Starting phenix.real_space_refine on Sun Mar 24 07:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axv_15704/03_2024/8axv_15704_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 S 324 5.16 5 C 25380 2.51 5 N 6972 2.21 5 O 7584 1.98 5 H 108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 277": "OD1" <-> "OD2" Residue "F ASP 322": "OD1" <-> "OD2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "G PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "I PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 277": "OD1" <-> "OD2" Residue "I TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 219": "OE1" <-> "OE2" Residue "K ASP 9": "OD1" <-> "OD2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 277": "OD1" <-> "OD2" Residue "K PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "L PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 277": "OD1" <-> "OD2" Residue "L TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40380 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "B" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "C" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "D" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "E" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "F" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "G" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "H" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "I" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "J" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "K" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "L" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1070 SG CYS A 141 187.510 120.733 31.564 1.00 88.37 S ATOM 4422 SG CYS B 141 167.166 160.687 31.536 1.00 80.35 S ATOM 7774 SG CYS C 141 129.437 185.181 31.563 1.00 82.61 S ATOM 11126 SG CYS D 141 84.483 187.511 31.563 1.00 86.70 S ATOM 14478 SG CYS E 141 44.529 167.168 31.538 1.00 79.51 S ATOM 17830 SG CYS F 141 20.036 129.436 31.560 1.00 82.22 S ATOM 21182 SG CYS G 141 17.706 84.483 31.564 1.00 87.52 S ATOM 24534 SG CYS H 141 38.048 44.523 31.538 1.00 78.23 S ATOM 27886 SG CYS I 141 75.780 20.035 31.559 1.00 82.61 S ATOM 31238 SG CYS J 141 120.732 17.706 31.564 1.00 88.07 S ATOM 34590 SG CYS K 141 160.693 38.048 31.537 1.00 78.16 S ATOM 37942 SG CYS L 141 185.183 75.780 31.561 1.00 82.57 S Time building chain proxies: 39.75, per 1000 atoms: 0.98 Number of scatterers: 40380 At special positions: 0 Unit cell: (206.394, 206.394, 83.061, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 324 16.00 O 7584 8.00 N 6972 7.00 C 25380 6.00 H 108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.54 Conformation dependent library (CDL) restraints added in 13.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 60 sheets defined 29.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 38 through 54 Processing helix chain 'A' and resid 89 through 104 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 336 through 346 removed outlier: 4.806A pdb=" N GLY A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 381 through 402 Proline residue: A 385 - end of helix removed outlier: 3.698A pdb=" N GLN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'B' and resid 89 through 104 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 336 through 346 removed outlier: 4.806A pdb=" N GLY B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 381 through 402 Proline residue: B 385 - end of helix removed outlier: 3.736A pdb=" N GLN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 38 through 53 Processing helix chain 'C' and resid 89 through 104 Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 255 No H-bonds generated for 'chain 'C' and resid 252 through 255' Processing helix chain 'C' and resid 336 through 346 removed outlier: 4.755A pdb=" N GLY C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 381 through 402 Proline residue: C 385 - end of helix removed outlier: 3.674A pdb=" N GLN C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 38 through 54 Processing helix chain 'D' and resid 89 through 104 Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 255 No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 336 through 346 removed outlier: 4.805A pdb=" N GLY D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 381 through 402 Proline residue: D 385 - end of helix removed outlier: 3.698A pdb=" N GLN D 389 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 38 through 53 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 255 No H-bonds generated for 'chain 'E' and resid 252 through 255' Processing helix chain 'E' and resid 336 through 346 removed outlier: 4.807A pdb=" N GLY E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 363 Processing helix chain 'E' and resid 381 through 402 Proline residue: E 385 - end of helix removed outlier: 3.737A pdb=" N GLN E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 38 through 53 Processing helix chain 'F' and resid 89 through 104 Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 255 No H-bonds generated for 'chain 'F' and resid 252 through 255' Processing helix chain 'F' and resid 336 through 346 removed outlier: 4.754A pdb=" N GLY F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 363 Processing helix chain 'F' and resid 381 through 402 Proline residue: F 385 - end of helix removed outlier: 3.659A pdb=" N GLN F 389 " --> pdb=" O PRO F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 38 through 54 Processing helix chain 'G' and resid 89 through 104 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 255 No H-bonds generated for 'chain 'G' and resid 252 through 255' Processing helix chain 'G' and resid 336 through 346 removed outlier: 4.804A pdb=" N GLY G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE G 345 " --> pdb=" O GLN G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 363 Processing helix chain 'G' and resid 381 through 402 Proline residue: G 385 - end of helix removed outlier: 3.698A pdb=" N GLN G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 468 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 38 through 54 Processing helix chain 'H' and resid 89 through 104 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 166 Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 255 No H-bonds generated for 'chain 'H' and resid 252 through 255' Processing helix chain 'H' and resid 336 through 346 removed outlier: 4.797A pdb=" N GLY H 344 " --> pdb=" O ASP H 340 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 363 Processing helix chain 'H' and resid 381 through 402 Proline residue: H 385 - end of helix removed outlier: 3.735A pdb=" N GLN H 389 " --> pdb=" O PRO H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 468 Processing helix chain 'I' and resid 13 through 21 Processing helix chain 'I' and resid 38 through 53 Processing helix chain 'I' and resid 89 through 104 Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 166 Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 255 No H-bonds generated for 'chain 'I' and resid 252 through 255' Processing helix chain 'I' and resid 336 through 346 removed outlier: 4.752A pdb=" N GLY I 344 " --> pdb=" O ASP I 340 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE I 345 " --> pdb=" O GLN I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 363 Processing helix chain 'I' and resid 381 through 402 Proline residue: I 385 - end of helix removed outlier: 3.655A pdb=" N GLN I 389 " --> pdb=" O PRO I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 468 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 38 through 54 Processing helix chain 'J' and resid 89 through 104 Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 166 Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 252 through 255 No H-bonds generated for 'chain 'J' and resid 252 through 255' Processing helix chain 'J' and resid 336 through 346 removed outlier: 4.805A pdb=" N GLY J 344 " --> pdb=" O ASP J 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE J 345 " --> pdb=" O GLN J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 363 Processing helix chain 'J' and resid 381 through 402 Proline residue: J 385 - end of helix removed outlier: 3.698A pdb=" N GLN J 389 " --> pdb=" O PRO J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 38 through 53 Processing helix chain 'K' and resid 89 through 104 Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 166 Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 255 No H-bonds generated for 'chain 'K' and resid 252 through 255' Processing helix chain 'K' and resid 336 through 346 removed outlier: 4.805A pdb=" N GLY K 344 " --> pdb=" O ASP K 340 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE K 345 " --> pdb=" O GLN K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 352 through 363 Processing helix chain 'K' and resid 381 through 402 Proline residue: K 385 - end of helix removed outlier: 3.737A pdb=" N GLN K 389 " --> pdb=" O PRO K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'L' and resid 89 through 104 Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 166 Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 255 No H-bonds generated for 'chain 'L' and resid 252 through 255' Processing helix chain 'L' and resid 336 through 346 removed outlier: 4.755A pdb=" N GLY L 344 " --> pdb=" O ASP L 340 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE L 345 " --> pdb=" O GLN L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 363 Processing helix chain 'L' and resid 381 through 402 Proline residue: L 385 - end of helix removed outlier: 3.670A pdb=" N GLN L 389 " --> pdb=" O PRO L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.873A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 324 through 333 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.875A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 303 through 308 removed outlier: 4.053A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 430 through 433 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.012A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.879A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.066A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 324 through 333 Processing sheet with id= P, first strand: chain 'D' and resid 4 through 6 Processing sheet with id= Q, first strand: chain 'D' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 189 through 192 removed outlier: 3.869A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 324 through 333 Processing sheet with id= U, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.997A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 192 removed outlier: 3.871A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 303 through 308 removed outlier: 4.050A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 430 through 433 Processing sheet with id= Z, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= AA, first strand: chain 'F' and resid 78 through 80 removed outlier: 7.007A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 189 through 192 removed outlier: 3.878A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 308 removed outlier: 4.065A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 324 through 333 Processing sheet with id= AE, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'G' and resid 78 through 80 removed outlier: 7.010A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.868A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 324 through 333 Processing sheet with id= AJ, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= AK, first strand: chain 'H' and resid 78 through 80 removed outlier: 7.004A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 189 through 192 removed outlier: 3.872A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 308 removed outlier: 4.046A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 430 through 433 Processing sheet with id= AO, first strand: chain 'I' and resid 4 through 6 Processing sheet with id= AP, first strand: chain 'I' and resid 78 through 80 removed outlier: 7.015A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 189 through 192 removed outlier: 3.879A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 308 removed outlier: 4.067A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 324 through 333 Processing sheet with id= AT, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= AU, first strand: chain 'J' and resid 78 through 80 removed outlier: 7.010A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 189 through 192 removed outlier: 3.868A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.994A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 324 through 333 Processing sheet with id= AY, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AZ, first strand: chain 'K' and resid 78 through 80 removed outlier: 7.006A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 189 through 192 removed outlier: 3.874A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 308 removed outlier: 4.044A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 430 through 433 Processing sheet with id= BD, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= BE, first strand: chain 'L' and resid 78 through 80 removed outlier: 7.012A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 189 through 192 removed outlier: 3.879A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 308 removed outlier: 4.074A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 333 1445 hydrogen bonds defined for protein. 4143 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: 16.76 Time building geometry restraints manager: 16.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 108 1.05 - 1.24: 5419 1.24 - 1.43: 11407 1.43 - 1.62: 23794 1.62 - 1.81: 480 Bond restraints: 41208 Sorted by residual: bond pdb=" C3 MY6 F1002 " pdb=" N2 MY6 F1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.17e+01 bond pdb=" C3 MY6 A1002 " pdb=" N2 MY6 A1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.16e+01 bond pdb=" C3 MY6 C1002 " pdb=" N2 MY6 C1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.16e+01 bond pdb=" C3 MY6 B1002 " pdb=" N2 MY6 B1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" C3 MY6 E1002 " pdb=" N2 MY6 E1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.12e+01 ... (remaining 41203 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.26: 1729 107.26 - 113.95: 23452 113.95 - 120.63: 15803 120.63 - 127.31: 14527 127.31 - 134.00: 433 Bond angle restraints: 55944 Sorted by residual: angle pdb=" N MET C 72 " pdb=" CA MET C 72 " pdb=" C MET C 72 " ideal model delta sigma weight residual 114.56 109.43 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" N MET I 72 " pdb=" CA MET I 72 " pdb=" C MET I 72 " ideal model delta sigma weight residual 114.56 109.54 5.02 1.27e+00 6.20e-01 1.56e+01 angle pdb=" N MET L 72 " pdb=" CA MET L 72 " pdb=" C MET L 72 " ideal model delta sigma weight residual 114.56 109.57 4.99 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N MET F 72 " pdb=" CA MET F 72 " pdb=" C MET F 72 " ideal model delta sigma weight residual 114.56 109.98 4.58 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C5 MY6 F1002 " pdb=" C6 MY6 F1002 " pdb=" N8 MY6 F1002 " ideal model delta sigma weight residual 109.68 119.82 -10.14 3.00e+00 1.11e-01 1.14e+01 ... (remaining 55939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 21226 17.72 - 35.44: 2725 35.44 - 53.16: 795 53.16 - 70.87: 177 70.87 - 88.59: 49 Dihedral angle restraints: 24972 sinusoidal: 9852 harmonic: 15120 Sorted by residual: dihedral pdb=" CA PRO I 193 " pdb=" C PRO I 193 " pdb=" N SER I 194 " pdb=" CA SER I 194 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N SER F 194 " pdb=" CA SER F 194 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N SER C 194 " pdb=" CA SER C 194 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 24969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3649 0.026 - 0.051: 1514 0.051 - 0.077: 596 0.077 - 0.103: 375 0.103 - 0.129: 166 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CA VAL H 431 " pdb=" N VAL H 431 " pdb=" C VAL H 431 " pdb=" CB VAL H 431 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL I 305 " pdb=" N VAL I 305 " pdb=" C VAL I 305 " pdb=" CB VAL I 305 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL F 305 " pdb=" N VAL F 305 " pdb=" C VAL F 305 " pdb=" CB VAL F 305 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 6297 not shown) Planarity restraints: 7104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 384 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO K 385 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 385 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 385 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 384 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO E 385 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 385 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 385 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 384 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 385 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " -0.023 5.00e-02 4.00e+02 ... (remaining 7101 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.48: 391 2.48 - 3.01: 25262 3.01 - 3.54: 48404 3.54 - 4.07: 76352 4.07 - 4.60: 111596 Nonbonded interactions: 262005 Sorted by model distance: nonbonded pdb=" OD1 ASP J 237 " pdb=" OG SER J 251 " model vdw 1.948 2.200 nonbonded pdb=" OD1 ASP G 237 " pdb=" OG SER G 251 " model vdw 1.950 2.200 nonbonded pdb=" OD1 ASP A 237 " pdb=" OG SER A 251 " model vdw 1.951 2.200 nonbonded pdb=" OD1 ASP D 237 " pdb=" OG SER D 251 " model vdw 1.951 2.200 nonbonded pdb=" OD1 ASP C 237 " pdb=" OG SER C 251 " model vdw 1.955 2.200 ... (remaining 262000 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' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'B' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'C' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'D' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'E' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'F' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'G' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'H' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'I' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'J' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'K' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) selection = (chain 'L' and (resid 3 through 314 or resid 316 through 469 or resid 1001 throu \ gh 1002)) } 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=0.00 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: 7.020 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: 0.980 Extract box with map and model: 28.380 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 140.570 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.007 0.191 41100 Z= 0.489 Angle : 0.568 10.136 55692 Z= 0.287 Chirality : 0.041 0.129 6300 Planarity : 0.004 0.042 7092 Dihedral : 17.869 88.594 15156 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 41.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.35 % Allowed : 30.69 % Favored : 66.96 % 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: -0.64 (0.12), residues: 5040 helix: 1.53 (0.14), residues: 1728 sheet: -0.53 (0.19), residues: 768 loop : -1.87 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 258 HIS 0.008 0.001 HIS H 429 PHE 0.017 0.001 PHE K 133 TYR 0.006 0.001 TYR H 382 ARG 0.005 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 592 time to evaluate : 4.628 Fit side-chains revert: symmetry clash REVERT: B 136 HIS cc_start: 0.5179 (m90) cc_final: 0.4806 (m90) REVERT: C 56 ASP cc_start: 0.6244 (m-30) cc_final: 0.5738 (t70) REVERT: C 72 MET cc_start: 0.6951 (tmt) cc_final: 0.6460 (mmp) REVERT: C 149 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6209 (mp) REVERT: D 149 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6523 (mp) REVERT: D 285 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: F 427 LYS cc_start: 0.6954 (mtpm) cc_final: 0.6388 (mtpt) REVERT: G 56 ASP cc_start: 0.5127 (t70) cc_final: 0.4767 (m-30) REVERT: L 322 ASP cc_start: 0.6498 (m-30) cc_final: 0.6287 (m-30) outliers start: 103 outliers final: 50 residues processed: 675 average time/residue: 1.1263 time to fit residues: 977.3384 Evaluate side-chains 512 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 459 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 242 SER Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 242 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 242 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 431 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 7.9990 chunk 382 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 294 optimal weight: 20.0000 chunk 457 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS A 429 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN C 19 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 265 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 429 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 HIS I 209 ASN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 GLN K 186 ASN ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 41100 Z= 0.512 Angle : 0.687 6.672 55692 Z= 0.364 Chirality : 0.050 0.327 6300 Planarity : 0.006 0.079 7092 Dihedral : 6.132 55.710 5660 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 44.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 6.31 % Allowed : 27.78 % Favored : 65.92 % 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: -1.08 (0.12), residues: 5040 helix: 1.17 (0.13), residues: 1668 sheet: -0.66 (0.19), residues: 768 loop : -2.11 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 199 HIS 0.006 0.001 HIS D 429 PHE 0.029 0.003 PHE D 183 TYR 0.023 0.003 TYR K 195 ARG 0.006 0.001 ARG C 434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 475 time to evaluate : 5.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 441 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: B 123 MET cc_start: 0.7149 (mmm) cc_final: 0.6765 (mpm) REVERT: C 56 ASP cc_start: 0.6379 (m-30) cc_final: 0.5778 (t70) REVERT: C 72 MET cc_start: 0.6930 (tmt) cc_final: 0.6510 (mmm) REVERT: C 123 MET cc_start: 0.7225 (mmm) cc_final: 0.6935 (mpm) REVERT: C 314 MET cc_start: 0.8600 (tmm) cc_final: 0.8368 (ttt) REVERT: D 285 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: D 441 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: E 123 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5324 (mpm) REVERT: E 314 MET cc_start: 0.8463 (tmm) cc_final: 0.8164 (tmm) REVERT: F 123 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5215 (mpm) REVERT: F 275 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6625 (mtp85) REVERT: G 53 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: G 89 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6475 (m-30) REVERT: G 136 HIS cc_start: 0.5583 (m90) cc_final: 0.5039 (m90) REVERT: G 285 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: G 441 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: H 84 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6603 (mpp) REVERT: H 441 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: I 275 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6895 (mtp85) REVERT: I 441 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: J 30 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5550 (mtm-85) REVERT: J 89 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: J 285 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: J 441 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7098 (mp10) REVERT: K 285 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7413 (m-80) REVERT: L 362 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6726 (mt) REVERT: L 465 ARG cc_start: 0.7015 (ppp80) cc_final: 0.6767 (ppp80) outliers start: 277 outliers final: 140 residues processed: 675 average time/residue: 1.1585 time to fit residues: 1002.8861 Evaluate side-chains 604 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 443 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 242 SER Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 275 ARG Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 242 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 44 SER Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 380 optimal weight: 6.9990 chunk 311 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 458 optimal weight: 3.9990 chunk 495 optimal weight: 0.5980 chunk 408 optimal weight: 1.9990 chunk 454 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 367 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 259 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS C 265 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 259 HIS H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 259 HIS L 265 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 41100 Z= 0.190 Angle : 0.468 5.309 55692 Z= 0.250 Chirality : 0.042 0.156 6300 Planarity : 0.004 0.050 7092 Dihedral : 5.347 56.587 5644 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 42.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.94 % Allowed : 30.35 % Favored : 65.71 % 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 (0.12), residues: 5040 helix: 1.98 (0.14), residues: 1668 sheet: -0.68 (0.19), residues: 780 loop : -1.87 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 199 HIS 0.004 0.001 HIS H 429 PHE 0.019 0.002 PHE A 183 TYR 0.012 0.001 TYR K 382 ARG 0.004 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 466 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: B 123 MET cc_start: 0.7127 (mmm) cc_final: 0.6757 (mpm) REVERT: C 56 ASP cc_start: 0.6448 (m-30) cc_final: 0.5826 (t70) REVERT: C 72 MET cc_start: 0.6971 (tmt) cc_final: 0.6659 (mmm) REVERT: C 441 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: D 285 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: D 441 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: E 123 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5450 (mpm) REVERT: E 441 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: F 123 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5426 (mpm) REVERT: F 275 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6457 (mtp85) REVERT: F 441 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: G 53 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: G 89 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: G 136 HIS cc_start: 0.5672 (m90) cc_final: 0.5069 (m90) REVERT: G 139 VAL cc_start: 0.7852 (t) cc_final: 0.7641 (p) REVERT: G 285 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: G 441 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: I 297 TYR cc_start: 0.6141 (m-10) cc_final: 0.5666 (m-10) REVERT: I 441 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: J 30 ARG cc_start: 0.5899 (OUTLIER) cc_final: 0.5637 (mtm-85) REVERT: J 285 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: J 441 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7158 (mp10) REVERT: K 441 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: L 362 LEU cc_start: 0.7042 (mp) cc_final: 0.6838 (mt) outliers start: 173 outliers final: 85 residues processed: 581 average time/residue: 1.2188 time to fit residues: 899.0311 Evaluate side-chains 547 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 444 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 92 ARG Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 411 ARG Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 6.9990 chunk 344 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 218 optimal weight: 0.8980 chunk 307 optimal weight: 10.0000 chunk 460 optimal weight: 2.9990 chunk 487 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 436 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 265 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 41100 Z= 0.359 Angle : 0.568 8.116 55692 Z= 0.303 Chirality : 0.045 0.218 6300 Planarity : 0.005 0.054 7092 Dihedral : 5.467 58.466 5615 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 44.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.46 % Allowed : 29.21 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 5040 helix: 1.76 (0.14), residues: 1668 sheet: -0.70 (0.19), residues: 768 loop : -2.03 (0.11), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 199 HIS 0.004 0.001 HIS G 307 PHE 0.023 0.002 PHE L 183 TYR 0.021 0.002 TYR L 195 ARG 0.003 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 463 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7418 (m-80) REVERT: A 441 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: B 123 MET cc_start: 0.7175 (mmm) cc_final: 0.6807 (mpm) REVERT: B 441 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7360 (mp10) REVERT: C 56 ASP cc_start: 0.6513 (m-30) cc_final: 0.6002 (t70) REVERT: C 72 MET cc_start: 0.7088 (tmt) cc_final: 0.6718 (mmm) REVERT: D 285 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: D 441 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: E 123 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.5569 (mpm) REVERT: E 314 MET cc_start: 0.8406 (tmm) cc_final: 0.8155 (tmm) REVERT: E 441 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: F 123 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5446 (mpm) REVERT: F 275 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6596 (mtp85) REVERT: G 89 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6647 (m-30) REVERT: G 285 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: G 441 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.6982 (mp10) REVERT: H 216 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: H 441 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: I 297 TYR cc_start: 0.6257 (m-10) cc_final: 0.5767 (m-10) REVERT: I 441 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: J 285 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: J 441 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7068 (mp10) REVERT: K 441 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7356 (mp10) outliers start: 240 outliers final: 142 residues processed: 632 average time/residue: 1.1867 time to fit residues: 957.6911 Evaluate side-chains 612 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 452 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 362 LEU Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 378 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 415 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 437 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS C 265 HIS ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41100 Z= 0.291 Angle : 0.517 6.275 55692 Z= 0.276 Chirality : 0.044 0.184 6300 Planarity : 0.004 0.050 7092 Dihedral : 5.352 58.718 5615 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 43.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.42 % Allowed : 29.14 % Favored : 65.44 % 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: -0.62 (0.12), residues: 5040 helix: 1.90 (0.14), residues: 1668 sheet: -0.75 (0.19), residues: 780 loop : -1.96 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 175 HIS 0.003 0.001 HIS E 164 PHE 0.022 0.002 PHE A 183 TYR 0.015 0.002 TYR L 195 ARG 0.003 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 462 time to evaluate : 4.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: A 441 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: B 441 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: C 56 ASP cc_start: 0.6519 (m-30) cc_final: 0.6007 (t70) REVERT: C 72 MET cc_start: 0.7019 (tmt) cc_final: 0.6657 (mmm) REVERT: C 441 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: D 285 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: D 441 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: E 123 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5427 (mpm) REVERT: E 167 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7463 (mm) REVERT: E 341 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6608 (mp-120) REVERT: E 441 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: F 123 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.5560 (mpm) REVERT: F 275 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6533 (mtp85) REVERT: F 441 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: G 89 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: G 285 TYR cc_start: 0.7599 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: H 441 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: I 297 TYR cc_start: 0.6173 (m-10) cc_final: 0.5751 (m-10) REVERT: I 441 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7656 (mp10) REVERT: J 136 HIS cc_start: 0.5876 (m90) cc_final: 0.5096 (m90) REVERT: J 285 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: K 441 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7413 (mp10) outliers start: 238 outliers final: 163 residues processed: 626 average time/residue: 1.1779 time to fit residues: 963.6185 Evaluate side-chains 634 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 452 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 345 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 411 ARG Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 188 MET Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 362 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 343 THR Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 0.4980 chunk 438 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 286 optimal weight: 0.0040 chunk 120 optimal weight: 5.9990 chunk 487 optimal weight: 3.9990 chunk 404 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 186 ASN C 31 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 41100 Z= 0.154 Angle : 0.441 5.567 55692 Z= 0.233 Chirality : 0.041 0.121 6300 Planarity : 0.004 0.048 7092 Dihedral : 4.902 58.963 5615 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 42.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.37 % Allowed : 31.26 % Favored : 65.37 % 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: -0.25 (0.12), residues: 5040 helix: 2.28 (0.14), residues: 1680 sheet: -0.62 (0.19), residues: 780 loop : -1.79 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 258 HIS 0.003 0.001 HIS L 308 PHE 0.016 0.001 PHE A 183 TYR 0.009 0.001 TYR K 382 ARG 0.003 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 478 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: A 441 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: B 441 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: C 56 ASP cc_start: 0.6529 (m-30) cc_final: 0.6008 (t70) REVERT: C 72 MET cc_start: 0.6972 (tmt) cc_final: 0.6684 (mmm) REVERT: C 441 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: D 285 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: D 441 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: E 123 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5559 (mpm) REVERT: E 441 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: F 441 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: G 285 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: I 297 TYR cc_start: 0.6054 (m-10) cc_final: 0.5734 (m-10) REVERT: I 441 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: J 136 HIS cc_start: 0.5920 (m90) cc_final: 0.5159 (m90) REVERT: J 285 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: K 441 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7462 (mp10) outliers start: 148 outliers final: 92 residues processed: 585 average time/residue: 1.1915 time to fit residues: 891.9321 Evaluate side-chains 564 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 459 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 401 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 277 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 275 optimal weight: 1.9990 chunk 410 optimal weight: 0.9990 chunk 272 optimal weight: 0.8980 chunk 485 optimal weight: 3.9990 chunk 304 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS C 265 HIS ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 341 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS H 429 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41100 Z= 0.207 Angle : 0.468 5.677 55692 Z= 0.247 Chirality : 0.042 0.141 6300 Planarity : 0.004 0.047 7092 Dihedral : 4.916 59.908 5612 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 42.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.30 % Allowed : 30.53 % Favored : 65.16 % 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: -0.20 (0.13), residues: 5040 helix: 2.33 (0.14), residues: 1680 sheet: -0.59 (0.19), residues: 780 loop : -1.77 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 175 HIS 0.003 0.001 HIS E 164 PHE 0.017 0.002 PHE L 183 TYR 0.012 0.001 TYR L 195 ARG 0.003 0.000 ARG I 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 459 time to evaluate : 4.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: B 441 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: C 56 ASP cc_start: 0.6644 (m-30) cc_final: 0.6092 (t70) REVERT: C 72 MET cc_start: 0.6941 (tmt) cc_final: 0.6660 (mmm) REVERT: C 441 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: D 285 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: E 123 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5599 (mpm) REVERT: E 441 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: F 441 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: G 285 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: H 216 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7085 (m-30) REVERT: H 275 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6670 (mtp85) REVERT: H 441 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: I 441 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: J 136 HIS cc_start: 0.5901 (m90) cc_final: 0.5154 (m90) REVERT: J 285 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: K 441 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: L 441 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7455 (mp10) outliers start: 189 outliers final: 142 residues processed: 601 average time/residue: 1.1189 time to fit residues: 871.4713 Evaluate side-chains 607 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 450 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 275 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 343 THR Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 20.0000 chunk 193 optimal weight: 0.8980 chunk 290 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 381 optimal weight: 8.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 341 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 41100 Z= 0.208 Angle : 0.468 6.373 55692 Z= 0.247 Chirality : 0.042 0.147 6300 Planarity : 0.004 0.047 7092 Dihedral : 4.896 59.110 5612 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 42.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.35 % Allowed : 30.44 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 5040 helix: 2.35 (0.14), residues: 1680 sheet: -0.62 (0.19), residues: 780 loop : -1.76 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 175 HIS 0.003 0.001 HIS A 308 PHE 0.018 0.002 PHE L 183 TYR 0.013 0.001 TYR L 195 ARG 0.002 0.000 ARG L 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 461 time to evaluate : 5.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 441 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: C 56 ASP cc_start: 0.6652 (m-30) cc_final: 0.6084 (t70) REVERT: C 441 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: D 285 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7278 (m-80) REVERT: E 123 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.5557 (mpm) REVERT: E 441 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: F 441 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: G 285 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: H 216 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: H 275 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6704 (mtp85) REVERT: H 441 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: I 441 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: J 136 HIS cc_start: 0.5805 (m90) cc_final: 0.5093 (m90) REVERT: J 285 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: K 275 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6646 (mtp85) REVERT: K 441 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: L 72 MET cc_start: 0.6948 (tmt) cc_final: 0.6623 (mmt) REVERT: L 441 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7506 (mp10) outliers start: 191 outliers final: 157 residues processed: 607 average time/residue: 1.1350 time to fit residues: 892.6285 Evaluate side-chains 623 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 451 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 275 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 275 ARG Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 343 THR Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 431 VAL Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 452 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 chunk 197 optimal weight: 3.9990 chunk 355 optimal weight: 2.9990 chunk 138 optimal weight: 0.0980 chunk 409 optimal weight: 1.9990 chunk 428 optimal weight: 2.9990 chunk 451 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 341 GLN ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 41100 Z= 0.141 Angle : 0.435 7.453 55692 Z= 0.228 Chirality : 0.041 0.123 6300 Planarity : 0.004 0.045 7092 Dihedral : 4.663 59.038 5612 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 42.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.19 % Allowed : 31.63 % Favored : 65.19 % 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: -0.00 (0.13), residues: 5040 helix: 2.52 (0.14), residues: 1680 sheet: -0.49 (0.19), residues: 780 loop : -1.66 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 258 HIS 0.004 0.001 HIS G 308 PHE 0.014 0.001 PHE A 183 TYR 0.008 0.001 TYR K 382 ARG 0.002 0.000 ARG I 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 465 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 441 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: C 56 ASP cc_start: 0.6642 (m-30) cc_final: 0.6074 (t70) REVERT: C 441 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: D 285 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: E 123 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5457 (mpm) REVERT: E 441 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: F 441 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: G 285 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: G 427 LYS cc_start: 0.7056 (mtpm) cc_final: 0.6700 (ttmt) REVERT: H 216 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: H 275 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6619 (mtp85) REVERT: H 441 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: I 441 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: J 136 HIS cc_start: 0.5779 (m90) cc_final: 0.5072 (m90) REVERT: J 285 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: K 275 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6626 (mtp85) REVERT: K 441 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: L 56 ASP cc_start: 0.6673 (m-30) cc_final: 0.6188 (t70) REVERT: L 72 MET cc_start: 0.6971 (tmt) cc_final: 0.6654 (mmt) REVERT: L 441 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7480 (mp10) outliers start: 140 outliers final: 102 residues processed: 574 average time/residue: 1.2111 time to fit residues: 885.4525 Evaluate side-chains 570 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 453 time to evaluate : 4.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 262 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 275 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 275 ARG Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 4.9990 chunk 478 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 502 optimal weight: 2.9990 chunk 462 optimal weight: 20.0000 chunk 399 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 308 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** D 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN ** F 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 GLN H 186 ASN ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 GLN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 41100 Z= 0.462 Angle : 0.634 6.968 55692 Z= 0.336 Chirality : 0.048 0.257 6300 Planarity : 0.006 0.072 7092 Dihedral : 5.482 59.650 5610 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 45.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.96 % Allowed : 30.90 % Favored : 65.14 % 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: -0.73 (0.12), residues: 5040 helix: 1.81 (0.14), residues: 1644 sheet: -0.78 (0.19), residues: 780 loop : -2.01 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP I 175 HIS 0.004 0.001 HIS E 164 PHE 0.026 0.003 PHE F 183 TYR 0.025 0.003 TYR L 195 ARG 0.003 0.000 ARG K 434 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 452 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5789 (m90) cc_final: 0.5050 (m90) REVERT: B 123 MET cc_start: 0.7185 (mmm) cc_final: 0.6887 (mpm) REVERT: B 441 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: C 56 ASP cc_start: 0.6714 (m-30) cc_final: 0.6130 (t70) REVERT: C 314 MET cc_start: 0.8496 (tmm) cc_final: 0.8268 (ttp) REVERT: D 285 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: E 123 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5454 (mpm) REVERT: E 441 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: G 285 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: H 133 PHE cc_start: 0.8139 (t80) cc_final: 0.7929 (t80) REVERT: H 216 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.7014 (m-30) REVERT: H 275 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6733 (mtp85) REVERT: H 441 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: I 441 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: J 53 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: J 136 HIS cc_start: 0.5878 (m90) cc_final: 0.5118 (m90) REVERT: J 285 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: K 53 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: K 275 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: K 341 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6580 (mp-120) REVERT: K 441 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: L 72 MET cc_start: 0.6989 (tmt) cc_final: 0.6744 (tpt) outliers start: 174 outliers final: 134 residues processed: 581 average time/residue: 1.0934 time to fit residues: 829.1514 Evaluate side-chains 596 residues out of total 4416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 447 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 274 CYS Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 149 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 275 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 330 VAL Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 275 ARG Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 341 GLN Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 330 VAL Chi-restraints excluded: chain L residue 343 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 431 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 122 optimal weight: 0.1980 chunk 368 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 111 optimal weight: 0.0970 chunk 400 optimal weight: 0.0010 chunk 167 optimal weight: 0.9990 chunk 411 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 73 optimal weight: 1.9990 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN B 186 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 341 GLN F 31 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.207599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140932 restraints weight = 86721.406| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.44 r_work: 0.3529 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 41100 Z= 0.110 Angle : 0.430 7.329 55692 Z= 0.226 Chirality : 0.040 0.120 6300 Planarity : 0.004 0.045 7092 Dihedral : 4.679 59.920 5610 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 42.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.23 % Allowed : 32.72 % Favored : 65.05 % 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: -0.06 (0.13), residues: 5040 helix: 2.55 (0.14), residues: 1656 sheet: -0.52 (0.19), residues: 780 loop : -1.72 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 258 HIS 0.005 0.001 HIS G 308 PHE 0.011 0.001 PHE H 133 TYR 0.007 0.001 TYR K 382 ARG 0.003 0.000 ARG J 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15279.32 seconds wall clock time: 276 minutes 33.31 seconds (16593.31 seconds total)