Starting phenix.real_space_refine on Tue Mar 19 01:35:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vak_21141/03_2024/6vak_21141.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.031 sd= 0.566 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 77 5.16 5 C 14707 2.51 5 N 3982 2.21 5 O 4015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 171": "OD1" <-> "OD2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 137": "OD1" <-> "OD2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "E GLU 262": "OE1" <-> "OE2" Residue "E TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 137": "OD1" <-> "OD2" Residue "F ASP 171": "OD1" <-> "OD2" Residue "F PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G ASP 171": "OD1" <-> "OD2" Residue "G PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H ASP 171": "OD1" <-> "OD2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I ASP 171": "OD1" <-> "OD2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 262": "OE1" <-> "OE2" Residue "I TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 137": "OD1" <-> "OD2" Residue "J ASP 171": "OD1" <-> "OD2" Residue "J PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 174": "OE1" <-> "OE2" Residue "J ARG 181": "NH1" <-> "NH2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "J GLU 262": "OE1" <-> "OE2" Residue "J TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 171": "OD1" <-> "OD2" Residue "K PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 174": "OE1" <-> "OE2" Residue "K ARG 181": "NH1" <-> "NH2" Residue "K GLU 183": "OE1" <-> "OE2" Residue "K PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 249": "NH1" <-> "NH2" Residue "K GLU 262": "OE1" <-> "OE2" Residue "K TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22781 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "F" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "J" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "K" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2071 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 11.89, per 1000 atoms: 0.52 Number of scatterers: 22781 At special positions: 0 Unit cell: (147.34, 147.34, 102.82, 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 77 16.00 O 4015 8.00 N 3982 7.00 C 14707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.04 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.04 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.04 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.04 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.04 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.04 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.04 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.04 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.04 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.62 Conformation dependent library (CDL) restraints added in 4.5 seconds 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 11 sheets defined 75.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 25 through 43 removed outlier: 4.097A pdb=" N ALA A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.507A pdb=" N ARG A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 208 " --> pdb=" O CYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR A 282 " --> pdb=" O TRP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA B 43 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.508A pdb=" N ARG B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 176 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR B 208 " --> pdb=" O CYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA B 218 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR B 282 " --> pdb=" O TRP B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Proline residue: C 114 - end of helix removed outlier: 3.508A pdb=" N ARG C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 176 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 208 " --> pdb=" O CYS C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA C 218 " --> pdb=" O TYR C 214 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR C 282 " --> pdb=" O TRP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA D 43 " --> pdb=" O PHE D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Proline residue: D 114 - end of helix removed outlier: 3.508A pdb=" N ARG D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL D 176 " --> pdb=" O PHE D 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR D 208 " --> pdb=" O CYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA D 218 " --> pdb=" O TYR D 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE D 250 " --> pdb=" O ASN D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR D 282 " --> pdb=" O TRP D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 87 " --> pdb=" O VAL E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix removed outlier: 3.508A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 153 through 159 Processing helix chain 'E' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL E 176 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR E 208 " --> pdb=" O CYS E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA E 218 " --> pdb=" O TYR E 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE E 250 " --> pdb=" O ASN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR E 282 " --> pdb=" O TRP E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN F 87 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Proline residue: F 114 - end of helix removed outlier: 3.507A pdb=" N ARG F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL F 176 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR F 208 " --> pdb=" O CYS F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA F 218 " --> pdb=" O TYR F 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE F 250 " --> pdb=" O ASN F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR F 282 " --> pdb=" O TRP F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA G 43 " --> pdb=" O PHE G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 76 through 87 removed outlier: 4.334A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 87 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 124 removed outlier: 5.595A pdb=" N ALA G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Proline residue: G 114 - end of helix removed outlier: 3.507A pdb=" N ARG G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 153 through 159 Processing helix chain 'G' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL G 176 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU G 183 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR G 208 " --> pdb=" O CYS G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA G 218 " --> pdb=" O TYR G 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE G 250 " --> pdb=" O ASN G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR G 282 " --> pdb=" O TRP G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY G 305 " --> pdb=" O LYS G 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA H 43 " --> pdb=" O PHE H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN H 87 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Proline residue: H 114 - end of helix removed outlier: 3.507A pdb=" N ARG H 124 " --> pdb=" O ILE H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 133 Processing helix chain 'H' and resid 153 through 159 Processing helix chain 'H' and resid 169 through 209 removed outlier: 3.646A pdb=" N GLU H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL H 176 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 208 " --> pdb=" O CYS H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 removed outlier: 4.035A pdb=" N GLU H 217 " --> pdb=" O SER H 213 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA H 218 " --> pdb=" O TYR H 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE H 250 " --> pdb=" O ASN H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR H 282 " --> pdb=" O TRP H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA I 43 " --> pdb=" O PHE I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 75 removed outlier: 4.173A pdb=" N LEU I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN I 87 " --> pdb=" O VAL I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix removed outlier: 3.507A pdb=" N ARG I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 133 Processing helix chain 'I' and resid 153 through 159 Processing helix chain 'I' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL I 176 " --> pdb=" O PHE I 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU I 183 " --> pdb=" O ARG I 179 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR I 208 " --> pdb=" O CYS I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA I 218 " --> pdb=" O TYR I 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE I 250 " --> pdb=" O ASN I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR I 282 " --> pdb=" O TRP I 278 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 305 removed outlier: 3.843A pdb=" N GLY I 305 " --> pdb=" O LYS I 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 43 removed outlier: 4.096A pdb=" N ALA J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 76 through 87 removed outlier: 4.333A pdb=" N TRP J 80 " --> pdb=" O ASN J 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN J 87 " --> pdb=" O VAL J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 124 removed outlier: 5.596A pdb=" N ALA J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Proline residue: J 114 - end of helix removed outlier: 3.508A pdb=" N ARG J 124 " --> pdb=" O ILE J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 133 Processing helix chain 'J' and resid 153 through 159 Processing helix chain 'J' and resid 169 through 209 removed outlier: 3.647A pdb=" N GLU J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 176 " --> pdb=" O PHE J 172 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU J 183 " --> pdb=" O ARG J 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR J 208 " --> pdb=" O CYS J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 252 removed outlier: 3.863A pdb=" N ALA J 218 " --> pdb=" O TYR J 214 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE J 250 " --> pdb=" O ASN J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 282 removed outlier: 3.656A pdb=" N THR J 282 " --> pdb=" O TRP J 278 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY J 305 " --> pdb=" O LYS J 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 43 removed outlier: 4.097A pdb=" N ALA K 43 " --> pdb=" O PHE K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 75 removed outlier: 4.174A pdb=" N LEU K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 76 through 87 removed outlier: 4.332A pdb=" N TRP K 80 " --> pdb=" O ASN K 76 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN K 87 " --> pdb=" O VAL K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 124 removed outlier: 5.597A pdb=" N ALA K 113 " --> pdb=" O ARG K 109 " (cutoff:3.500A) Proline residue: K 114 - end of helix removed outlier: 3.508A pdb=" N ARG K 124 " --> pdb=" O ILE K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 133 Processing helix chain 'K' and resid 153 through 159 Processing helix chain 'K' and resid 169 through 209 removed outlier: 3.646A pdb=" N GLU K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL K 176 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU K 183 " --> pdb=" O ARG K 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR K 208 " --> pdb=" O CYS K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 252 removed outlier: 3.864A pdb=" N ALA K 218 " --> pdb=" O TYR K 214 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE K 250 " --> pdb=" O ASN K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 282 removed outlier: 3.655A pdb=" N THR K 282 " --> pdb=" O TRP K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 305 removed outlier: 3.842A pdb=" N GLY K 305 " --> pdb=" O LYS K 301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG A 288 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG B 288 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG C 288 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG D 288 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG E 288 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG F 288 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG G 288 " --> pdb=" O LEU G 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 288 through 289 removed outlier: 4.086A pdb=" N ARG H 288 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 288 through 289 removed outlier: 4.088A pdb=" N ARG I 288 " --> pdb=" O LEU I 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 288 through 289 removed outlier: 4.088A pdb=" N ARG J 288 " --> pdb=" O LEU J 295 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 288 through 289 removed outlier: 4.087A pdb=" N ARG K 288 " --> pdb=" O LEU K 295 " (cutoff:3.500A) 1563 hydrogen bonds defined for protein. 4689 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: 6.80 Time building geometry restraints manager: 10.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7480 1.34 - 1.46: 5771 1.46 - 1.58: 10047 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 23375 Sorted by residual: bond pdb=" N GLU A 126 " pdb=" CA GLU A 126 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.38e+00 bond pdb=" N GLU E 126 " pdb=" CA GLU E 126 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" N LYS G 163 " pdb=" CA LYS G 163 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.33e+00 bond pdb=" N LYS F 163 " pdb=" CA LYS F 163 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.29e+00 bond pdb=" N GLU C 126 " pdb=" CA GLU C 126 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 ... (remaining 23370 not shown) Histogram of bond angle deviations from ideal: 102.43 - 108.78: 1278 108.78 - 115.13: 13152 115.13 - 121.48: 12629 121.48 - 127.83: 4579 127.83 - 134.17: 328 Bond angle restraints: 31966 Sorted by residual: angle pdb=" N ALA K 127 " pdb=" CA ALA K 127 " pdb=" C ALA K 127 " ideal model delta sigma weight residual 113.18 109.09 4.09 1.33e+00 5.65e-01 9.47e+00 angle pdb=" C GLU A 164 " pdb=" N ASN A 165 " pdb=" CA ASN A 165 " ideal model delta sigma weight residual 123.46 119.32 4.14 1.35e+00 5.49e-01 9.40e+00 angle pdb=" C GLU J 164 " pdb=" N ASN J 165 " pdb=" CA ASN J 165 " ideal model delta sigma weight residual 123.46 119.33 4.13 1.35e+00 5.49e-01 9.37e+00 angle pdb=" C GLU F 164 " pdb=" N ASN F 165 " pdb=" CA ASN F 165 " ideal model delta sigma weight residual 123.46 119.35 4.11 1.35e+00 5.49e-01 9.28e+00 angle pdb=" C GLU I 164 " pdb=" N ASN I 165 " pdb=" CA ASN I 165 " ideal model delta sigma weight residual 123.46 119.35 4.11 1.35e+00 5.49e-01 9.27e+00 ... (remaining 31961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 12408 16.83 - 33.67: 968 33.67 - 50.50: 275 50.50 - 67.33: 11 67.33 - 84.17: 55 Dihedral angle restraints: 13717 sinusoidal: 4972 harmonic: 8745 Sorted by residual: dihedral pdb=" CB GLU F 261 " pdb=" CG GLU F 261 " pdb=" CD GLU F 261 " pdb=" OE1 GLU F 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.17 84.17 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CB GLU B 261 " pdb=" CG GLU B 261 " pdb=" CD GLU B 261 " pdb=" OE1 GLU B 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.15 84.15 1 3.00e+01 1.11e-03 9.58e+00 dihedral pdb=" CB GLU I 261 " pdb=" CG GLU I 261 " pdb=" CD GLU I 261 " pdb=" OE1 GLU I 261 " ideal model delta sinusoidal sigma weight residual 0.00 -84.14 84.14 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 13714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2252 0.026 - 0.052: 851 0.052 - 0.077: 322 0.077 - 0.103: 97 0.103 - 0.129: 97 Chirality restraints: 3619 Sorted by residual: chirality pdb=" CA PRO G 50 " pdb=" N PRO G 50 " pdb=" C PRO G 50 " pdb=" CB PRO G 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO J 50 " pdb=" N PRO J 50 " pdb=" C PRO J 50 " pdb=" CB PRO J 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA PRO D 50 " pdb=" N PRO D 50 " pdb=" C PRO D 50 " pdb=" CB PRO D 50 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 3616 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 160 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 161 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 160 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO J 161 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 161 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 161 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 160 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO D 161 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 161 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 161 " -0.025 5.00e-02 4.00e+02 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 215 2.62 - 3.19: 21381 3.19 - 3.76: 34640 3.76 - 4.33: 43772 4.33 - 4.90: 73603 Nonbonded interactions: 173611 Sorted by model distance: nonbonded pdb=" O VAL C 129 " pdb=" OG SER C 133 " model vdw 2.047 2.440 nonbonded pdb=" O VAL E 129 " pdb=" OG SER E 133 " model vdw 2.047 2.440 nonbonded pdb=" O VAL I 129 " pdb=" OG SER I 133 " model vdw 2.047 2.440 nonbonded pdb=" O VAL H 129 " pdb=" OG SER H 133 " model vdw 2.047 2.440 nonbonded pdb=" O VAL F 129 " pdb=" OG SER F 133 " model vdw 2.047 2.440 ... (remaining 173606 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 4.960 Check model and map are aligned: 0.310 Set scattering table: 0.220 Process input model: 59.400 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.004 0.029 23375 Z= 0.270 Angle : 0.765 6.719 31966 Z= 0.453 Chirality : 0.037 0.129 3619 Planarity : 0.005 0.045 4125 Dihedral : 14.359 84.169 7997 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.96 % Allowed : 4.30 % Favored : 92.75 % 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: -2.80 (0.13), residues: 2948 helix: -1.10 (0.10), residues: 2112 sheet: None (None), residues: 0 loop : -3.64 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 189 HIS 0.005 0.001 HIS J 238 PHE 0.021 0.001 PHE A 172 TYR 0.014 0.001 TYR J 287 ARG 0.003 0.000 ARG F 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 444 time to evaluate : 2.426 Fit side-chains REVERT: A 190 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (tt) REVERT: B 190 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8456 (tt) REVERT: B 205 LEU cc_start: 0.8435 (tp) cc_final: 0.8157 (tt) REVERT: C 190 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8322 (tt) REVERT: D 121 SER cc_start: 0.9053 (t) cc_final: 0.8838 (p) REVERT: E 190 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8144 (tt) REVERT: E 285 TYR cc_start: 0.7781 (t80) cc_final: 0.7386 (t80) REVERT: G 190 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8339 (mp) REVERT: H 190 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8290 (mp) REVERT: H 206 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7962 (tttt) REVERT: I 190 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7808 (mp) outliers start: 66 outliers final: 13 residues processed: 502 average time/residue: 0.2813 time to fit residues: 230.8057 Evaluate side-chains 288 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 268 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 81 ASN A 222 GLN A 229 GLN B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 238 HIS B 277 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 222 GLN C 238 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 238 HIS ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN E 238 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN F 238 HIS F 266 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN G 238 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN H 222 GLN H 238 HIS ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 ASN I 207 HIS I 238 HIS ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN J 207 HIS J 238 HIS J 246 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 ASN K 207 HIS K 238 HIS K 246 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23375 Z= 0.247 Angle : 0.616 7.030 31966 Z= 0.308 Chirality : 0.037 0.161 3619 Planarity : 0.004 0.046 4125 Dihedral : 5.318 48.104 3304 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.67 % Allowed : 12.72 % Favored : 83.61 % 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: -0.49 (0.15), residues: 2948 helix: 0.58 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.94 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 302 HIS 0.005 0.001 HIS J 207 PHE 0.017 0.001 PHE E 172 TYR 0.016 0.001 TYR F 208 ARG 0.002 0.000 ARG G 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 318 time to evaluate : 2.493 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: B 205 LEU cc_start: 0.8650 (tp) cc_final: 0.8450 (tt) outliers start: 82 outliers final: 56 residues processed: 366 average time/residue: 0.2642 time to fit residues: 162.9626 Evaluate side-chains 310 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 254 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 80.0000 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 0.0010 chunk 267 optimal weight: 0.0770 chunk 92 optimal weight: 10.0000 chunk 216 optimal weight: 80.0000 overall best weight: 1.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 238 HIS A 246 ASN B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN D 45 HIS ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN G 222 GLN G 246 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN H 246 ASN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 ASN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 ASN ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23375 Z= 0.169 Angle : 0.556 6.862 31966 Z= 0.276 Chirality : 0.035 0.169 3619 Planarity : 0.004 0.050 4125 Dihedral : 4.148 15.770 3267 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.67 % Allowed : 17.20 % Favored : 79.13 % 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: 0.80 (0.16), residues: 2948 helix: 1.57 (0.11), residues: 2178 sheet: None (None), residues: 0 loop : -2.61 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP J 302 HIS 0.004 0.001 HIS A 238 PHE 0.013 0.001 PHE E 148 TYR 0.020 0.001 TYR H 285 ARG 0.002 0.000 ARG K 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 307 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 GLU cc_start: 0.7858 (pp20) cc_final: 0.7534 (pt0) REVERT: B 205 LEU cc_start: 0.8574 (tp) cc_final: 0.8318 (tt) REVERT: E 285 TYR cc_start: 0.7672 (t80) cc_final: 0.7274 (t80) outliers start: 82 outliers final: 69 residues processed: 347 average time/residue: 0.2703 time to fit residues: 156.6365 Evaluate side-chains 341 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 4.9990 chunk 271 optimal weight: 40.0000 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 GLN B 45 HIS B 246 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 277 GLN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23375 Z= 0.258 Angle : 0.572 6.193 31966 Z= 0.287 Chirality : 0.036 0.166 3619 Planarity : 0.004 0.045 4125 Dihedral : 4.132 14.959 3267 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.70 % Allowed : 18.45 % Favored : 76.85 % 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: 1.06 (0.16), residues: 2948 helix: 1.79 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.56 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 189 HIS 0.002 0.001 HIS I 238 PHE 0.014 0.001 PHE E 148 TYR 0.028 0.001 TYR C 285 ARG 0.001 0.000 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 294 time to evaluate : 2.577 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: B 126 GLU cc_start: 0.7929 (pp20) cc_final: 0.7628 (pt0) REVERT: E 285 TYR cc_start: 0.7669 (t80) cc_final: 0.7258 (t80) REVERT: F 148 PHE cc_start: 0.6315 (m-80) cc_final: 0.5956 (m-80) REVERT: F 205 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8237 (mp) REVERT: G 285 TYR cc_start: 0.7547 (t80) cc_final: 0.7308 (t80) REVERT: I 85 GLU cc_start: 0.7892 (tp30) cc_final: 0.7354 (tp30) outliers start: 105 outliers final: 81 residues processed: 349 average time/residue: 0.2779 time to fit residues: 165.0350 Evaluate side-chains 354 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 272 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 4.9990 chunk 162 optimal weight: 70.0000 chunk 4 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 0 optimal weight: 60.0000 chunk 146 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS B 207 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 23375 Z= 0.382 Angle : 0.612 6.460 31966 Z= 0.312 Chirality : 0.038 0.176 3619 Planarity : 0.004 0.043 4125 Dihedral : 4.324 15.848 3267 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.60 % Allowed : 18.18 % Favored : 76.22 % 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: 0.97 (0.16), residues: 2948 helix: 1.73 (0.11), residues: 2156 sheet: None (None), residues: 0 loop : -2.56 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 302 HIS 0.003 0.001 HIS I 238 PHE 0.015 0.001 PHE E 148 TYR 0.026 0.002 TYR C 285 ARG 0.002 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 262 time to evaluate : 2.596 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: B 126 GLU cc_start: 0.7882 (pp20) cc_final: 0.7656 (pt0) REVERT: F 148 PHE cc_start: 0.6514 (m-80) cc_final: 0.6306 (m-80) REVERT: F 205 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (mp) outliers start: 125 outliers final: 107 residues processed: 322 average time/residue: 0.2725 time to fit residues: 148.9595 Evaluate side-chains 360 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 252 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 207 HIS Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 207 HIS Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 148 PHE Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 287 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 222 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23375 Z= 0.223 Angle : 0.552 5.868 31966 Z= 0.276 Chirality : 0.035 0.169 3619 Planarity : 0.004 0.046 4125 Dihedral : 4.040 15.349 3267 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.61 % Allowed : 19.35 % Favored : 76.04 % 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: 1.41 (0.16), residues: 2948 helix: 2.02 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 278 HIS 0.002 0.001 HIS A 45 PHE 0.012 0.001 PHE E 148 TYR 0.028 0.001 TYR H 285 ARG 0.001 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 273 time to evaluate : 2.637 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: E 285 TYR cc_start: 0.7645 (t80) cc_final: 0.7163 (t80) REVERT: F 205 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8231 (mp) REVERT: I 121 SER cc_start: 0.9022 (t) cc_final: 0.8725 (p) outliers start: 103 outliers final: 85 residues processed: 324 average time/residue: 0.2756 time to fit residues: 149.8582 Evaluate side-chains 346 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 260 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 8.9990 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS I 277 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23375 Z= 0.286 Angle : 0.567 5.533 31966 Z= 0.286 Chirality : 0.036 0.160 3619 Planarity : 0.004 0.046 4125 Dihedral : 4.050 15.350 3267 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.79 % Allowed : 19.79 % Favored : 75.41 % 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: 1.40 (0.16), residues: 2948 helix: 2.00 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.33 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 189 HIS 0.003 0.001 HIS F 238 PHE 0.015 0.001 PHE E 148 TYR 0.024 0.001 TYR C 285 ARG 0.001 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 262 time to evaluate : 2.828 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: F 205 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8254 (mp) REVERT: I 121 SER cc_start: 0.9038 (t) cc_final: 0.8731 (p) outliers start: 107 outliers final: 97 residues processed: 316 average time/residue: 0.2700 time to fit residues: 144.8258 Evaluate side-chains 356 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 258 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 74 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 202 THR Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 0.3980 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23375 Z= 0.165 Angle : 0.525 5.398 31966 Z= 0.260 Chirality : 0.034 0.161 3619 Planarity : 0.004 0.048 4125 Dihedral : 3.768 15.752 3267 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.30 % Allowed : 20.51 % Favored : 75.19 % 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: 1.83 (0.16), residues: 2948 helix: 2.32 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.20 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 80 HIS 0.006 0.001 HIS A 238 PHE 0.010 0.001 PHE E 148 TYR 0.027 0.001 TYR H 285 ARG 0.001 0.000 ARG D 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 270 time to evaluate : 2.775 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: A 148 PHE cc_start: 0.5324 (OUTLIER) cc_final: 0.3458 (t80) REVERT: I 121 SER cc_start: 0.9039 (t) cc_final: 0.8737 (p) outliers start: 96 outliers final: 82 residues processed: 315 average time/residue: 0.2705 time to fit residues: 144.4394 Evaluate side-chains 342 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 259 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 291 GLN Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 209 optimal weight: 0.9990 chunk 81 optimal weight: 70.0000 chunk 241 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 300 HIS F 304 GLN H 277 GLN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23375 Z= 0.196 Angle : 0.528 5.410 31966 Z= 0.262 Chirality : 0.034 0.158 3619 Planarity : 0.004 0.046 4125 Dihedral : 3.734 15.423 3267 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.99 % Allowed : 21.23 % Favored : 74.79 % 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: 1.92 (0.16), residues: 2948 helix: 2.39 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.14 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 189 HIS 0.003 0.001 HIS H 238 PHE 0.011 0.001 PHE J 148 TYR 0.028 0.001 TYR H 285 ARG 0.001 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 264 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 85 residues processed: 308 average time/residue: 0.2716 time to fit residues: 140.3087 Evaluate side-chains 343 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 258 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 202 THR Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 GLN Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 148 PHE Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain J residue 291 GLN Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.0030 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 295 optimal weight: 0.0770 chunk 272 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 overall best weight: 1.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS B 45 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 HIS F 304 GLN H 277 GLN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23375 Z= 0.172 Angle : 0.521 5.377 31966 Z= 0.258 Chirality : 0.034 0.158 3619 Planarity : 0.004 0.047 4125 Dihedral : 3.662 15.494 3267 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.85 % Allowed : 21.23 % Favored : 74.92 % 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: 2.08 (0.16), residues: 2948 helix: 2.49 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 80 HIS 0.004 0.001 HIS J 238 PHE 0.009 0.001 PHE J 148 TYR 0.026 0.001 TYR H 285 ARG 0.001 0.000 ARG H 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5896 Ramachandran restraints generated. 2948 Oldfield, 0 Emsley, 2948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 259 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 81 residues processed: 302 average time/residue: 0.2687 time to fit residues: 135.2603 Evaluate side-chains 339 residues out of total 2519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 258 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 291 GLN Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 121 SER Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 291 GLN Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 259 ASP Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 291 GLN Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 259 ASP Chi-restraints excluded: chain I residue 291 GLN Chi-restraints excluded: chain J residue 48 CYS Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 259 ASP Chi-restraints excluded: chain K residue 48 CYS Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 259 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 GLN ** I 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090631 restraints weight = 39187.642| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.64 r_work: 0.2917 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23375 Z= 0.225 Angle : 0.535 5.430 31966 Z= 0.267 Chirality : 0.035 0.159 3619 Planarity : 0.004 0.046 4125 Dihedral : 3.710 15.093 3267 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.94 % Allowed : 21.05 % Favored : 75.01 % 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: 2.01 (0.16), residues: 2948 helix: 2.43 (0.11), residues: 2167 sheet: None (None), residues: 0 loop : -2.04 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 189 HIS 0.005 0.001 HIS B 45 PHE 0.013 0.001 PHE A 148 TYR 0.027 0.001 TYR H 285 ARG 0.001 0.000 ARG B 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.38 seconds wall clock time: 76 minutes 35.85 seconds (4595.85 seconds total)