0.7505 (t) outliers start: 118 outliers final: 72 residues processed: 608 average time/residue: 0.9208 time to fit residues: 653.9645 Evaluate side-chains 599 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 526 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 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 115 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR 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 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 28 THR 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 57 THR 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 84 SER 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 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 97 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 115 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 O residue 97 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 42 SER 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 Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain R residue 42 SER 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 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE 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 V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 88 THR 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: 0.0970 chunk 173 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 244 optimal weight: 40.0000 chunk 120 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 overall best weight: 6.0186 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18952 Z= 0.273 Angle : 0.570 9.981 25898 Z= 0.327 Chirality : 0.046 0.217 3335 Planarity : 0.003 0.050 3197 Dihedral : 4.689 20.623 2737 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 7.65 % Allowed : 21.84 % Favored : 70.51 % 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: -1.19 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.67 (0.13), residues: 1426 loop : -2.95 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 27 PHE 0.013 0.002 PHE V 92 TYR 0.018 0.002 TYR S 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 688 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 535 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8944 (p) REVERT: D 91 ARG cc_start: 0.8237 (mtm180) cc_final: 0.7968 (mtm180) REVERT: E 52 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8496 (ttmm) REVERT: L 90 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7695 (ptt90) REVERT: P 52 LYS cc_start: 0.9153 (ptmm) cc_final: 0.8874 (ptmm) REVERT: P 90 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8092 (ptt180) REVERT: R 22 LYS cc_start: 0.9006 (tttt) cc_final: 0.8466 (tttp) REVERT: R 42 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8516 (t) REVERT: U 90 ARG cc_start: 0.8840 (ptt180) cc_final: 0.6922 (ptt-90) REVERT: W 10 CYS cc_start: 0.8074 (p) cc_final: 0.7637 (t) outliers start: 153 outliers final: 114 residues processed: 606 average time/residue: 0.8481 time to fit residues: 607.0269 Evaluate side-chains 631 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 512 time to evaluate : 2.026 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 17 THR 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 115 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 D residue 98 LEU Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 115 THR 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 57 THR 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 48 SER Chi-restraints excluded: chain I residue 84 SER 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 48 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 26 ASP 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 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 97 ILE Chi-restraints excluded: chain M residue 115 THR 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 115 THR Chi-restraints excluded: chain O residue 52 LYS 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 O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 CYS Chi-restraints excluded: chain S residue 83 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 45 ILE 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 86 SER Chi-restraints excluded: chain T residue 88 THR 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 78 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 115 THR 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: 10.0000 chunk 182 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18952 Z= 0.328 Angle : 0.596 12.761 25898 Z= 0.341 Chirality : 0.047 0.235 3335 Planarity : 0.003 0.053 3197 Dihedral : 4.851 21.343 2737 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 9.25 % Allowed : 21.69 % Favored : 69.07 % 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: -1.22 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.66 (0.13), residues: 1426 loop : -2.99 (0.15), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 27 PHE 0.012 0.002 PHE H 64 TYR 0.017 0.002 TYR H 65 ARG 0.009 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 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 708 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 523 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9155 (OUTLIER) cc_final: 0.8931 (p) REVERT: E 52 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8508 (ttmm) REVERT: E 54 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: E 90 ARG cc_start: 0.8353 (ptm-80) cc_final: 0.8059 (ptm-80) REVERT: F 105 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8465 (p) REVERT: I 18 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (pt) REVERT: L 90 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7637 (ptt90) REVERT: P 52 LYS cc_start: 0.9142 (ptmm) cc_final: 0.8842 (ptmm) REVERT: P 90 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8118 (ptt180) REVERT: P 91 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: R 21 ASP cc_start: 0.8584 (m-30) cc_final: 0.8279 (m-30) REVERT: R 22 LYS cc_start: 0.9008 (tttt) cc_final: 0.8458 (tttp) REVERT: W 10 CYS cc_start: 0.7933 (p) cc_final: 0.7641 (t) outliers start: 185 outliers final: 134 residues processed: 615 average time/residue: 0.8509 time to fit residues: 619.6334 Evaluate side-chains 653 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 511 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 THR 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 48 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 B residue 88 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 72 THR 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 115 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 D residue 98 LEU Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP 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 G residue 115 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 57 THR 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 H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 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 K residue 86 SER Chi-restraints excluded: chain L residue 26 ASP 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 97 ILE Chi-restraints excluded: chain M residue 115 THR 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 115 THR Chi-restraints excluded: chain O residue 52 LYS Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 CYS 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 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 U residue 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 88 THR Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 82 optimal weight: 0.8980 chunk 220 optimal weight: 60.0000 chunk 48 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 244 optimal weight: 20.0000 chunk 203 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 overall best weight: 7.5792 ------------------------------------------------------------------------------- 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: 0.8391 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18952 Z= 0.327 Angle : 0.600 14.034 25898 Z= 0.342 Chirality : 0.047 0.252 3335 Planarity : 0.003 0.060 3197 Dihedral : 4.878 21.717 2737 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 9.40 % Allowed : 22.39 % Favored : 68.22 % 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: 0.67 (0.13), residues: 1426 loop : -3.03 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 27 PHE 0.013 0.002 PHE S 64 TYR 0.021 0.002 TYR S 50 ARG 0.012 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 6 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 709 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 521 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8934 (p) REVERT: E 52 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8502 (ttmm) REVERT: E 54 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: E 90 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (ptt-90) REVERT: G 43 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: I 18 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8504 (pt) REVERT: I 100 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8163 (p) REVERT: L 90 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7642 (ptt90) REVERT: N 91 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8331 (mtm-85) REVERT: P 52 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8828 (ptmm) REVERT: P 90 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8127 (ptt180) REVERT: P 91 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7770 (mtp85) REVERT: R 21 ASP cc_start: 0.8604 (m-30) cc_final: 0.8283 (m-30) REVERT: R 22 LYS cc_start: 0.9019 (tttt) cc_final: 0.8464 (tttp) REVERT: R 52 LYS cc_start: 0.8244 (pttm) cc_final: 0.8026 (pttm) REVERT: W 10 CYS cc_start: 0.7901 (p) cc_final: 0.7646 (t) outliers start: 188 outliers final: 141 residues processed: 615 average time/residue: 0.8329 time to fit residues: 606.4792 Evaluate side-chains 658 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 507 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 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 B residue 88 THR 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 115 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 THR 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 H residue 94 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN 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 K residue 77 ILE Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 26 ASP 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 L residue 115 THR Chi-restraints excluded: chain M residue 18 ILE 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 97 ILE Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 24 CYS 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 N residue 115 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 CYS Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 U residue 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER 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 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 236 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18952 Z= 0.380 Angle : 0.627 13.259 25898 Z= 0.357 Chirality : 0.048 0.245 3335 Planarity : 0.004 0.066 3197 Dihedral : 5.036 22.386 2737 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 9.55 % Allowed : 22.29 % Favored : 68.17 % 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: -1.27 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.66 (0.13), residues: 1426 loop : -3.08 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 27 PHE 0.015 0.002 PHE S 64 TYR 0.014 0.002 TYR I 114 ARG 0.013 0.001 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 7 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 709 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 518 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8443 (ptp90) REVERT: C 84 SER cc_start: 0.9175 (OUTLIER) cc_final: 0.8946 (p) REVERT: E 52 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8592 (ttmm) REVERT: F 105 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8500 (p) REVERT: G 43 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: I 18 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8504 (pt) REVERT: L 90 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7693 (ptt90) REVERT: N 91 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8252 (mtm-85) REVERT: P 52 LYS cc_start: 0.9122 (ptmm) cc_final: 0.8814 (ptmm) REVERT: P 90 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8151 (ptt180) REVERT: P 91 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7748 (mtp85) REVERT: R 22 LYS cc_start: 0.9018 (tttt) cc_final: 0.8452 (tttp) REVERT: V 98 LEU cc_start: 0.8407 (tp) cc_final: 0.8198 (tm) REVERT: W 10 CYS cc_start: 0.7825 (p) cc_final: 0.7569 (t) outliers start: 191 outliers final: 148 residues processed: 617 average time/residue: 0.8434 time to fit residues: 613.6583 Evaluate side-chains 664 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 507 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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 90 ARG Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 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 B residue 88 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 43 GLN 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 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 72 THR 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 H residue 94 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN 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 K residue 77 ILE Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 26 ASP 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 L residue 115 THR Chi-restraints excluded: chain M residue 18 ILE 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 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 23 VAL 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 N residue 115 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 48 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 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 S residue 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 28 THR Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 U residue 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER 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 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 150 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18952 Z= 0.251 Angle : 0.578 10.756 25898 Z= 0.330 Chirality : 0.046 0.277 3335 Planarity : 0.003 0.065 3197 Dihedral : 4.752 20.696 2737 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 8.60 % Allowed : 23.44 % Favored : 67.97 % 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: -1.19 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.74 (0.13), residues: 1426 loop : -3.07 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 27 PHE 0.013 0.001 PHE S 64 TYR 0.022 0.002 TYR E 65 ARG 0.014 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 8 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 711 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 539 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8927 (p) REVERT: D 114 TYR cc_start: 0.8627 (p90) cc_final: 0.8374 (p90) REVERT: E 52 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8505 (ttmm) REVERT: G 43 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: I 18 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8505 (pt) REVERT: L 90 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7582 (ptt90) REVERT: P 52 LYS cc_start: 0.9100 (ptmm) cc_final: 0.8796 (ptmm) REVERT: P 90 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8100 (ptt180) REVERT: P 91 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7749 (mtp85) REVERT: R 22 LYS cc_start: 0.9013 (tttt) cc_final: 0.8475 (tttp) REVERT: T 90 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8721 (ptt180) REVERT: U 90 ARG cc_start: 0.8852 (ptt180) cc_final: 0.6915 (ptt-90) REVERT: W 10 CYS cc_start: 0.7822 (p) cc_final: 0.7569 (t) outliers start: 172 outliers final: 141 residues processed: 628 average time/residue: 0.8554 time to fit residues: 634.2461 Evaluate side-chains 666 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 517 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 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 9 SER Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 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 H residue 84 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN 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 K residue 86 SER Chi-restraints excluded: chain L residue 26 ASP 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 L residue 115 THR Chi-restraints excluded: chain M residue 23 VAL 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 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP 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 N residue 115 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 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 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ILE 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 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 233 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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: 0.8404 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18952 Z= 0.360 Angle : 0.638 10.992 25898 Z= 0.361 Chirality : 0.048 0.276 3335 Planarity : 0.003 0.073 3197 Dihedral : 4.990 22.154 2737 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 8.75 % Allowed : 23.74 % Favored : 67.52 % 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: -1.25 (0.15), residues: 2530 helix: None (None), residues: 0 sheet: 0.70 (0.13), residues: 1426 loop : -3.11 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 27 PHE 0.016 0.002 PHE S 64 TYR 0.038 0.002 TYR K 37 ARG 0.014 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 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 690 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 515 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8430 (ptp90) REVERT: D 114 TYR cc_start: 0.8663 (p90) cc_final: 0.8447 (p90) REVERT: E 52 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8535 (ttmm) REVERT: G 43 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: I 18 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8498 (pt) REVERT: L 90 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7640 (ptt90) REVERT: P 52 LYS cc_start: 0.9118 (ptmm) cc_final: 0.8818 (ptmm) REVERT: P 90 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8144 (ptt180) REVERT: P 91 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7766 (mtp85) REVERT: R 21 ASP cc_start: 0.8555 (m-30) cc_final: 0.8177 (m-30) REVERT: R 22 LYS cc_start: 0.9022 (tttt) cc_final: 0.8450 (tttp) REVERT: T 90 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8751 (ptt180) REVERT: W 10 CYS cc_start: 0.7849 (p) cc_final: 0.7550 (t) outliers start: 175 outliers final: 152 residues processed: 610 average time/residue: 0.8473 time to fit residues: 612.2433 Evaluate side-chains 667 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 507 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 90 ARG Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 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 B residue 88 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 43 GLN 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 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 THR 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 72 THR 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 H residue 84 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 97 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN 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 K residue 77 ILE Chi-restraints excluded: chain L residue 26 ASP 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 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 18 ILE 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 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 54 ASP 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 N residue 115 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 72 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS 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 R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 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 S residue 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ILE 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 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 240 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 200 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18952 Z= 0.256 Angle : 0.593 10.748 25898 Z= 0.336 Chirality : 0.047 0.269 3335 Planarity : 0.003 0.071 3197 Dihedral : 4.765 20.752 2737 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 7.85 % Allowed : 24.44 % Favored : 67.72 % 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: -1.18 (0.16), residues: 2530 helix: None (None), residues: 0 sheet: 0.77 (0.13), residues: 1426 loop : -3.11 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 27 PHE 0.013 0.001 PHE S 64 TYR 0.023 0.002 TYR E 65 ARG 0.015 0.001 ARG B 91 ********************** REFINEMENT MACRO_CYCLE 10 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 675 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 518 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8940 (p) REVERT: D 114 TYR cc_start: 0.8629 (p90) cc_final: 0.8373 (p90) REVERT: E 52 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8535 (ttmm) REVERT: I 18 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8500 (pt) REVERT: L 90 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7578 (ptt90) REVERT: P 52 LYS cc_start: 0.9104 (ptmm) cc_final: 0.8806 (ptmm) REVERT: P 90 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8114 (ptt180) REVERT: P 91 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7755 (mtp85) REVERT: R 22 LYS cc_start: 0.8983 (tttt) cc_final: 0.8458 (tttp) REVERT: R 52 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7936 (pttm) REVERT: U 90 ARG cc_start: 0.8859 (ptt180) cc_final: 0.6919 (ptt-90) REVERT: W 10 CYS cc_start: 0.7838 (p) cc_final: 0.7542 (t) outliers start: 157 outliers final: 137 residues processed: 599 average time/residue: 0.8489 time to fit residues: 599.3909 Evaluate side-chains 652 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 508 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 LYS Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain F residue 48 SER Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 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 H residue 84 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain I residue 48 SER Chi-restraints excluded: chain I residue 84 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 16 LYS Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 43 GLN 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 K residue 77 ILE Chi-restraints excluded: chain L residue 26 ASP 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 86 SER Chi-restraints excluded: chain L residue 90 ARG Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain M residue 18 ILE 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 83 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 111 THR Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 54 ASP 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 N residue 115 THR Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 SER Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 115 THR 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 90 ARG Chi-restraints excluded: chain P residue 91 ARG Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 84 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 24 CYS Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 10 CYS Chi-restraints excluded: chain S residue 24 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 97 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain T residue 23 VAL Chi-restraints excluded: chain T residue 45 ILE 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 98 LEU 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 115 THR Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain V residue 115 THR Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 69 VAL Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 9.9990 chunk 61 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 176 optimal weight: 40.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.129799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108064 restraints weight = 24640.621| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.66 r_work: 0.3045 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18952 Z= 0.353 Angle : 0.634 11.047 25898 Z= 0.359 Chirality : 0.048 0.268 3335 Planarity : 0.004 0.072 3197 Dihedral : 4.984 22.058 2737 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 8.15 % Allowed : 24.54 % Favored : 67.32 % 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: 0.72 (0.13), residues: 1426 loop : -3.16 (0.14), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 27 PHE 0.016 0.002 PHE S 64 TYR 0.027 0.002 TYR K 37 ARG 0.015 0.001 ARG B 91 =============================================================================== Job complete usr+sys time: 8672.06 seconds wall clock time: 154 minutes 29.78 seconds (9269.78 seconds total)