Starting phenix.real_space_refine on Sat Feb 24 03:35:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj8_25157/02_2024/7sj8_25157.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.317 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 P 30 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25802 2.51 5 N 7026 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 160": "OD1" <-> "OD2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 160": "OD1" <-> "OD2" Residue "K TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "K PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 160": "OD1" <-> "OD2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "L PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 359": "NH1" <-> "NH2" Residue "I PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3418 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.94, per 1000 atoms: 0.51 Number of scatterers: 41056 At special positions: 0 Unit cell: (171.12, 103.04, 210.68, 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) S 282 16.00 P 30 15.00 Mg 6 11.99 O 7910 8.00 N 7026 7.00 C 25802 6.00 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=0, symmetry=0 Time building additional restraints: 17.98 Conformation dependent library (CDL) restraints added in 8.0 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 36 sheets defined 54.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.679A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.625A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 143 through 161 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.615A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 71 through 81 removed outlier: 4.641A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 129 Processing helix chain 'J' and resid 143 through 161 Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 205 through 216 Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 298 through 301' Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.625A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 129 Processing helix chain 'K' and resid 143 through 161 Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 205 through 216 Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.679A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 298 through 301' Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.883A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 71 through 81 removed outlier: 4.641A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 143 through 161 Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 205 through 216 Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 removed outlier: 3.615A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 298 through 301' Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.510A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.144A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.658A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.690A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 3.963A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 159 Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.660A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 322 through 337 Processing helix chain 'G' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE G 341 " --> pdb=" O SER G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 341' Processing helix chain 'G' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 400 removed outlier: 3.828A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.961A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 Processing helix chain 'H' and resid 338 through 341 removed outlier: 3.607A pdb=" N PHE H 341 " --> pdb=" O SER H 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 338 through 341' Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.512A pdb=" N PHE H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 40 through 46 removed outlier: 4.144A pdb=" N LEU I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 293 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.690A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.963A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.660A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.605A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA7, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB1, first strand: chain 'J' and resid 92 through 94 Processing sheet with id=AB2, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AB4, first strand: chain 'K' and resid 92 through 94 Processing sheet with id=AB5, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AB7, first strand: chain 'L' and resid 92 through 94 Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'L' and resid 269 through 273 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AD7, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 54 2226 hydrogen bonds defined for protein. 6354 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: 16.56 Time building geometry restraints manager: 18.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13597 1.34 - 1.46: 7156 1.46 - 1.57: 20753 1.57 - 1.69: 48 1.69 - 1.81: 444 Bond restraints: 41998 Sorted by residual: bond pdb=" N ARG F 359 " pdb=" CA ARG F 359 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.37e+00 bond pdb=" CA PHE A 169 " pdb=" CB PHE A 169 " ideal model delta sigma weight residual 1.531 1.469 0.061 3.12e-02 1.03e+03 3.86e+00 bond pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" CA PHE C 169 " pdb=" CB PHE C 169 " ideal model delta sigma weight residual 1.531 1.470 0.061 3.12e-02 1.03e+03 3.83e+00 ... (remaining 41993 not shown) Histogram of bond angle deviations from ideal: 99.30 - 106.71: 1423 106.71 - 114.12: 24331 114.12 - 121.52: 21996 121.52 - 128.93: 8975 128.93 - 136.34: 310 Bond angle restraints: 57035 Sorted by residual: angle pdb=" C PRO H 358 " pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C PRO D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C PRO I 357 " pdb=" N PRO I 358 " pdb=" CA PRO I 358 " ideal model delta sigma weight residual 119.84 125.09 -5.25 1.25e+00 6.40e-01 1.76e+01 angle pdb=" N GLY I 360 " pdb=" CA GLY I 360 " pdb=" C GLY I 360 " ideal model delta sigma weight residual 114.95 109.19 5.76 1.41e+00 5.03e-01 1.67e+01 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.80 118.89 -8.09 2.13e+00 2.20e-01 1.44e+01 ... (remaining 57030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 24204 28.64 - 57.28: 651 57.28 - 85.92: 66 85.92 - 114.56: 12 114.56 - 143.20: 12 Dihedral angle restraints: 24945 sinusoidal: 9957 harmonic: 14988 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.53 -143.20 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.55 -143.19 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.55 -143.18 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 24942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5373 0.065 - 0.129: 846 0.129 - 0.194: 16 0.194 - 0.258: 0 0.258 - 0.323: 5 Chirality restraints: 6240 Sorted by residual: chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ARG H 359 " pdb=" N ARG H 359 " pdb=" C ARG H 359 " pdb=" CB ARG H 359 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 6237 not shown) Planarity restraints: 7411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 380 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ARG B 380 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG B 380 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 381 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 358 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C PRO H 358 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO H 358 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG H 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 380 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ARG F 380 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG F 380 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE F 381 " -0.008 2.00e-02 2.50e+03 ... (remaining 7408 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 511 2.51 - 3.10: 33177 3.10 - 3.70: 65739 3.70 - 4.30: 90910 4.30 - 4.90: 154739 Nonbonded interactions: 345076 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.906 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.907 2.170 ... (remaining 345071 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 1 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 441 or resid 501 through 502)) selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.680 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: 0.050 Extract box with map and model: 29.700 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 109.050 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.370 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.005 0.061 41998 Z= 0.341 Angle : 0.600 8.939 57035 Z= 0.337 Chirality : 0.043 0.323 6240 Planarity : 0.004 0.035 7411 Dihedral : 13.420 143.203 15321 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 6.00 % Allowed : 6.77 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -1.01 (0.12), residues: 5136 helix: 0.47 (0.10), residues: 2442 sheet: -1.24 (0.19), residues: 738 loop : -1.85 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS D 264 PHE 0.011 0.001 PHE F 367 TYR 0.010 0.001 TYR D 36 ARG 0.003 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2374 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 2109 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7611 (mp0) cc_final: 0.6830 (mm-30) REVERT: A 6 SER cc_start: 0.9179 (m) cc_final: 0.8802 (p) REVERT: A 33 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 77 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8918 (tp30) REVERT: A 90 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7782 (tm-30) REVERT: A 103 TYR cc_start: 0.8942 (t80) cc_final: 0.8527 (t80) REVERT: A 120 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8056 (t70) REVERT: A 121 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7864 (tpt170) REVERT: A 209 ILE cc_start: 0.9121 (mt) cc_final: 0.8857 (mm) REVERT: A 224 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: A 316 CYS cc_start: 0.7923 (t) cc_final: 0.7722 (t) REVERT: A 423 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 430 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9185 (tptt) REVERT: C 1 MET cc_start: 0.7549 (ptp) cc_final: 0.7112 (ptp) REVERT: C 6 SER cc_start: 0.9123 (m) cc_final: 0.8772 (p) REVERT: C 11 GLN cc_start: 0.8380 (tt0) cc_final: 0.8121 (tt0) REVERT: C 60 LYS cc_start: 0.8677 (tttp) cc_final: 0.8047 (tttt) REVERT: C 101 ASN cc_start: 0.9204 (m-40) cc_final: 0.8871 (m-40) REVERT: C 269 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8240 (pp) REVERT: C 358 GLN cc_start: 0.9284 (tp40) cc_final: 0.8980 (tp40) REVERT: C 414 GLU cc_start: 0.7630 (tt0) cc_final: 0.7409 (mt-10) REVERT: E 1 MET cc_start: 0.7555 (ptp) cc_final: 0.7072 (ptp) REVERT: E 3 GLU cc_start: 0.7752 (mp0) cc_final: 0.6501 (mm-30) REVERT: E 6 SER cc_start: 0.9186 (m) cc_final: 0.8776 (p) REVERT: E 18 ASN cc_start: 0.9031 (m-40) cc_final: 0.8753 (m110) REVERT: E 33 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8366 (p0) REVERT: E 55 GLU cc_start: 0.8559 (tt0) cc_final: 0.8188 (tp30) REVERT: E 69 ASP cc_start: 0.8282 (t0) cc_final: 0.8081 (t0) REVERT: E 90 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7694 (tm-30) REVERT: E 129 CYS cc_start: 0.7103 (m) cc_final: 0.6900 (m) REVERT: E 154 MET cc_start: 0.8895 (mmm) cc_final: 0.8665 (mmm) REVERT: E 156 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8622 (mmm-85) REVERT: E 167 LEU cc_start: 0.9498 (mt) cc_final: 0.9080 (mt) REVERT: E 169 PHE cc_start: 0.8790 (m-80) cc_final: 0.8356 (m-80) REVERT: E 209 ILE cc_start: 0.9280 (mt) cc_final: 0.8926 (mt) REVERT: E 220 GLU cc_start: 0.7363 (mp0) cc_final: 0.7099 (mp0) REVERT: E 309 HIS cc_start: 0.8256 (m170) cc_final: 0.8048 (m90) REVERT: E 358 GLN cc_start: 0.9363 (tp40) cc_final: 0.9140 (tp40) REVERT: E 382 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8714 (p) REVERT: E 386 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: E 423 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8478 (mt-10) REVERT: E 430 LYS cc_start: 0.9600 (ttmt) cc_final: 0.9338 (tptt) REVERT: J 3 GLU cc_start: 0.7521 (mp0) cc_final: 0.6116 (mm-30) REVERT: J 33 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.7955 (p0) REVERT: J 69 ASP cc_start: 0.7948 (t0) cc_final: 0.7653 (t0) REVERT: J 75 ILE cc_start: 0.9407 (mm) cc_final: 0.9157 (mt) REVERT: J 90 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7781 (tp30) REVERT: J 129 CYS cc_start: 0.6887 (m) cc_final: 0.5329 (m) REVERT: J 198 SER cc_start: 0.7668 (p) cc_final: 0.7148 (p) REVERT: J 220 GLU cc_start: 0.7724 (mp0) cc_final: 0.7448 (mp0) REVERT: J 244 PHE cc_start: 0.8669 (m-80) cc_final: 0.8173 (m-80) REVERT: J 280 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8044 (mtmm) REVERT: J 291 ILE cc_start: 0.9387 (pt) cc_final: 0.8625 (pt) REVERT: J 295 CYS cc_start: 0.8682 (m) cc_final: 0.8397 (m) REVERT: J 296 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7903 (t80) REVERT: J 302 MET cc_start: 0.7818 (mtt) cc_final: 0.7608 (mtt) REVERT: J 316 CYS cc_start: 0.8485 (t) cc_final: 0.8114 (t) REVERT: J 342 GLN cc_start: 0.8996 (pt0) cc_final: 0.8669 (pm20) REVERT: J 346 TRP cc_start: 0.8291 (p-90) cc_final: 0.4954 (t-100) REVERT: J 430 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9336 (tptt) REVERT: K 24 TYR cc_start: 0.8799 (m-10) cc_final: 0.8503 (m-80) REVERT: K 33 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.7886 (p0) REVERT: K 88 HIS cc_start: 0.8504 (t70) cc_final: 0.8221 (t70) REVERT: K 90 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7664 (tp30) REVERT: K 103 TYR cc_start: 0.8587 (t80) cc_final: 0.8237 (t80) REVERT: K 198 SER cc_start: 0.7848 (p) cc_final: 0.6958 (p) REVERT: K 256 GLN cc_start: 0.9019 (pt0) cc_final: 0.8641 (tm-30) REVERT: K 295 CYS cc_start: 0.8688 (m) cc_final: 0.8476 (m) REVERT: K 296 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7987 (t80) REVERT: K 311 LYS cc_start: 0.8564 (mttm) cc_final: 0.8113 (mtpp) REVERT: K 346 TRP cc_start: 0.8583 (p-90) cc_final: 0.4750 (t-100) REVERT: K 430 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9209 (tptt) REVERT: K 433 GLU cc_start: 0.9121 (tt0) cc_final: 0.8898 (tp30) REVERT: L 11 GLN cc_start: 0.8106 (tt0) cc_final: 0.7783 (tt0) REVERT: L 69 ASP cc_start: 0.7718 (t0) cc_final: 0.7503 (t0) REVERT: L 88 HIS cc_start: 0.8747 (t70) cc_final: 0.8117 (t70) REVERT: L 90 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8038 (tp30) REVERT: L 198 SER cc_start: 0.7868 (p) cc_final: 0.7433 (p) REVERT: L 224 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7878 (m-10) REVERT: L 244 PHE cc_start: 0.8873 (m-80) cc_final: 0.8321 (m-80) REVERT: L 257 THR cc_start: 0.9003 (m) cc_final: 0.8796 (p) REVERT: L 295 CYS cc_start: 0.8681 (m) cc_final: 0.8444 (m) REVERT: L 311 LYS cc_start: 0.8536 (mttm) cc_final: 0.7995 (mtpp) REVERT: L 346 TRP cc_start: 0.8416 (p-90) cc_final: 0.4979 (t-100) REVERT: L 417 GLU cc_start: 0.8749 (tt0) cc_final: 0.8440 (mt-10) REVERT: F 2 ARG cc_start: 0.8298 (mtm180) cc_final: 0.7986 (mtm180) REVERT: F 19 LYS cc_start: 0.8453 (tptt) cc_final: 0.7912 (mmmt) REVERT: F 20 PHE cc_start: 0.8864 (t80) cc_final: 0.8662 (t80) REVERT: F 22 GLU cc_start: 0.7829 (tt0) cc_final: 0.7019 (tt0) REVERT: F 50 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: F 99 ASN cc_start: 0.8178 (t0) cc_final: 0.7939 (t0) REVERT: F 106 TYR cc_start: 0.8004 (m-80) cc_final: 0.7693 (m-10) REVERT: F 134 GLN cc_start: 0.8245 (pt0) cc_final: 0.7968 (pt0) REVERT: F 159 TYR cc_start: 0.8631 (m-80) cc_final: 0.8204 (m-80) REVERT: F 226 ASN cc_start: 0.9058 (m-40) cc_final: 0.8805 (m-40) REVERT: F 251 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8396 (mtp85) REVERT: F 252 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8483 (mtpp) REVERT: F 364 SER cc_start: 0.8790 (p) cc_final: 0.8536 (m) REVERT: F 401 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7646 (mm-30) REVERT: D 8 GLN cc_start: 0.8055 (mt0) cc_final: 0.7685 (mt0) REVERT: D 26 ASP cc_start: 0.8377 (m-30) cc_final: 0.6973 (m-30) REVERT: D 99 ASN cc_start: 0.8314 (t0) cc_final: 0.7972 (t0) REVERT: D 123 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8353 (mm-30) REVERT: D 279 GLN cc_start: 0.8609 (pt0) cc_final: 0.8143 (pt0) REVERT: D 306 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8197 (mtt90) REVERT: D 310 TYR cc_start: 0.8857 (m-80) cc_final: 0.8602 (m-80) REVERT: D 329 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8157 (mm-40) REVERT: G 6 HIS cc_start: 0.8687 (t70) cc_final: 0.8158 (t70) REVERT: G 7 ILE cc_start: 0.9064 (mt) cc_final: 0.8792 (mt) REVERT: G 8 GLN cc_start: 0.8497 (mt0) cc_final: 0.7905 (mt0) REVERT: G 14 ASN cc_start: 0.8980 (m-40) cc_final: 0.8749 (m-40) REVERT: G 27 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8459 (mt-10) REVERT: G 31 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8267 (t0) REVERT: G 67 ASP cc_start: 0.8566 (t0) cc_final: 0.8073 (t0) REVERT: G 69 GLU cc_start: 0.8089 (pt0) cc_final: 0.7779 (mp0) REVERT: G 108 GLU cc_start: 0.9088 (tp30) cc_final: 0.8547 (tp30) REVERT: G 121 ARG cc_start: 0.8788 (ttm110) cc_final: 0.8016 (mtm180) REVERT: G 123 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9317 (tp30) REVERT: G 129 CYS cc_start: 0.7674 (t) cc_final: 0.7323 (t) REVERT: G 136 THR cc_start: 0.8813 (m) cc_final: 0.8374 (p) REVERT: G 143 THR cc_start: 0.8618 (m) cc_final: 0.8413 (m) REVERT: G 147 MET cc_start: 0.8794 (ttt) cc_final: 0.8593 (ttt) REVERT: G 164 MET cc_start: 0.8861 (tpp) cc_final: 0.8623 (mtm) REVERT: G 184 ASN cc_start: 0.9066 (m-40) cc_final: 0.8514 (p0) REVERT: G 194 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8629 (mt-10) REVERT: G 197 ASP cc_start: 0.8046 (m-30) cc_final: 0.7808 (m-30) REVERT: G 207 LEU cc_start: 0.9447 (mp) cc_final: 0.9087 (mp) REVERT: G 209 ASP cc_start: 0.8667 (t0) cc_final: 0.8282 (t70) REVERT: G 211 CYS cc_start: 0.8916 (m) cc_final: 0.8700 (m) REVERT: G 213 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7163 (ttp-110) REVERT: G 288 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8012 (tm-30) REVERT: G 379 LYS cc_start: 0.9418 (mtpt) cc_final: 0.8967 (mtmm) REVERT: G 395 LEU cc_start: 0.9375 (tp) cc_final: 0.9128 (tp) REVERT: G 401 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7932 (mm-30) REVERT: G 404 ASP cc_start: 0.8135 (p0) cc_final: 0.7508 (p0) REVERT: G 426 GLN cc_start: 0.8117 (tt0) cc_final: 0.7801 (tp40) REVERT: H 20 PHE cc_start: 0.9325 (t80) cc_final: 0.9067 (t80) REVERT: H 26 ASP cc_start: 0.8806 (m-30) cc_final: 0.8555 (t70) REVERT: H 27 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8195 (mt-10) REVERT: H 31 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8041 (t0) REVERT: H 50 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: H 67 ASP cc_start: 0.8409 (t0) cc_final: 0.8146 (t0) REVERT: H 68 LEU cc_start: 0.8320 (mt) cc_final: 0.8113 (mp) REVERT: H 108 GLU cc_start: 0.8758 (tp30) cc_final: 0.8545 (tp30) REVERT: H 121 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8160 (mtm180) REVERT: H 130 LEU cc_start: 0.8802 (tp) cc_final: 0.8547 (tp) REVERT: H 181 GLU cc_start: 0.8572 (pt0) cc_final: 0.8326 (pt0) REVERT: H 184 ASN cc_start: 0.8969 (m-40) cc_final: 0.8455 (p0) REVERT: H 194 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8522 (mt-10) REVERT: H 207 LEU cc_start: 0.9438 (mp) cc_final: 0.9235 (mp) REVERT: H 209 ASP cc_start: 0.8689 (t0) cc_final: 0.7863 (t0) REVERT: H 213 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7745 (ttp-110) REVERT: H 252 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8439 (mtpp) REVERT: H 304 ASP cc_start: 0.8428 (t0) cc_final: 0.7764 (t70) REVERT: H 306 ARG cc_start: 0.9003 (mtt90) cc_final: 0.8515 (mtm-85) REVERT: H 395 LEU cc_start: 0.9326 (tp) cc_final: 0.9087 (tp) REVERT: H 404 ASP cc_start: 0.8492 (p0) cc_final: 0.7845 (p0) REVERT: H 407 GLU cc_start: 0.9078 (tp30) cc_final: 0.8826 (mm-30) REVERT: H 410 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8940 (mt-10) REVERT: I 26 ASP cc_start: 0.8865 (m-30) cc_final: 0.8664 (t70) REVERT: I 31 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8293 (t0) REVERT: I 67 ASP cc_start: 0.8558 (t0) cc_final: 0.8258 (t0) REVERT: I 88 ASP cc_start: 0.7707 (p0) cc_final: 0.7267 (p0) REVERT: I 108 GLU cc_start: 0.8937 (tp30) cc_final: 0.8613 (tp30) REVERT: I 121 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8081 (mtm180) REVERT: I 123 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9015 (mm-30) REVERT: I 129 CYS cc_start: 0.7738 (t) cc_final: 0.7505 (t) REVERT: I 181 GLU cc_start: 0.8842 (pt0) cc_final: 0.8606 (pt0) REVERT: I 184 ASN cc_start: 0.9004 (m-40) cc_final: 0.8420 (p0) REVERT: I 209 ASP cc_start: 0.8786 (t0) cc_final: 0.8163 (t0) REVERT: I 213 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7876 (ttp-110) REVERT: I 252 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8565 (mttp) REVERT: I 304 ASP cc_start: 0.8609 (t0) cc_final: 0.8105 (t70) REVERT: I 306 ARG cc_start: 0.9048 (mtt90) cc_final: 0.8653 (mtm-85) REVERT: I 343 GLU cc_start: 0.8735 (tp30) cc_final: 0.8535 (tp30) REVERT: I 395 LEU cc_start: 0.9375 (tp) cc_final: 0.9174 (tp) REVERT: I 401 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8109 (mm-30) REVERT: I 404 ASP cc_start: 0.8396 (p0) cc_final: 0.7638 (p0) REVERT: I 407 GLU cc_start: 0.9241 (tp30) cc_final: 0.9014 (mm-30) REVERT: B 26 ASP cc_start: 0.8410 (m-30) cc_final: 0.7001 (m-30) REVERT: B 27 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8348 (mt-10) REVERT: B 316 VAL cc_start: 0.9381 (t) cc_final: 0.9158 (m) REVERT: B 329 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8160 (mm-40) REVERT: B 412 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7740 (tm-30) REVERT: B 424 GLN cc_start: 0.8384 (tt0) cc_final: 0.8114 (tt0) outliers start: 265 outliers final: 120 residues processed: 2281 average time/residue: 0.5544 time to fit residues: 2020.9796 Evaluate side-chains 1637 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1500 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 216 ASN Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.0470 chunk 386 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 399 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 243 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN J 206 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN D 298 ASN D 307 HIS D 329 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN B 57 HIS B 99 ASN B 165 ASN B 298 ASN B 307 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 41998 Z= 0.274 Angle : 0.629 10.343 57035 Z= 0.325 Chirality : 0.045 0.201 6240 Planarity : 0.005 0.067 7411 Dihedral : 11.064 143.498 5998 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 7.49 % Allowed : 17.09 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.39 (0.12), residues: 5136 helix: 1.19 (0.10), residues: 2436 sheet: -1.16 (0.18), residues: 804 loop : -1.75 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 21 HIS 0.006 0.001 HIS F 6 PHE 0.025 0.001 PHE L 255 TYR 0.022 0.001 TYR C 210 ARG 0.011 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2034 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1703 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8030 (p0) REVERT: A 76 ASP cc_start: 0.8774 (m-30) cc_final: 0.8559 (m-30) REVERT: A 90 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7797 (tm-30) REVERT: A 96 LYS cc_start: 0.8780 (tppt) cc_final: 0.8515 (tppp) REVERT: A 103 TYR cc_start: 0.8840 (t80) cc_final: 0.8394 (t80) REVERT: A 120 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8156 (t70) REVERT: A 121 ARG cc_start: 0.8277 (mmm160) cc_final: 0.7887 (tpt170) REVERT: A 169 PHE cc_start: 0.8582 (m-80) cc_final: 0.8325 (m-80) REVERT: A 211 ASP cc_start: 0.8952 (t0) cc_final: 0.8506 (t70) REVERT: A 224 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: A 302 MET cc_start: 0.8337 (mtt) cc_final: 0.8048 (mtm) REVERT: A 357 TYR cc_start: 0.8640 (m-80) cc_final: 0.8399 (m-80) REVERT: A 372 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7144 (mm-40) REVERT: A 386 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: A 430 LYS cc_start: 0.9401 (ttmt) cc_final: 0.9106 (tptt) REVERT: C 66 VAL cc_start: 0.9267 (t) cc_final: 0.9036 (p) REVERT: C 69 ASP cc_start: 0.8469 (t0) cc_final: 0.8245 (t0) REVERT: C 76 ASP cc_start: 0.8741 (m-30) cc_final: 0.8500 (m-30) REVERT: C 156 ARG cc_start: 0.8714 (mmt90) cc_final: 0.8336 (mmm-85) REVERT: C 269 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8214 (pp) REVERT: C 306 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7935 (p0) REVERT: E 6 SER cc_start: 0.9124 (m) cc_final: 0.8704 (p) REVERT: E 18 ASN cc_start: 0.8948 (m-40) cc_final: 0.8704 (m110) REVERT: E 33 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8623 (p0) REVERT: E 55 GLU cc_start: 0.8575 (tt0) cc_final: 0.8184 (tp30) REVERT: E 69 ASP cc_start: 0.8556 (t0) cc_final: 0.8327 (t0) REVERT: E 90 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7699 (tm-30) REVERT: E 156 ARG cc_start: 0.8960 (mmt90) cc_final: 0.8650 (mmm-85) REVERT: E 207 GLU cc_start: 0.8497 (tt0) cc_final: 0.8062 (tt0) REVERT: E 255 PHE cc_start: 0.8260 (m-80) cc_final: 0.8049 (m-80) REVERT: E 290 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: E 352 LYS cc_start: 0.8727 (tttp) cc_final: 0.8144 (tttp) REVERT: E 386 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7865 (tp30) REVERT: E 430 LYS cc_start: 0.9576 (ttmt) cc_final: 0.9296 (tptt) REVERT: J 33 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.7878 (p0) REVERT: J 75 ILE cc_start: 0.9347 (mm) cc_final: 0.9068 (mt) REVERT: J 109 THR cc_start: 0.9130 (m) cc_final: 0.8552 (p) REVERT: J 198 SER cc_start: 0.7793 (p) cc_final: 0.7305 (p) REVERT: J 214 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8010 (ttp80) REVERT: J 244 PHE cc_start: 0.8673 (m-80) cc_final: 0.8160 (m-80) REVERT: J 296 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7593 (t80) REVERT: J 308 ARG cc_start: 0.8708 (mpp80) cc_final: 0.8025 (ptp90) REVERT: J 346 TRP cc_start: 0.8461 (p-90) cc_final: 0.4889 (t-100) REVERT: J 430 LYS cc_start: 0.9537 (ttmt) cc_final: 0.9256 (tptt) REVERT: J 432 TYR cc_start: 0.8618 (m-80) cc_final: 0.7792 (t80) REVERT: K 33 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8528 (p0) REVERT: K 90 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7666 (tp30) REVERT: K 256 GLN cc_start: 0.9144 (pt0) cc_final: 0.8745 (tm-30) REVERT: K 346 TRP cc_start: 0.8629 (p-90) cc_final: 0.4568 (t-100) REVERT: K 357 TYR cc_start: 0.8532 (m-80) cc_final: 0.8189 (m-80) REVERT: K 430 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9191 (tptt) REVERT: K 433 GLU cc_start: 0.9108 (tt0) cc_final: 0.8840 (tp30) REVERT: L 33 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8339 (p0) REVERT: L 69 ASP cc_start: 0.8149 (t0) cc_final: 0.7826 (t0) REVERT: L 90 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7990 (tp30) REVERT: L 103 TYR cc_start: 0.8657 (t80) cc_final: 0.8132 (t80) REVERT: L 224 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7768 (m-10) REVERT: L 244 PHE cc_start: 0.8826 (m-80) cc_final: 0.8205 (m-80) REVERT: L 255 PHE cc_start: 0.8794 (m-80) cc_final: 0.8591 (m-80) REVERT: L 297 GLU cc_start: 0.9138 (tp30) cc_final: 0.8890 (tp30) REVERT: L 346 TRP cc_start: 0.8380 (p-90) cc_final: 0.4795 (t-100) REVERT: L 352 LYS cc_start: 0.3473 (mmtt) cc_final: 0.2919 (mptt) REVERT: L 370 LYS cc_start: 0.7836 (tptp) cc_final: 0.7613 (tptp) REVERT: L 372 GLN cc_start: 0.8106 (mp-120) cc_final: 0.7736 (mp10) REVERT: L 394 LYS cc_start: 0.8976 (mppt) cc_final: 0.8648 (mppt) REVERT: F 2 ARG cc_start: 0.8376 (mtm180) cc_final: 0.8078 (mtm180) REVERT: F 14 ASN cc_start: 0.8495 (m-40) cc_final: 0.8265 (m-40) REVERT: F 50 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: F 134 GLN cc_start: 0.8216 (pt0) cc_final: 0.7992 (pt0) REVERT: F 226 ASN cc_start: 0.9073 (m-40) cc_final: 0.8681 (m-40) REVERT: F 324 LYS cc_start: 0.9170 (tptp) cc_final: 0.8839 (tptp) REVERT: D 99 ASN cc_start: 0.8157 (t0) cc_final: 0.7828 (t0) REVERT: D 108 GLU cc_start: 0.8144 (tp30) cc_final: 0.7887 (tp30) REVERT: D 207 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9182 (mm) REVERT: D 279 GLN cc_start: 0.8558 (pt0) cc_final: 0.8248 (pt0) REVERT: D 323 MET cc_start: 0.7782 (mpp) cc_final: 0.7224 (mpp) REVERT: D 324 LYS cc_start: 0.9334 (tptp) cc_final: 0.9117 (tptp) REVERT: D 375 GLN cc_start: 0.8518 (pp30) cc_final: 0.7119 (pp30) REVERT: D 379 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8324 (mtmt) REVERT: D 392 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8761 (mmtt) REVERT: G 31 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8262 (t0) REVERT: G 121 ARG cc_start: 0.8773 (ttm110) cc_final: 0.8229 (mtm180) REVERT: G 123 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9265 (tp30) REVERT: G 143 THR cc_start: 0.8621 (m) cc_final: 0.8308 (m) REVERT: G 194 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8734 (mt-10) REVERT: G 197 ASP cc_start: 0.8267 (m-30) cc_final: 0.7807 (m-30) REVERT: G 207 LEU cc_start: 0.9445 (mp) cc_final: 0.9088 (mp) REVERT: G 209 ASP cc_start: 0.8631 (t0) cc_final: 0.8177 (t0) REVERT: G 211 CYS cc_start: 0.8887 (m) cc_final: 0.8681 (m) REVERT: G 226 ASN cc_start: 0.9002 (m-40) cc_final: 0.8731 (m-40) REVERT: G 297 LYS cc_start: 0.9073 (tppt) cc_final: 0.8573 (tppt) REVERT: G 325 GLU cc_start: 0.8851 (tt0) cc_final: 0.8514 (tt0) REVERT: G 351 VAL cc_start: 0.9119 (t) cc_final: 0.8916 (p) REVERT: G 370 ASN cc_start: 0.8428 (t0) cc_final: 0.8194 (t0) REVERT: G 375 GLN cc_start: 0.8116 (pp30) cc_final: 0.6968 (pp30) REVERT: G 379 LYS cc_start: 0.9363 (mtpt) cc_final: 0.8556 (mtmm) REVERT: G 403 MET cc_start: 0.7741 (mtp) cc_final: 0.7208 (ttp) REVERT: H 20 PHE cc_start: 0.9241 (t80) cc_final: 0.8997 (t80) REVERT: H 31 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8383 (m-30) REVERT: H 50 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: H 198 GLU cc_start: 0.8638 (pt0) cc_final: 0.8403 (pt0) REVERT: H 323 MET cc_start: 0.8468 (mmm) cc_final: 0.8225 (mpp) REVERT: H 383 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8443 (tm-30) REVERT: H 392 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8745 (mtpt) REVERT: H 405 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7322 (tm-30) REVERT: H 426 GLN cc_start: 0.7873 (tt0) cc_final: 0.7611 (tp40) REVERT: I 31 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: I 67 ASP cc_start: 0.8436 (t0) cc_final: 0.7914 (t0) REVERT: I 68 LEU cc_start: 0.8368 (mm) cc_final: 0.7989 (mp) REVERT: I 69 GLU cc_start: 0.7885 (mp0) cc_final: 0.7095 (mp0) REVERT: I 77 ARG cc_start: 0.9298 (ttm170) cc_final: 0.8974 (ttm110) REVERT: I 108 GLU cc_start: 0.8727 (tp30) cc_final: 0.8508 (tp30) REVERT: I 121 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8250 (mtm180) REVERT: I 123 GLU cc_start: 0.9448 (mm-30) cc_final: 0.8943 (mm-30) REVERT: I 209 ASP cc_start: 0.8724 (t0) cc_final: 0.8127 (t0) REVERT: I 383 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8595 (tm-30) REVERT: I 403 MET cc_start: 0.7495 (ttm) cc_final: 0.7183 (ttm) REVERT: I 404 ASP cc_start: 0.8580 (p0) cc_final: 0.7595 (p0) REVERT: I 407 GLU cc_start: 0.9182 (tp30) cc_final: 0.8965 (mm-30) REVERT: B 108 GLU cc_start: 0.8143 (tp30) cc_final: 0.7866 (tp30) REVERT: B 328 GLU cc_start: 0.8141 (tt0) cc_final: 0.7600 (tt0) REVERT: B 329 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8037 (mm-40) REVERT: B 375 GLN cc_start: 0.8330 (pp30) cc_final: 0.7319 (pp30) REVERT: B 379 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8182 (mtpt) REVERT: B 424 GLN cc_start: 0.8501 (tt0) cc_final: 0.8127 (tt0) outliers start: 331 outliers final: 202 residues processed: 1891 average time/residue: 0.5655 time to fit residues: 1733.5903 Evaluate side-chains 1684 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1462 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 463 optimal weight: 6.9990 chunk 501 optimal weight: 10.0000 chunk 413 optimal weight: 30.0000 chunk 460 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 372 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 285 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 227 HIS D 298 ASN D 307 HIS D 329 GLN D 337 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 245 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 298 ASN B 307 HIS B 329 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41998 Z= 0.291 Angle : 0.630 10.335 57035 Z= 0.327 Chirality : 0.045 0.194 6240 Planarity : 0.004 0.046 7411 Dihedral : 10.736 144.888 5952 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 8.11 % Allowed : 19.95 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.43 (0.12), residues: 5136 helix: 1.14 (0.10), residues: 2430 sheet: -1.19 (0.19), residues: 786 loop : -1.73 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.010 0.001 HIS G 57 PHE 0.021 0.002 PHE J 255 TYR 0.040 0.001 TYR C 210 ARG 0.007 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1876 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1518 time to evaluate : 4.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8082 (p0) REVERT: A 90 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7809 (tm-30) REVERT: A 96 LYS cc_start: 0.8746 (tppt) cc_final: 0.8402 (tppp) REVERT: A 103 TYR cc_start: 0.8830 (t80) cc_final: 0.8517 (t80) REVERT: A 120 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8104 (t70) REVERT: A 121 ARG cc_start: 0.8318 (mmm160) cc_final: 0.7908 (tpt170) REVERT: A 169 PHE cc_start: 0.8616 (m-80) cc_final: 0.8389 (m-80) REVERT: A 336 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8634 (mmmt) REVERT: A 357 TYR cc_start: 0.8656 (m-80) cc_final: 0.8374 (m-80) REVERT: A 413 MET cc_start: 0.8566 (mtm) cc_final: 0.8197 (mtt) REVERT: A 430 LYS cc_start: 0.9377 (ttmt) cc_final: 0.9112 (tptt) REVERT: C 156 ARG cc_start: 0.8749 (mmt90) cc_final: 0.8405 (mmm-85) REVERT: C 169 PHE cc_start: 0.8582 (m-80) cc_final: 0.8228 (m-80) REVERT: C 269 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 417 GLU cc_start: 0.8483 (mp0) cc_final: 0.8174 (mp0) REVERT: E 6 SER cc_start: 0.9156 (m) cc_final: 0.8727 (p) REVERT: E 18 ASN cc_start: 0.8956 (m-40) cc_final: 0.8732 (m110) REVERT: E 33 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8499 (p0) REVERT: E 51 THR cc_start: 0.9381 (m) cc_final: 0.9140 (t) REVERT: E 55 GLU cc_start: 0.8586 (tt0) cc_final: 0.8173 (tp30) REVERT: E 69 ASP cc_start: 0.8643 (t0) cc_final: 0.8428 (t0) REVERT: E 90 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7680 (tm-30) REVERT: E 156 ARG cc_start: 0.8944 (mmt90) cc_final: 0.8642 (mmm-85) REVERT: E 207 GLU cc_start: 0.8510 (tt0) cc_final: 0.8202 (tt0) REVERT: E 290 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: E 313 MET cc_start: 0.8544 (mtm) cc_final: 0.8316 (mtm) REVERT: E 327 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8161 (p0) REVERT: E 386 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7852 (tp30) REVERT: E 430 LYS cc_start: 0.9578 (ttmt) cc_final: 0.9262 (tptt) REVERT: J 75 ILE cc_start: 0.9343 (mm) cc_final: 0.9070 (mt) REVERT: J 90 GLU cc_start: 0.8017 (tp30) cc_final: 0.7715 (tp30) REVERT: J 108 TYR cc_start: 0.8925 (m-80) cc_final: 0.8604 (m-80) REVERT: J 168 GLU cc_start: 0.8689 (mp0) cc_final: 0.8252 (pm20) REVERT: J 244 PHE cc_start: 0.8667 (m-80) cc_final: 0.8147 (m-80) REVERT: J 346 TRP cc_start: 0.8450 (p-90) cc_final: 0.4752 (t-100) REVERT: J 430 LYS cc_start: 0.9540 (ttmt) cc_final: 0.9243 (tptt) REVERT: J 432 TYR cc_start: 0.8576 (m-80) cc_final: 0.7669 (t80) REVERT: J 433 GLU cc_start: 0.9050 (tp30) cc_final: 0.8806 (tp30) REVERT: K 33 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (p0) REVERT: K 90 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7738 (tp30) REVERT: K 256 GLN cc_start: 0.9130 (pt0) cc_final: 0.8691 (tm-30) REVERT: K 346 TRP cc_start: 0.8537 (p-90) cc_final: 0.4499 (t-100) REVERT: K 357 TYR cc_start: 0.8579 (m-80) cc_final: 0.8194 (m-80) REVERT: K 425 MET cc_start: 0.8638 (tpt) cc_final: 0.8435 (tpp) REVERT: K 430 LYS cc_start: 0.9453 (ttmt) cc_final: 0.9158 (tptt) REVERT: K 433 GLU cc_start: 0.9080 (tt0) cc_final: 0.8822 (tp30) REVERT: L 11 GLN cc_start: 0.7920 (tt0) cc_final: 0.7633 (tt0) REVERT: L 69 ASP cc_start: 0.8241 (t0) cc_final: 0.7867 (t0) REVERT: L 90 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7913 (tp30) REVERT: L 224 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: L 251 ASP cc_start: 0.7988 (m-30) cc_final: 0.7755 (m-30) REVERT: L 297 GLU cc_start: 0.9152 (tp30) cc_final: 0.8934 (tp30) REVERT: L 346 TRP cc_start: 0.8479 (p-90) cc_final: 0.4781 (t-100) REVERT: L 394 LYS cc_start: 0.8977 (mppt) cc_final: 0.8669 (mppt) REVERT: L 414 GLU cc_start: 0.8226 (mp0) cc_final: 0.7908 (mp0) REVERT: L 417 GLU cc_start: 0.8192 (mp0) cc_final: 0.7584 (mp0) REVERT: L 433 GLU cc_start: 0.8877 (tp30) cc_final: 0.8644 (tp30) REVERT: F 2 ARG cc_start: 0.8334 (mtm180) cc_final: 0.8064 (mtm180) REVERT: F 226 ASN cc_start: 0.8985 (m-40) cc_final: 0.8673 (m-40) REVERT: F 251 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8351 (mtp85) REVERT: F 310 TYR cc_start: 0.8883 (m-80) cc_final: 0.8640 (m-80) REVERT: F 329 GLN cc_start: 0.9122 (tp40) cc_final: 0.8904 (mm-40) REVERT: F 375 GLN cc_start: 0.8454 (pp30) cc_final: 0.8014 (pp30) REVERT: F 406 MET cc_start: 0.8475 (tpp) cc_final: 0.7531 (tpp) REVERT: F 410 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7917 (mt-10) REVERT: D 77 ARG cc_start: 0.9156 (ttm110) cc_final: 0.8950 (ttm110) REVERT: D 99 ASN cc_start: 0.8267 (t0) cc_final: 0.7873 (t0) REVERT: D 162 ARG cc_start: 0.8343 (mmp80) cc_final: 0.8083 (mmp80) REVERT: D 167 PHE cc_start: 0.8495 (m-80) cc_final: 0.8172 (m-10) REVERT: D 279 GLN cc_start: 0.8640 (pt0) cc_final: 0.8332 (pt0) REVERT: D 323 MET cc_start: 0.7946 (mpp) cc_final: 0.7065 (mpp) REVERT: D 364 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8506 (m) REVERT: D 375 GLN cc_start: 0.8453 (pp30) cc_final: 0.7263 (pp30) REVERT: D 379 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8440 (mtpt) REVERT: D 405 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7758 (tm-30) REVERT: D 422 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7821 (t80) REVERT: G 14 ASN cc_start: 0.8892 (m-40) cc_final: 0.8670 (m-40) REVERT: G 31 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: G 67 ASP cc_start: 0.8630 (t0) cc_final: 0.8047 (t0) REVERT: G 121 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8327 (mtm180) REVERT: G 143 THR cc_start: 0.8553 (m) cc_final: 0.8320 (m) REVERT: G 164 MET cc_start: 0.8163 (mtm) cc_final: 0.7956 (mtt) REVERT: G 194 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8619 (mt-10) REVERT: G 207 LEU cc_start: 0.9474 (mp) cc_final: 0.9089 (mp) REVERT: G 209 ASP cc_start: 0.8725 (t0) cc_final: 0.8440 (t0) REVERT: G 213 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7664 (ttp-110) REVERT: G 226 ASN cc_start: 0.9011 (m-40) cc_final: 0.8735 (m-40) REVERT: G 291 GLN cc_start: 0.8842 (mp10) cc_final: 0.8616 (mp10) REVERT: G 297 LYS cc_start: 0.9104 (tppt) cc_final: 0.8792 (tppt) REVERT: G 310 TYR cc_start: 0.9110 (m-80) cc_final: 0.8695 (m-80) REVERT: G 375 GLN cc_start: 0.8125 (pp30) cc_final: 0.7561 (pp30) REVERT: G 403 MET cc_start: 0.7821 (mtp) cc_final: 0.7131 (ttp) REVERT: G 404 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8321 (p0) REVERT: H 20 PHE cc_start: 0.9228 (t80) cc_final: 0.8973 (t80) REVERT: H 31 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: H 50 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7744 (m-80) REVERT: H 67 ASP cc_start: 0.8334 (t0) cc_final: 0.7906 (t70) REVERT: H 121 ARG cc_start: 0.8753 (ttm110) cc_final: 0.8356 (mtm180) REVERT: H 198 GLU cc_start: 0.8797 (pt0) cc_final: 0.8405 (pt0) REVERT: H 226 ASN cc_start: 0.8998 (m-40) cc_final: 0.8684 (m-40) REVERT: H 299 MET cc_start: 0.7999 (mmm) cc_final: 0.7675 (mmm) REVERT: H 323 MET cc_start: 0.8410 (mmm) cc_final: 0.8054 (mpp) REVERT: H 375 GLN cc_start: 0.8341 (pp30) cc_final: 0.7969 (pp30) REVERT: H 388 MET cc_start: 0.8525 (mtp) cc_final: 0.7996 (mmt) REVERT: H 410 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8839 (mt-10) REVERT: H 426 GLN cc_start: 0.7878 (tt0) cc_final: 0.7612 (tp40) REVERT: I 31 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (m-30) REVERT: I 121 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8334 (mtm180) REVERT: I 198 GLU cc_start: 0.8677 (pt0) cc_final: 0.8364 (pt0) REVERT: I 291 GLN cc_start: 0.8683 (mp10) cc_final: 0.8393 (mp10) REVERT: I 299 MET cc_start: 0.8200 (mmm) cc_final: 0.7788 (mmm) REVERT: I 375 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8109 (pp30) REVERT: I 395 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8900 (mt) REVERT: B 50 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: B 65 LEU cc_start: 0.8467 (mp) cc_final: 0.8219 (mt) REVERT: B 167 PHE cc_start: 0.8261 (m-80) cc_final: 0.8004 (m-10) REVERT: B 328 GLU cc_start: 0.8109 (tt0) cc_final: 0.7784 (tt0) REVERT: B 329 GLN cc_start: 0.9010 (mm110) cc_final: 0.8010 (mm-40) REVERT: B 375 GLN cc_start: 0.8436 (pp30) cc_final: 0.7661 (pp30) REVERT: B 424 GLN cc_start: 0.8486 (tt0) cc_final: 0.8100 (tt0) outliers start: 358 outliers final: 240 residues processed: 1726 average time/residue: 0.5315 time to fit residues: 1488.4857 Evaluate side-chains 1680 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1420 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 305 CYS Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 376 CYS Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 7.9990 chunk 348 optimal weight: 0.9980 chunk 240 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 465 optimal weight: 7.9990 chunk 492 optimal weight: 0.0270 chunk 243 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 309 HIS ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 GLN J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 300 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS F 134 GLN F 190 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN G 307 HIS ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS I 375 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 298 ASN B 307 HIS B 375 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41998 Z= 0.232 Angle : 0.613 10.543 57035 Z= 0.314 Chirality : 0.045 0.225 6240 Planarity : 0.004 0.045 7411 Dihedral : 10.377 144.324 5924 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 7.02 % Allowed : 22.93 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.36 (0.12), residues: 5136 helix: 1.17 (0.10), residues: 2436 sheet: -1.07 (0.19), residues: 786 loop : -1.70 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.007 0.001 HIS G 57 PHE 0.034 0.001 PHE J 255 TYR 0.045 0.001 TYR C 210 ARG 0.006 0.000 ARG A 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1538 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7549 (p0) REVERT: A 69 ASP cc_start: 0.8068 (t0) cc_final: 0.7862 (t0) REVERT: A 90 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7640 (tm-30) REVERT: A 96 LYS cc_start: 0.8745 (tppt) cc_final: 0.8532 (tppp) REVERT: A 120 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (t70) REVERT: A 121 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7744 (tpt170) REVERT: A 169 PHE cc_start: 0.8549 (m-80) cc_final: 0.8225 (m-80) REVERT: A 336 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8637 (mmmt) REVERT: A 357 TYR cc_start: 0.8616 (m-80) cc_final: 0.8376 (m-80) REVERT: A 386 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: A 430 LYS cc_start: 0.9375 (ttmt) cc_final: 0.9108 (tptt) REVERT: C 169 PHE cc_start: 0.8526 (m-80) cc_final: 0.8248 (m-80) REVERT: C 221 ARG cc_start: 0.7485 (mmm-85) cc_final: 0.7277 (mmm-85) REVERT: C 269 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8441 (pp) REVERT: C 336 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8705 (mmmm) REVERT: C 417 GLU cc_start: 0.8552 (mp0) cc_final: 0.8282 (mp0) REVERT: E 33 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8404 (p0) REVERT: E 51 THR cc_start: 0.9399 (m) cc_final: 0.9179 (t) REVERT: E 55 GLU cc_start: 0.8565 (tt0) cc_final: 0.8350 (tp30) REVERT: E 76 ASP cc_start: 0.8690 (m-30) cc_final: 0.8468 (m-30) REVERT: E 88 HIS cc_start: 0.6342 (OUTLIER) cc_final: 0.4940 (t70) REVERT: E 90 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7773 (tm-30) REVERT: E 156 ARG cc_start: 0.8934 (mmt90) cc_final: 0.8627 (mmm-85) REVERT: E 207 GLU cc_start: 0.8457 (tt0) cc_final: 0.8223 (tt0) REVERT: E 306 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (p0) REVERT: E 313 MET cc_start: 0.8433 (mtm) cc_final: 0.8207 (mtm) REVERT: E 352 LYS cc_start: 0.8761 (tptt) cc_final: 0.8087 (tppt) REVERT: E 430 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9267 (tptt) REVERT: J 75 ILE cc_start: 0.9306 (mm) cc_final: 0.9056 (mt) REVERT: J 88 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.5362 (t70) REVERT: J 90 GLU cc_start: 0.8015 (tp30) cc_final: 0.7790 (tp30) REVERT: J 108 TYR cc_start: 0.8953 (m-80) cc_final: 0.8590 (m-80) REVERT: J 210 TYR cc_start: 0.8537 (m-10) cc_final: 0.8209 (m-80) REVERT: J 244 PHE cc_start: 0.8635 (m-80) cc_final: 0.8141 (m-80) REVERT: J 339 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7308 (ptm160) REVERT: J 346 TRP cc_start: 0.8510 (p-90) cc_final: 0.4662 (t-100) REVERT: J 430 LYS cc_start: 0.9546 (ttmt) cc_final: 0.9256 (tptt) REVERT: J 432 TYR cc_start: 0.8546 (m-80) cc_final: 0.7919 (t80) REVERT: J 433 GLU cc_start: 0.9022 (tp30) cc_final: 0.8812 (tp30) REVERT: K 33 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8376 (p0) REVERT: K 90 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7726 (tp30) REVERT: K 108 TYR cc_start: 0.8784 (m-80) cc_final: 0.8554 (m-80) REVERT: K 154 MET cc_start: 0.8444 (mmm) cc_final: 0.8240 (mmm) REVERT: K 256 GLN cc_start: 0.9152 (pt0) cc_final: 0.8799 (tm-30) REVERT: K 279 GLU cc_start: 0.7774 (pp20) cc_final: 0.7487 (pp20) REVERT: K 300 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (t0) REVERT: K 346 TRP cc_start: 0.8516 (p-90) cc_final: 0.4393 (t-100) REVERT: K 357 TYR cc_start: 0.8529 (m-80) cc_final: 0.8138 (m-80) REVERT: K 430 LYS cc_start: 0.9469 (ttmt) cc_final: 0.9159 (tptt) REVERT: K 433 GLU cc_start: 0.9053 (tt0) cc_final: 0.8794 (tp30) REVERT: L 224 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: L 346 TRP cc_start: 0.8535 (p-90) cc_final: 0.4717 (t-100) REVERT: L 433 GLU cc_start: 0.8862 (tp30) cc_final: 0.8638 (tp30) REVERT: F 200 TYR cc_start: 0.8329 (m-80) cc_final: 0.7727 (m-80) REVERT: F 226 ASN cc_start: 0.8947 (m-40) cc_final: 0.8635 (m-40) REVERT: F 251 ARG cc_start: 0.8624 (mtp-110) cc_final: 0.8365 (mtp85) REVERT: F 279 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: F 310 TYR cc_start: 0.8851 (m-80) cc_final: 0.8578 (m-80) REVERT: F 329 GLN cc_start: 0.9136 (tp40) cc_final: 0.8927 (tp40) REVERT: F 376 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 99 ASN cc_start: 0.8251 (t0) cc_final: 0.7866 (t0) REVERT: D 122 LYS cc_start: 0.8841 (pttp) cc_final: 0.8574 (ptmm) REVERT: D 162 ARG cc_start: 0.8256 (mmp80) cc_final: 0.7682 (mmp80) REVERT: D 167 PHE cc_start: 0.8496 (m-80) cc_final: 0.7850 (m-10) REVERT: D 279 GLN cc_start: 0.8615 (pt0) cc_final: 0.8377 (pt0) REVERT: D 323 MET cc_start: 0.7950 (mpp) cc_final: 0.7126 (mpp) REVERT: D 329 GLN cc_start: 0.9034 (mm110) cc_final: 0.8725 (tp40) REVERT: D 364 SER cc_start: 0.8751 (p) cc_final: 0.8493 (m) REVERT: D 375 GLN cc_start: 0.8361 (pp30) cc_final: 0.7117 (pp30) REVERT: D 379 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8594 (mtmt) REVERT: D 405 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 422 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7840 (t80) REVERT: G 14 ASN cc_start: 0.8927 (m-40) cc_final: 0.8676 (m-40) REVERT: G 31 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: G 67 ASP cc_start: 0.8685 (t0) cc_final: 0.8110 (t0) REVERT: G 69 GLU cc_start: 0.8391 (mp0) cc_final: 0.7809 (mp0) REVERT: G 84 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8243 (pt) REVERT: G 121 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8381 (mtm180) REVERT: G 143 THR cc_start: 0.8577 (m) cc_final: 0.8293 (m) REVERT: G 164 MET cc_start: 0.8254 (mtm) cc_final: 0.8039 (mtt) REVERT: G 194 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8619 (mt-10) REVERT: G 209 ASP cc_start: 0.8746 (t0) cc_final: 0.8312 (t0) REVERT: G 213 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7554 (ttp-110) REVERT: G 226 ASN cc_start: 0.8999 (m-40) cc_final: 0.8725 (m-40) REVERT: G 297 LYS cc_start: 0.9063 (tppt) cc_final: 0.8687 (tppt) REVERT: G 310 TYR cc_start: 0.9102 (m-80) cc_final: 0.8692 (m-80) REVERT: G 375 GLN cc_start: 0.8107 (pp30) cc_final: 0.7489 (pp30) REVERT: G 403 MET cc_start: 0.7794 (mtp) cc_final: 0.7211 (ttp) REVERT: H 31 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: H 50 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: H 121 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8425 (mtm180) REVERT: H 274 THR cc_start: 0.8980 (p) cc_final: 0.8386 (t) REVERT: H 282 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7892 (ttp80) REVERT: H 291 GLN cc_start: 0.8953 (mp10) cc_final: 0.8726 (mp10) REVERT: H 323 MET cc_start: 0.8277 (mmm) cc_final: 0.8020 (mpp) REVERT: H 388 MET cc_start: 0.8553 (mtp) cc_final: 0.8037 (mmt) REVERT: H 410 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8747 (mt-10) REVERT: H 426 GLN cc_start: 0.7835 (tt0) cc_final: 0.7582 (tp40) REVERT: I 121 ARG cc_start: 0.8804 (ttm110) cc_final: 0.8397 (mtm180) REVERT: I 198 GLU cc_start: 0.8640 (pt0) cc_final: 0.8338 (pt0) REVERT: I 288 GLU cc_start: 0.9089 (tt0) cc_final: 0.8793 (tm-30) REVERT: I 291 GLN cc_start: 0.8707 (mp10) cc_final: 0.8309 (mp10) REVERT: I 299 MET cc_start: 0.8169 (mmm) cc_final: 0.7706 (mmm) REVERT: I 329 GLN cc_start: 0.9314 (mm-40) cc_final: 0.9094 (mm-40) REVERT: I 363 MET cc_start: 0.8381 (ptp) cc_final: 0.7869 (ptt) REVERT: I 395 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8874 (mt) REVERT: B 50 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: B 121 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8301 (mtm-85) REVERT: B 323 MET cc_start: 0.7867 (mpt) cc_final: 0.7211 (mpp) REVERT: B 328 GLU cc_start: 0.8325 (tt0) cc_final: 0.7985 (tt0) REVERT: B 329 GLN cc_start: 0.9066 (mm110) cc_final: 0.8214 (mm-40) REVERT: B 375 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.6722 (pp30) REVERT: B 377 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 379 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8084 (mtmt) REVERT: B 424 GLN cc_start: 0.8465 (tt0) cc_final: 0.8009 (tt0) outliers start: 310 outliers final: 223 residues processed: 1721 average time/residue: 0.5394 time to fit residues: 1506.5001 Evaluate side-chains 1669 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1422 time to evaluate : 5.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 306 ASP Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 395 LEU Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 420 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 442 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS C 8 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 285 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 ASN I 375 GLN B 57 HIS B 298 ASN B 307 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41998 Z= 0.236 Angle : 0.623 9.986 57035 Z= 0.320 Chirality : 0.045 0.227 6240 Planarity : 0.004 0.059 7411 Dihedral : 10.116 144.224 5895 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.66 % Rotamer: Outliers : 7.49 % Allowed : 23.59 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.41 (0.12), residues: 5136 helix: 1.08 (0.10), residues: 2496 sheet: -0.96 (0.19), residues: 774 loop : -1.82 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 21 HIS 0.017 0.001 HIS A 309 PHE 0.041 0.002 PHE L 255 TYR 0.047 0.001 TYR C 210 ARG 0.007 0.000 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1519 time to evaluate : 5.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8192 (p0) REVERT: A 69 ASP cc_start: 0.8321 (t0) cc_final: 0.8110 (t0) REVERT: A 70 LEU cc_start: 0.8951 (mt) cc_final: 0.8722 (mp) REVERT: A 90 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7816 (tm-30) REVERT: A 96 LYS cc_start: 0.8730 (tppt) cc_final: 0.8413 (tppp) REVERT: A 103 TYR cc_start: 0.8754 (t80) cc_final: 0.8338 (t80) REVERT: A 120 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8120 (t0) REVERT: A 121 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7852 (tpt170) REVERT: A 169 PHE cc_start: 0.8479 (m-80) cc_final: 0.8232 (m-80) REVERT: A 301 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: A 357 TYR cc_start: 0.8570 (m-80) cc_final: 0.8369 (m-80) REVERT: A 386 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: A 402 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8382 (mmt-90) REVERT: A 430 LYS cc_start: 0.9374 (ttmt) cc_final: 0.9112 (tptt) REVERT: C 90 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7932 (tp30) REVERT: C 169 PHE cc_start: 0.8539 (m-80) cc_final: 0.8328 (m-80) REVERT: C 269 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8446 (pp) REVERT: C 417 GLU cc_start: 0.8593 (mp0) cc_final: 0.8284 (mp0) REVERT: E 33 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8419 (p0) REVERT: E 51 THR cc_start: 0.9398 (m) cc_final: 0.9192 (t) REVERT: E 55 GLU cc_start: 0.8557 (tt0) cc_final: 0.8298 (tp30) REVERT: E 76 ASP cc_start: 0.8658 (m-30) cc_final: 0.8433 (m-30) REVERT: E 88 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.4976 (t70) REVERT: E 90 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7782 (tm-30) REVERT: E 214 ARG cc_start: 0.8762 (tmm-80) cc_final: 0.7982 (tmm-80) REVERT: E 248 LEU cc_start: 0.9202 (tp) cc_final: 0.8972 (tt) REVERT: E 269 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 430 LYS cc_start: 0.9570 (ttmt) cc_final: 0.9266 (tptt) REVERT: J 33 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.7966 (p0) REVERT: J 88 HIS cc_start: 0.6951 (OUTLIER) cc_final: 0.5275 (t70) REVERT: J 90 GLU cc_start: 0.8003 (tp30) cc_final: 0.7773 (tp30) REVERT: J 108 TYR cc_start: 0.8893 (m-80) cc_final: 0.8592 (m-80) REVERT: J 210 TYR cc_start: 0.8555 (m-10) cc_final: 0.8339 (m-80) REVERT: J 224 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: J 339 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7309 (ptm160) REVERT: J 346 TRP cc_start: 0.8542 (p-90) cc_final: 0.4673 (t-100) REVERT: J 351 PHE cc_start: 0.7986 (m-80) cc_final: 0.7645 (m-80) REVERT: J 386 GLU cc_start: 0.8854 (tt0) cc_final: 0.8650 (pt0) REVERT: J 430 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9245 (tptt) REVERT: J 432 TYR cc_start: 0.8529 (m-80) cc_final: 0.7883 (t80) REVERT: K 33 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8433 (p0) REVERT: K 90 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7630 (tp30) REVERT: K 256 GLN cc_start: 0.9117 (pt0) cc_final: 0.8799 (tm-30) REVERT: K 300 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8547 (t0) REVERT: K 346 TRP cc_start: 0.8507 (p-90) cc_final: 0.4357 (t-100) REVERT: K 357 TYR cc_start: 0.8484 (m-80) cc_final: 0.8104 (m-80) REVERT: K 430 LYS cc_start: 0.9484 (ttmt) cc_final: 0.9164 (tptt) REVERT: K 432 TYR cc_start: 0.8562 (m-80) cc_final: 0.7889 (t80) REVERT: K 433 GLU cc_start: 0.9019 (tt0) cc_final: 0.8779 (tp30) REVERT: L 113 GLU cc_start: 0.8659 (mp0) cc_final: 0.8377 (mp0) REVERT: L 154 MET cc_start: 0.8730 (mmm) cc_final: 0.8423 (mmp) REVERT: L 224 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7729 (m-10) REVERT: L 259 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9225 (mm) REVERT: L 346 TRP cc_start: 0.8567 (p-90) cc_final: 0.4688 (t-100) REVERT: L 394 LYS cc_start: 0.9389 (mppt) cc_final: 0.9038 (mppt) REVERT: L 433 GLU cc_start: 0.8853 (tp30) cc_final: 0.8644 (tp30) REVERT: F 226 ASN cc_start: 0.8948 (m-40) cc_final: 0.8630 (m-40) REVERT: F 251 ARG cc_start: 0.8654 (mtp-110) cc_final: 0.8377 (mtp85) REVERT: F 279 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: F 310 TYR cc_start: 0.8868 (m-80) cc_final: 0.8627 (m-80) REVERT: F 406 MET cc_start: 0.8537 (tpp) cc_final: 0.7842 (tpp) REVERT: F 410 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 44 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8208 (mp) REVERT: D 99 ASN cc_start: 0.8268 (t0) cc_final: 0.7873 (t0) REVERT: D 122 LYS cc_start: 0.8804 (pttp) cc_final: 0.8560 (ptmm) REVERT: D 279 GLN cc_start: 0.8546 (pt0) cc_final: 0.8345 (pt0) REVERT: D 323 MET cc_start: 0.7803 (mpp) cc_final: 0.7192 (mpp) REVERT: D 329 GLN cc_start: 0.9061 (mm110) cc_final: 0.8745 (tp40) REVERT: D 364 SER cc_start: 0.8795 (OUTLIER) cc_final: 0.8515 (m) REVERT: D 375 GLN cc_start: 0.8334 (pp30) cc_final: 0.7077 (pp30) REVERT: D 379 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8680 (mtmt) REVERT: D 405 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 422 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7863 (t80) REVERT: G 31 ASP cc_start: 0.8904 (m-30) cc_final: 0.8482 (m-30) REVERT: G 50 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: G 67 ASP cc_start: 0.8678 (t0) cc_final: 0.8212 (t0) REVERT: G 121 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8400 (mtm180) REVERT: G 129 CYS cc_start: 0.7514 (t) cc_final: 0.7135 (p) REVERT: G 164 MET cc_start: 0.8431 (mtm) cc_final: 0.8161 (mtt) REVERT: G 194 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8626 (mt-10) REVERT: G 209 ASP cc_start: 0.8819 (t0) cc_final: 0.8393 (t0) REVERT: G 213 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7519 (ttp-110) REVERT: G 226 ASN cc_start: 0.8985 (m-40) cc_final: 0.8705 (m-40) REVERT: G 297 LYS cc_start: 0.9022 (tppt) cc_final: 0.8566 (tppt) REVERT: G 310 TYR cc_start: 0.9126 (m-80) cc_final: 0.8779 (m-80) REVERT: G 324 LYS cc_start: 0.8930 (tttp) cc_final: 0.8582 (ttpt) REVERT: G 375 GLN cc_start: 0.8119 (pp30) cc_final: 0.6849 (pp30) REVERT: G 379 LYS cc_start: 0.9396 (mtpt) cc_final: 0.8560 (mtmm) REVERT: G 388 MET cc_start: 0.4825 (mmt) cc_final: 0.4494 (mmt) REVERT: G 403 MET cc_start: 0.7836 (mtp) cc_final: 0.7110 (ttp) REVERT: G 404 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8200 (p0) REVERT: G 405 GLU cc_start: 0.8049 (pp20) cc_final: 0.7816 (pp20) REVERT: H 31 ASP cc_start: 0.8699 (m-30) cc_final: 0.8454 (m-30) REVERT: H 50 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: H 67 ASP cc_start: 0.8449 (t0) cc_final: 0.7977 (t0) REVERT: H 73 MET cc_start: 0.8898 (mmm) cc_final: 0.8593 (mtm) REVERT: H 121 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8513 (mtm180) REVERT: H 194 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8735 (mt-10) REVERT: H 198 GLU cc_start: 0.8745 (pt0) cc_final: 0.8323 (pt0) REVERT: H 274 THR cc_start: 0.8987 (p) cc_final: 0.8409 (t) REVERT: H 282 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7838 (ttp80) REVERT: H 291 GLN cc_start: 0.8942 (mp10) cc_final: 0.8736 (mp10) REVERT: H 323 MET cc_start: 0.8403 (mmm) cc_final: 0.7975 (mpp) REVERT: H 344 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8228 (p-90) REVERT: H 375 GLN cc_start: 0.8321 (pp30) cc_final: 0.7872 (pp30) REVERT: H 388 MET cc_start: 0.8581 (mtp) cc_final: 0.8055 (mmt) REVERT: H 410 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8765 (mt-10) REVERT: H 426 GLN cc_start: 0.7867 (tt0) cc_final: 0.7604 (tp40) REVERT: I 67 ASP cc_start: 0.8047 (t0) cc_final: 0.7750 (t70) REVERT: I 121 ARG cc_start: 0.8814 (ttm110) cc_final: 0.8421 (mtm180) REVERT: I 198 GLU cc_start: 0.8567 (pt0) cc_final: 0.8268 (pt0) REVERT: I 291 GLN cc_start: 0.8689 (mt0) cc_final: 0.8229 (mp10) REVERT: I 329 GLN cc_start: 0.9280 (mm-40) cc_final: 0.9020 (mm-40) REVERT: I 363 MET cc_start: 0.8425 (ptp) cc_final: 0.7986 (ptt) REVERT: B 50 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: B 328 GLU cc_start: 0.8329 (tt0) cc_final: 0.7985 (tt0) REVERT: B 329 GLN cc_start: 0.9090 (mm110) cc_final: 0.8229 (mm-40) REVERT: B 370 ASN cc_start: 0.7898 (t0) cc_final: 0.7473 (t0) REVERT: B 406 MET cc_start: 0.8316 (tpp) cc_final: 0.7361 (tpp) REVERT: B 424 GLN cc_start: 0.8475 (tt0) cc_final: 0.7994 (tt0) outliers start: 331 outliers final: 240 residues processed: 1709 average time/residue: 0.5366 time to fit residues: 1495.9749 Evaluate side-chains 1677 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1411 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 224 TYR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 279 GLN Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 20.0000 chunk 443 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 493 optimal weight: 0.9980 chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 285 GLN C 293 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 249 ASN K 300 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 298 ASN B 307 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 41998 Z= 0.304 Angle : 0.664 10.491 57035 Z= 0.341 Chirality : 0.046 0.227 6240 Planarity : 0.005 0.060 7411 Dihedral : 10.140 145.102 5879 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 7.65 % Allowed : 24.81 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 5136 helix: 0.95 (0.10), residues: 2508 sheet: -1.02 (0.19), residues: 786 loop : -1.75 (0.15), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 388 HIS 0.008 0.001 HIS B 6 PHE 0.039 0.002 PHE L 255 TYR 0.052 0.002 TYR C 210 ARG 0.007 0.001 ARG I 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1783 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1445 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8657 (OUTLIER) cc_final: 0.8340 (p0) REVERT: A 69 ASP cc_start: 0.8280 (t0) cc_final: 0.8044 (t0) REVERT: A 90 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7848 (tm-30) REVERT: A 96 LYS cc_start: 0.8730 (tppt) cc_final: 0.8456 (tppp) REVERT: A 103 TYR cc_start: 0.8681 (t80) cc_final: 0.8347 (t80) REVERT: A 120 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 121 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7845 (tpt170) REVERT: A 357 TYR cc_start: 0.8645 (m-80) cc_final: 0.8399 (m-80) REVERT: A 386 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: A 430 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9146 (tptt) REVERT: C 90 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7991 (tp30) REVERT: C 123 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8467 (tpp80) REVERT: C 169 PHE cc_start: 0.8606 (m-80) cc_final: 0.8326 (m-80) REVERT: C 269 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 417 GLU cc_start: 0.8655 (mp0) cc_final: 0.8345 (mp0) REVERT: E 55 GLU cc_start: 0.8563 (tt0) cc_final: 0.8232 (tp30) REVERT: E 76 ASP cc_start: 0.8727 (m-30) cc_final: 0.8505 (m-30) REVERT: E 88 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.4753 (t70) REVERT: E 90 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7826 (tm-30) REVERT: E 214 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8201 (tmm-80) REVERT: E 248 LEU cc_start: 0.9244 (tp) cc_final: 0.9020 (tt) REVERT: E 269 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8602 (pp) REVERT: E 309 HIS cc_start: 0.8162 (m90) cc_final: 0.7827 (m170) REVERT: E 327 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8544 (p0) REVERT: E 430 LYS cc_start: 0.9567 (ttmt) cc_final: 0.9280 (tptt) REVERT: J 88 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.5107 (t70) REVERT: J 90 GLU cc_start: 0.8024 (tp30) cc_final: 0.7759 (tp30) REVERT: J 108 TYR cc_start: 0.8882 (m-80) cc_final: 0.8641 (m-80) REVERT: J 176 GLN cc_start: 0.8712 (mp10) cc_final: 0.8454 (mp10) REVERT: J 339 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7278 (ptm160) REVERT: J 346 TRP cc_start: 0.8574 (p-90) cc_final: 0.4673 (t-100) REVERT: J 386 GLU cc_start: 0.8824 (tt0) cc_final: 0.8568 (pt0) REVERT: J 413 MET cc_start: 0.8564 (tpp) cc_final: 0.8216 (mmm) REVERT: J 430 LYS cc_start: 0.9561 (ttmt) cc_final: 0.9266 (tptt) REVERT: J 432 TYR cc_start: 0.8548 (m-80) cc_final: 0.7896 (t80) REVERT: K 90 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7638 (tp30) REVERT: K 108 TYR cc_start: 0.8910 (m-80) cc_final: 0.8213 (m-10) REVERT: K 112 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8488 (mmtm) REVERT: K 256 GLN cc_start: 0.9144 (pt0) cc_final: 0.8802 (tm-30) REVERT: K 308 ARG cc_start: 0.8868 (mpp80) cc_final: 0.8610 (mpp80) REVERT: K 346 TRP cc_start: 0.8494 (p-90) cc_final: 0.4360 (t-100) REVERT: K 357 TYR cc_start: 0.8535 (m-80) cc_final: 0.8134 (m-80) REVERT: K 430 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9183 (tptt) REVERT: K 432 TYR cc_start: 0.8566 (m-80) cc_final: 0.7898 (t80) REVERT: K 433 GLU cc_start: 0.9040 (tt0) cc_final: 0.8793 (tp30) REVERT: L 90 GLU cc_start: 0.8208 (tp30) cc_final: 0.7941 (tp30) REVERT: L 110 ILE cc_start: 0.9182 (mm) cc_final: 0.8966 (mm) REVERT: L 113 GLU cc_start: 0.8721 (mp0) cc_final: 0.8483 (mp0) REVERT: L 224 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: L 259 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9225 (mm) REVERT: L 346 TRP cc_start: 0.8504 (p-90) cc_final: 0.4706 (t-100) REVERT: L 352 LYS cc_start: 0.2956 (mmtt) cc_final: 0.2208 (mmtm) REVERT: L 413 MET cc_start: 0.8411 (mmm) cc_final: 0.8197 (mmm) REVERT: F 22 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7554 (tm-30) REVERT: F 159 TYR cc_start: 0.8631 (m-80) cc_final: 0.8247 (m-80) REVERT: F 251 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.8410 (mtp85) REVERT: F 329 GLN cc_start: 0.9030 (tp40) cc_final: 0.8546 (mm-40) REVERT: F 375 GLN cc_start: 0.8399 (pp30) cc_final: 0.7947 (pp30) REVERT: F 406 MET cc_start: 0.8556 (tpp) cc_final: 0.7718 (tpp) REVERT: D 99 ASN cc_start: 0.8358 (t0) cc_final: 0.7953 (t0) REVERT: D 279 GLN cc_start: 0.8548 (pt0) cc_final: 0.8309 (pt0) REVERT: D 323 MET cc_start: 0.7823 (mpp) cc_final: 0.7279 (mpp) REVERT: D 344 TRP cc_start: 0.8819 (OUTLIER) cc_final: 0.8095 (p-90) REVERT: D 364 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8540 (m) REVERT: D 375 GLN cc_start: 0.8307 (pp30) cc_final: 0.7109 (pp30) REVERT: D 379 LYS cc_start: 0.9204 (mtpt) cc_final: 0.8518 (mtpt) REVERT: D 405 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 422 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7847 (t80) REVERT: G 3 GLU cc_start: 0.6635 (mp0) cc_final: 0.6164 (mp0) REVERT: G 31 ASP cc_start: 0.8911 (m-30) cc_final: 0.8479 (m-30) REVERT: G 50 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: G 67 ASP cc_start: 0.8643 (t0) cc_final: 0.8276 (t0) REVERT: G 121 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8409 (mtm180) REVERT: G 129 CYS cc_start: 0.7497 (t) cc_final: 0.6447 (p) REVERT: G 164 MET cc_start: 0.8479 (mtm) cc_final: 0.8176 (mtt) REVERT: G 194 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8630 (mt-10) REVERT: G 226 ASN cc_start: 0.8968 (m-40) cc_final: 0.8688 (m-40) REVERT: G 310 TYR cc_start: 0.9159 (m-10) cc_final: 0.8827 (m-80) REVERT: G 379 LYS cc_start: 0.9407 (mtpt) cc_final: 0.8903 (mtmm) REVERT: G 403 MET cc_start: 0.7856 (mtp) cc_final: 0.7164 (ttp) REVERT: G 404 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8191 (p0) REVERT: H 31 ASP cc_start: 0.8748 (m-30) cc_final: 0.8521 (m-30) REVERT: H 50 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: H 67 ASP cc_start: 0.8509 (t0) cc_final: 0.7986 (t70) REVERT: H 73 MET cc_start: 0.8906 (mmm) cc_final: 0.8600 (mtm) REVERT: H 121 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8509 (mtm180) REVERT: H 194 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8727 (mt-10) REVERT: H 198 GLU cc_start: 0.8855 (pt0) cc_final: 0.8325 (pt0) REVERT: H 208 TYR cc_start: 0.9086 (m-10) cc_final: 0.8496 (m-80) REVERT: H 282 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: H 291 GLN cc_start: 0.8933 (mp10) cc_final: 0.8706 (mp10) REVERT: H 344 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.8296 (p-90) REVERT: H 370 ASN cc_start: 0.8446 (t0) cc_final: 0.8116 (t0) REVERT: H 375 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6503 (pp30) REVERT: H 379 LYS cc_start: 0.9527 (ttmt) cc_final: 0.8888 (mtmm) REVERT: H 388 MET cc_start: 0.8526 (mtp) cc_final: 0.8058 (mmt) REVERT: H 407 GLU cc_start: 0.8933 (tp30) cc_final: 0.8717 (mm-30) REVERT: H 426 GLN cc_start: 0.7900 (tt0) cc_final: 0.7621 (tp40) REVERT: I 73 MET cc_start: 0.8824 (mmm) cc_final: 0.8498 (mtm) REVERT: I 121 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8446 (mtm180) REVERT: I 195 ASN cc_start: 0.9204 (m-40) cc_final: 0.8982 (m-40) REVERT: I 291 GLN cc_start: 0.8719 (mt0) cc_final: 0.8184 (mp10) REVERT: I 321 MET cc_start: 0.8714 (ptp) cc_final: 0.8470 (ptp) REVERT: I 329 GLN cc_start: 0.9295 (mm-40) cc_final: 0.9031 (mm-40) REVERT: I 363 MET cc_start: 0.8473 (ptp) cc_final: 0.7855 (ptt) REVERT: I 375 GLN cc_start: 0.8297 (pp30) cc_final: 0.7856 (pp30) REVERT: B 50 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: B 122 LYS cc_start: 0.8823 (pttp) cc_final: 0.8491 (ptmm) REVERT: B 257 MET cc_start: 0.8607 (mmp) cc_final: 0.8335 (mmm) REVERT: B 325 GLU cc_start: 0.8513 (pt0) cc_final: 0.8069 (pt0) REVERT: B 328 GLU cc_start: 0.8335 (tt0) cc_final: 0.7973 (tt0) REVERT: B 329 GLN cc_start: 0.9112 (mm110) cc_final: 0.8220 (mm-40) REVERT: B 375 GLN cc_start: 0.8353 (pp30) cc_final: 0.7665 (pp30) REVERT: B 406 MET cc_start: 0.8298 (tpp) cc_final: 0.7434 (tpp) REVERT: B 424 GLN cc_start: 0.8512 (tt0) cc_final: 0.8013 (tt0) outliers start: 338 outliers final: 263 residues processed: 1632 average time/residue: 0.5654 time to fit residues: 1503.3138 Evaluate side-chains 1661 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1376 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 372 GLN Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 280 LYS Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 336 LYS Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 202 ILE Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 360 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 415 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 491 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS F 337 ASN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 337 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41998 Z= 0.235 Angle : 0.657 11.464 57035 Z= 0.334 Chirality : 0.045 0.226 6240 Planarity : 0.005 0.050 7411 Dihedral : 9.943 146.300 5871 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.26 % Favored : 95.70 % Rotamer: Outliers : 6.84 % Allowed : 26.67 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 5136 helix: 1.18 (0.10), residues: 2442 sheet: -0.76 (0.19), residues: 756 loop : -1.68 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 344 HIS 0.009 0.001 HIS F 6 PHE 0.034 0.002 PHE L 255 TYR 0.055 0.001 TYR C 210 ARG 0.007 0.000 ARG H 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1453 time to evaluate : 5.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.8285 (t0) cc_final: 0.8026 (t0) REVERT: A 90 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7800 (tm-30) REVERT: A 96 LYS cc_start: 0.8776 (tppt) cc_final: 0.8492 (tppp) REVERT: A 103 TYR cc_start: 0.8697 (t80) cc_final: 0.8322 (t80) REVERT: A 112 LYS cc_start: 0.8843 (mttt) cc_final: 0.8597 (mttt) REVERT: A 120 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8111 (t0) REVERT: A 121 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7914 (tpt170) REVERT: A 153 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9272 (mp) REVERT: A 214 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8370 (tmm-80) REVERT: A 357 TYR cc_start: 0.8583 (m-80) cc_final: 0.8351 (m-80) REVERT: A 386 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: A 413 MET cc_start: 0.8731 (mtt) cc_final: 0.8517 (mtt) REVERT: A 430 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9148 (tptt) REVERT: C 90 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7972 (tp30) REVERT: C 123 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8450 (tpp80) REVERT: C 169 PHE cc_start: 0.8548 (m-80) cc_final: 0.8339 (m-80) REVERT: C 256 GLN cc_start: 0.9218 (pt0) cc_final: 0.8915 (pm20) REVERT: C 269 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 309 HIS cc_start: 0.8198 (m90) cc_final: 0.7738 (m90) REVERT: C 417 GLU cc_start: 0.8632 (mp0) cc_final: 0.8324 (mp0) REVERT: E 55 GLU cc_start: 0.8495 (tt0) cc_final: 0.8279 (tp30) REVERT: E 76 ASP cc_start: 0.8674 (m-30) cc_final: 0.8467 (m-30) REVERT: E 88 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.4936 (t70) REVERT: E 90 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7756 (tm-30) REVERT: E 210 TYR cc_start: 0.8958 (m-10) cc_final: 0.8705 (m-80) REVERT: E 214 ARG cc_start: 0.8856 (tmm-80) cc_final: 0.8115 (tmm-80) REVERT: E 248 LEU cc_start: 0.9231 (tp) cc_final: 0.9004 (tt) REVERT: E 269 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8548 (pp) REVERT: E 309 HIS cc_start: 0.8220 (m90) cc_final: 0.8004 (m-70) REVERT: E 313 MET cc_start: 0.8424 (mtm) cc_final: 0.8077 (mtm) REVERT: E 430 LYS cc_start: 0.9572 (ttmt) cc_final: 0.9272 (tptt) REVERT: J 33 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8095 (p0) REVERT: J 88 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.5157 (t70) REVERT: J 90 GLU cc_start: 0.8048 (tp30) cc_final: 0.7821 (tp30) REVERT: J 108 TYR cc_start: 0.8839 (m-80) cc_final: 0.8580 (m-80) REVERT: J 176 GLN cc_start: 0.8927 (mp10) cc_final: 0.8534 (mp10) REVERT: J 210 TYR cc_start: 0.8550 (m-10) cc_final: 0.8317 (m-80) REVERT: J 339 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7252 (ptm160) REVERT: J 346 TRP cc_start: 0.8590 (p-90) cc_final: 0.4596 (t-100) REVERT: J 413 MET cc_start: 0.8604 (tpp) cc_final: 0.8385 (mmm) REVERT: J 430 LYS cc_start: 0.9553 (ttmt) cc_final: 0.9244 (tptt) REVERT: J 432 TYR cc_start: 0.8515 (m-80) cc_final: 0.7872 (t80) REVERT: K 90 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: K 256 GLN cc_start: 0.9134 (pt0) cc_final: 0.8846 (tm-30) REVERT: K 346 TRP cc_start: 0.8424 (p-90) cc_final: 0.4314 (t-100) REVERT: K 357 TYR cc_start: 0.8342 (m-80) cc_final: 0.7973 (m-80) REVERT: K 408 TYR cc_start: 0.8942 (m-80) cc_final: 0.8380 (m-80) REVERT: K 415 GLU cc_start: 0.6227 (tm-30) cc_final: 0.5824 (tm-30) REVERT: K 417 GLU cc_start: 0.8546 (tt0) cc_final: 0.8204 (tt0) REVERT: K 430 LYS cc_start: 0.9491 (ttmt) cc_final: 0.9142 (tptt) REVERT: K 432 TYR cc_start: 0.8555 (m-80) cc_final: 0.7860 (t80) REVERT: K 433 GLU cc_start: 0.9014 (tt0) cc_final: 0.8758 (tp30) REVERT: L 90 GLU cc_start: 0.8246 (tp30) cc_final: 0.7954 (tp30) REVERT: L 154 MET cc_start: 0.8652 (mmm) cc_final: 0.8382 (mmp) REVERT: L 224 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: L 346 TRP cc_start: 0.8483 (p-90) cc_final: 0.4642 (t-100) REVERT: L 352 LYS cc_start: 0.2969 (mmtt) cc_final: 0.2746 (mmtt) REVERT: L 394 LYS cc_start: 0.9411 (mppt) cc_final: 0.9008 (mppt) REVERT: L 399 TYR cc_start: 0.8390 (t80) cc_final: 0.8171 (t80) REVERT: F 159 TYR cc_start: 0.8647 (m-80) cc_final: 0.8177 (m-80) REVERT: F 226 ASN cc_start: 0.8988 (m-40) cc_final: 0.8650 (m-40) REVERT: F 251 ARG cc_start: 0.8695 (mtp-110) cc_final: 0.8395 (mtp85) REVERT: F 406 MET cc_start: 0.8562 (tpp) cc_final: 0.7809 (tpp) REVERT: F 410 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8253 (mt-10) REVERT: D 99 ASN cc_start: 0.8298 (t0) cc_final: 0.7902 (t0) REVERT: D 122 LYS cc_start: 0.8829 (pttp) cc_final: 0.8520 (ptmm) REVERT: D 257 MET cc_start: 0.8319 (mmm) cc_final: 0.7949 (mmp) REVERT: D 279 GLN cc_start: 0.8491 (pt0) cc_final: 0.8244 (pt0) REVERT: D 323 MET cc_start: 0.7715 (mpp) cc_final: 0.6841 (mpp) REVERT: D 328 GLU cc_start: 0.8559 (pp20) cc_final: 0.8240 (pp20) REVERT: D 329 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8757 (tp40) REVERT: D 344 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.8072 (p-90) REVERT: D 364 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8570 (m) REVERT: D 375 GLN cc_start: 0.8273 (pp30) cc_final: 0.6939 (pp30) REVERT: D 376 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7521 (mt-10) REVERT: D 379 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8671 (mtmt) REVERT: D 405 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7814 (tm-30) REVERT: D 422 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7817 (t80) REVERT: G 3 GLU cc_start: 0.6627 (mp0) cc_final: 0.6244 (mp0) REVERT: G 14 ASN cc_start: 0.8889 (m-40) cc_final: 0.8631 (m-40) REVERT: G 31 ASP cc_start: 0.8909 (m-30) cc_final: 0.8469 (m-30) REVERT: G 50 TYR cc_start: 0.8403 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: G 67 ASP cc_start: 0.8644 (t0) cc_final: 0.8291 (t0) REVERT: G 101 TRP cc_start: 0.9186 (t60) cc_final: 0.8974 (t60) REVERT: G 121 ARG cc_start: 0.8868 (ttm110) cc_final: 0.8413 (mtm180) REVERT: G 129 CYS cc_start: 0.7458 (t) cc_final: 0.6719 (p) REVERT: G 164 MET cc_start: 0.8452 (mtm) cc_final: 0.8166 (mtt) REVERT: G 194 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8645 (mt-10) REVERT: G 226 ASN cc_start: 0.8957 (m-40) cc_final: 0.8689 (m-40) REVERT: G 297 LYS cc_start: 0.9078 (tppt) cc_final: 0.8807 (tppt) REVERT: G 310 TYR cc_start: 0.9143 (m-10) cc_final: 0.8837 (m-80) REVERT: G 375 GLN cc_start: 0.8386 (pp30) cc_final: 0.8083 (pp30) REVERT: G 403 MET cc_start: 0.7823 (mtp) cc_final: 0.7203 (ttp) REVERT: G 404 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8065 (p0) REVERT: G 406 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7702 (tpt) REVERT: H 31 ASP cc_start: 0.8766 (m-30) cc_final: 0.8471 (m-30) REVERT: H 50 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7907 (m-80) REVERT: H 67 ASP cc_start: 0.8489 (t0) cc_final: 0.8055 (t0) REVERT: H 73 MET cc_start: 0.8847 (mmm) cc_final: 0.8575 (mtm) REVERT: H 121 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8527 (mtm180) REVERT: H 198 GLU cc_start: 0.8740 (pt0) cc_final: 0.8502 (pt0) REVERT: H 208 TYR cc_start: 0.9080 (m-10) cc_final: 0.8570 (m-80) REVERT: H 282 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7842 (ttp80) REVERT: H 291 GLN cc_start: 0.8939 (mp10) cc_final: 0.8716 (mp10) REVERT: H 344 TRP cc_start: 0.9033 (OUTLIER) cc_final: 0.8225 (p-90) REVERT: H 370 ASN cc_start: 0.8413 (t0) cc_final: 0.8029 (t0) REVERT: H 375 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7798 (pp30) REVERT: H 426 GLN cc_start: 0.7835 (tt0) cc_final: 0.7534 (tm-30) REVERT: I 73 MET cc_start: 0.8875 (mmm) cc_final: 0.8462 (mtm) REVERT: I 121 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8411 (mtm180) REVERT: I 291 GLN cc_start: 0.8746 (mt0) cc_final: 0.8218 (mp10) REVERT: I 329 GLN cc_start: 0.9286 (mm-40) cc_final: 0.9070 (mm-40) REVERT: I 363 MET cc_start: 0.8401 (ptp) cc_final: 0.7971 (ptt) REVERT: B 50 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: B 328 GLU cc_start: 0.8303 (tt0) cc_final: 0.7936 (tt0) REVERT: B 329 GLN cc_start: 0.9100 (mm110) cc_final: 0.8210 (mm-40) REVERT: B 406 MET cc_start: 0.8261 (tpp) cc_final: 0.7474 (tpp) REVERT: B 410 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 424 GLN cc_start: 0.8533 (tt0) cc_final: 0.8020 (tt0) outliers start: 302 outliers final: 239 residues processed: 1624 average time/residue: 0.5293 time to fit residues: 1396.1057 Evaluate side-chains 1645 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1384 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 386 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 HIS J 300 ASN J 393 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 393 HIS ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN G 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 41998 Z= 0.309 Angle : 0.695 11.650 57035 Z= 0.356 Chirality : 0.046 0.231 6240 Planarity : 0.005 0.051 7411 Dihedral : 10.054 146.912 5862 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.74 % Rotamer: Outliers : 7.15 % Allowed : 27.26 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 5136 helix: 1.17 (0.10), residues: 2412 sheet: -0.68 (0.19), residues: 768 loop : -1.64 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 344 HIS 0.012 0.001 HIS F 6 PHE 0.041 0.002 PHE L 255 TYR 0.060 0.002 TYR C 210 ARG 0.010 0.001 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1724 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1408 time to evaluate : 5.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8432 (p0) REVERT: A 69 ASP cc_start: 0.8314 (t0) cc_final: 0.8070 (t0) REVERT: A 90 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7816 (tm-30) REVERT: A 96 LYS cc_start: 0.8807 (tppt) cc_final: 0.8601 (tppp) REVERT: A 103 TYR cc_start: 0.8723 (t80) cc_final: 0.8318 (t80) REVERT: A 120 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8213 (t0) REVERT: A 121 ARG cc_start: 0.8372 (mmm160) cc_final: 0.7959 (tpt170) REVERT: A 138 PHE cc_start: 0.8240 (m-80) cc_final: 0.7958 (m-80) REVERT: A 153 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9383 (mp) REVERT: A 214 ARG cc_start: 0.8782 (tmm-80) cc_final: 0.8426 (tmm-80) REVERT: A 357 TYR cc_start: 0.8678 (m-80) cc_final: 0.8409 (m-80) REVERT: A 386 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: A 430 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9183 (tptt) REVERT: C 90 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8031 (tp30) REVERT: C 123 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8460 (tpp80) REVERT: C 256 GLN cc_start: 0.9211 (pt0) cc_final: 0.8902 (pm20) REVERT: C 269 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8488 (pp) REVERT: C 309 HIS cc_start: 0.8233 (m90) cc_final: 0.7712 (m90) REVERT: C 417 GLU cc_start: 0.8671 (mp0) cc_final: 0.8348 (mp0) REVERT: E 76 ASP cc_start: 0.8720 (m-30) cc_final: 0.8500 (m-30) REVERT: E 90 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7798 (tm-30) REVERT: E 210 TYR cc_start: 0.8976 (m-10) cc_final: 0.8708 (m-80) REVERT: E 214 ARG cc_start: 0.8804 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: E 248 LEU cc_start: 0.9243 (tp) cc_final: 0.8984 (tt) REVERT: E 309 HIS cc_start: 0.8191 (m90) cc_final: 0.7927 (m-70) REVERT: E 313 MET cc_start: 0.8495 (mtm) cc_final: 0.8160 (mtm) REVERT: E 430 LYS cc_start: 0.9576 (ttmt) cc_final: 0.9279 (tptt) REVERT: J 33 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8116 (p0) REVERT: J 88 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.5030 (t70) REVERT: J 90 GLU cc_start: 0.8027 (tp30) cc_final: 0.7794 (tp30) REVERT: J 108 TYR cc_start: 0.8869 (m-80) cc_final: 0.8609 (m-80) REVERT: J 176 GLN cc_start: 0.9013 (mp10) cc_final: 0.8552 (mp10) REVERT: J 210 TYR cc_start: 0.8588 (m-10) cc_final: 0.8262 (m-80) REVERT: J 339 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7302 (ptm160) REVERT: J 346 TRP cc_start: 0.8611 (p-90) cc_final: 0.4618 (t-100) REVERT: J 430 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9240 (tptt) REVERT: J 432 TYR cc_start: 0.8557 (m-80) cc_final: 0.8015 (t80) REVERT: K 90 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: K 256 GLN cc_start: 0.9202 (pt0) cc_final: 0.8849 (tm-30) REVERT: K 346 TRP cc_start: 0.8457 (p-90) cc_final: 0.4310 (t-100) REVERT: K 357 TYR cc_start: 0.8387 (m-80) cc_final: 0.8062 (m-80) REVERT: K 430 LYS cc_start: 0.9508 (ttmt) cc_final: 0.9165 (tptt) REVERT: K 432 TYR cc_start: 0.8579 (m-80) cc_final: 0.7932 (t80) REVERT: K 433 GLU cc_start: 0.9033 (tt0) cc_final: 0.8773 (tp30) REVERT: L 11 GLN cc_start: 0.7919 (tt0) cc_final: 0.7715 (tt0) REVERT: L 109 THR cc_start: 0.8669 (m) cc_final: 0.8198 (p) REVERT: L 113 GLU cc_start: 0.8701 (mp0) cc_final: 0.8451 (mp0) REVERT: L 224 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8014 (m-10) REVERT: L 232 SER cc_start: 0.9189 (m) cc_final: 0.8743 (p) REVERT: L 259 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9256 (mm) REVERT: L 346 TRP cc_start: 0.8527 (p-90) cc_final: 0.4638 (t-100) REVERT: L 352 LYS cc_start: 0.3160 (mmtt) cc_final: 0.2661 (mmtt) REVERT: L 394 LYS cc_start: 0.9414 (mppt) cc_final: 0.9025 (mppt) REVERT: F 122 LYS cc_start: 0.8946 (pttm) cc_final: 0.8623 (ptmm) REVERT: F 159 TYR cc_start: 0.8633 (m-80) cc_final: 0.8203 (m-80) REVERT: F 166 THR cc_start: 0.8959 (m) cc_final: 0.8337 (p) REVERT: F 213 ARG cc_start: 0.7609 (ttp-110) cc_final: 0.7269 (ttp-110) REVERT: F 226 ASN cc_start: 0.9128 (m-40) cc_final: 0.8719 (m-40) REVERT: F 251 ARG cc_start: 0.8742 (mtp-110) cc_final: 0.8412 (mtp85) REVERT: F 329 GLN cc_start: 0.9011 (tp40) cc_final: 0.8594 (mm-40) REVERT: F 375 GLN cc_start: 0.8398 (pp30) cc_final: 0.8055 (pp30) REVERT: F 406 MET cc_start: 0.8614 (tpp) cc_final: 0.7824 (tpp) REVERT: F 410 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8214 (mt-10) REVERT: D 99 ASN cc_start: 0.8381 (t0) cc_final: 0.7995 (t0) REVERT: D 122 LYS cc_start: 0.8842 (pttp) cc_final: 0.8628 (ptmm) REVERT: D 123 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: D 257 MET cc_start: 0.8442 (mmm) cc_final: 0.8061 (mmp) REVERT: D 279 GLN cc_start: 0.8506 (pt0) cc_final: 0.8283 (pt0) REVERT: D 323 MET cc_start: 0.7778 (mpp) cc_final: 0.7295 (mpp) REVERT: D 328 GLU cc_start: 0.8576 (pp20) cc_final: 0.8210 (pp20) REVERT: D 329 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8729 (tp40) REVERT: D 344 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.8065 (p-90) REVERT: D 364 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8587 (m) REVERT: D 375 GLN cc_start: 0.8318 (pp30) cc_final: 0.7155 (pp30) REVERT: D 376 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7820 (mt-10) REVERT: D 379 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8538 (mtpt) REVERT: D 405 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 422 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7834 (t80) REVERT: G 14 ASN cc_start: 0.8870 (m-40) cc_final: 0.8626 (m-40) REVERT: G 31 ASP cc_start: 0.8913 (m-30) cc_final: 0.8467 (m-30) REVERT: G 50 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: G 67 ASP cc_start: 0.8540 (t0) cc_final: 0.8268 (t0) REVERT: G 121 ARG cc_start: 0.8880 (ttm110) cc_final: 0.8450 (mtm180) REVERT: G 164 MET cc_start: 0.8508 (mtm) cc_final: 0.8206 (mtt) REVERT: G 174 LYS cc_start: 0.9351 (mtmm) cc_final: 0.8786 (mtmm) REVERT: G 209 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8745 (p0) REVERT: G 226 ASN cc_start: 0.9037 (m-40) cc_final: 0.8748 (m-40) REVERT: G 232 THR cc_start: 0.8755 (m) cc_final: 0.8533 (m) REVERT: G 291 GLN cc_start: 0.8728 (mp10) cc_final: 0.8522 (mp10) REVERT: G 297 LYS cc_start: 0.9074 (tppt) cc_final: 0.8721 (tppt) REVERT: G 310 TYR cc_start: 0.9186 (m-10) cc_final: 0.8892 (m-80) REVERT: G 379 LYS cc_start: 0.9495 (mtpt) cc_final: 0.9064 (mtmm) REVERT: G 403 MET cc_start: 0.7862 (mtp) cc_final: 0.7187 (ttp) REVERT: G 404 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8087 (p0) REVERT: H 31 ASP cc_start: 0.8773 (m-30) cc_final: 0.8533 (m-30) REVERT: H 67 ASP cc_start: 0.8417 (t0) cc_final: 0.8040 (t0) REVERT: H 73 MET cc_start: 0.8808 (mmm) cc_final: 0.8581 (mtm) REVERT: H 121 ARG cc_start: 0.8835 (ttm110) cc_final: 0.8558 (mtm180) REVERT: H 198 GLU cc_start: 0.8804 (pt0) cc_final: 0.8271 (pt0) REVERT: H 208 TYR cc_start: 0.9094 (m-10) cc_final: 0.8617 (m-80) REVERT: H 282 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7913 (ttp80) REVERT: H 291 GLN cc_start: 0.8946 (mp10) cc_final: 0.8723 (mp10) REVERT: H 344 TRP cc_start: 0.9062 (OUTLIER) cc_final: 0.8308 (p-90) REVERT: H 370 ASN cc_start: 0.8438 (t0) cc_final: 0.8054 (t0) REVERT: H 375 GLN cc_start: 0.8299 (pp30) cc_final: 0.7793 (pp30) REVERT: H 376 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8265 (mt-10) REVERT: H 388 MET cc_start: 0.8536 (mtp) cc_final: 0.8051 (mmt) REVERT: H 426 GLN cc_start: 0.7886 (tt0) cc_final: 0.7575 (tm-30) REVERT: I 73 MET cc_start: 0.8877 (mmm) cc_final: 0.8481 (mtm) REVERT: I 121 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8569 (mtm180) REVERT: I 195 ASN cc_start: 0.9242 (m-40) cc_final: 0.8994 (m-40) REVERT: I 291 GLN cc_start: 0.8772 (mt0) cc_final: 0.8211 (mp10) REVERT: I 329 GLN cc_start: 0.9288 (mm-40) cc_final: 0.9079 (mm-40) REVERT: I 363 MET cc_start: 0.8441 (ptp) cc_final: 0.7902 (ptt) REVERT: I 410 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8321 (mp0) REVERT: B 50 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: B 122 LYS cc_start: 0.8846 (pttp) cc_final: 0.8462 (ptmm) REVERT: B 284 LEU cc_start: 0.7745 (pt) cc_final: 0.7431 (pt) REVERT: B 328 GLU cc_start: 0.8304 (tt0) cc_final: 0.7930 (tt0) REVERT: B 329 GLN cc_start: 0.9131 (mm110) cc_final: 0.8296 (mm-40) REVERT: B 406 MET cc_start: 0.8370 (tpp) cc_final: 0.7571 (tpp) REVERT: B 410 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 424 GLN cc_start: 0.8593 (tt0) cc_final: 0.8071 (tt0) outliers start: 316 outliers final: 261 residues processed: 1591 average time/residue: 0.5226 time to fit residues: 1357.0279 Evaluate side-chains 1656 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1374 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 304 LYS Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 205 GLU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 9.9990 chunk 470 optimal weight: 1.9990 chunk 429 optimal weight: 10.0000 chunk 458 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 chunk 359 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 413 optimal weight: 4.9990 chunk 433 optimal weight: 6.9990 chunk 456 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 192 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 HIS C 285 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 393 HIS ** L 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS D 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 227 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 41998 Z= 0.273 Angle : 0.704 12.191 57035 Z= 0.358 Chirality : 0.046 0.224 6240 Planarity : 0.005 0.053 7411 Dihedral : 9.921 146.116 5856 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 6.54 % Allowed : 28.41 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.26 (0.12), residues: 5136 helix: 1.19 (0.10), residues: 2412 sheet: -0.99 (0.19), residues: 750 loop : -1.54 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 344 HIS 0.010 0.001 HIS D 190 PHE 0.042 0.002 PHE L 255 TYR 0.068 0.002 TYR L 210 ARG 0.008 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1713 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1424 time to evaluate : 4.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8409 (p0) REVERT: A 69 ASP cc_start: 0.8310 (t0) cc_final: 0.8042 (t0) REVERT: A 90 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7788 (tm-30) REVERT: A 96 LYS cc_start: 0.8855 (tppt) cc_final: 0.8638 (tppp) REVERT: A 103 TYR cc_start: 0.8659 (t80) cc_final: 0.8298 (t80) REVERT: A 120 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8259 (t0) REVERT: A 121 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7967 (tpt170) REVERT: A 153 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9341 (mp) REVERT: A 357 TYR cc_start: 0.8641 (m-80) cc_final: 0.8377 (m-80) REVERT: A 386 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: A 402 ARG cc_start: 0.8752 (mmt-90) cc_final: 0.8530 (mmt-90) REVERT: A 430 LYS cc_start: 0.9431 (ttmt) cc_final: 0.9191 (tptt) REVERT: C 52 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: C 90 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8011 (tp30) REVERT: C 123 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8468 (tpp80) REVERT: C 138 PHE cc_start: 0.8409 (m-80) cc_final: 0.7999 (m-80) REVERT: C 269 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8512 (pp) REVERT: C 309 HIS cc_start: 0.8229 (m90) cc_final: 0.7694 (m90) REVERT: C 417 GLU cc_start: 0.8620 (mp0) cc_final: 0.8327 (mp0) REVERT: E 76 ASP cc_start: 0.8709 (m-30) cc_final: 0.8484 (m-30) REVERT: E 90 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7773 (tm-30) REVERT: E 214 ARG cc_start: 0.8870 (tmm-80) cc_final: 0.8153 (tmm-80) REVERT: E 248 LEU cc_start: 0.9241 (tp) cc_final: 0.9013 (tt) REVERT: E 309 HIS cc_start: 0.8167 (m90) cc_final: 0.7898 (m-70) REVERT: E 313 MET cc_start: 0.8471 (mtm) cc_final: 0.8132 (mtm) REVERT: E 357 TYR cc_start: 0.8515 (m-80) cc_final: 0.8306 (m-80) REVERT: E 408 TYR cc_start: 0.9246 (m-80) cc_final: 0.9026 (m-80) REVERT: E 430 LYS cc_start: 0.9574 (ttmt) cc_final: 0.9280 (tptt) REVERT: J 33 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8121 (p0) REVERT: J 88 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.5108 (t70) REVERT: J 210 TYR cc_start: 0.8521 (m-10) cc_final: 0.8209 (m-80) REVERT: J 248 LEU cc_start: 0.9074 (tp) cc_final: 0.8683 (tt) REVERT: J 300 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8704 (t0) REVERT: J 339 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7263 (ptm160) REVERT: J 346 TRP cc_start: 0.8617 (p-90) cc_final: 0.4552 (t-100) REVERT: J 381 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7533 (p) REVERT: J 413 MET cc_start: 0.8502 (mmm) cc_final: 0.8252 (mmm) REVERT: J 430 LYS cc_start: 0.9552 (ttmt) cc_final: 0.9228 (tptt) REVERT: J 432 TYR cc_start: 0.8545 (m-80) cc_final: 0.7970 (t80) REVERT: K 90 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: K 251 ASP cc_start: 0.8233 (t70) cc_final: 0.7974 (p0) REVERT: K 256 GLN cc_start: 0.9201 (pt0) cc_final: 0.8859 (tm-30) REVERT: K 346 TRP cc_start: 0.8440 (p-90) cc_final: 0.4283 (t-100) REVERT: K 357 TYR cc_start: 0.8396 (m-80) cc_final: 0.8022 (m-80) REVERT: K 430 LYS cc_start: 0.9505 (ttmt) cc_final: 0.9150 (tptt) REVERT: K 432 TYR cc_start: 0.8532 (m-80) cc_final: 0.7926 (t80) REVERT: K 433 GLU cc_start: 0.9038 (tt0) cc_final: 0.8765 (tp30) REVERT: L 109 THR cc_start: 0.8687 (m) cc_final: 0.8098 (p) REVERT: L 113 GLU cc_start: 0.8719 (mp0) cc_final: 0.8336 (mp0) REVERT: L 224 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7939 (m-10) REVERT: L 232 SER cc_start: 0.9161 (m) cc_final: 0.8709 (p) REVERT: L 259 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9246 (mm) REVERT: L 346 TRP cc_start: 0.8404 (p-90) cc_final: 0.4634 (t-100) REVERT: L 352 LYS cc_start: 0.3098 (mmtt) cc_final: 0.2712 (mptt) REVERT: L 372 GLN cc_start: 0.8685 (mp10) cc_final: 0.8483 (pm20) REVERT: L 394 LYS cc_start: 0.9419 (mppt) cc_final: 0.9021 (mppt) REVERT: F 122 LYS cc_start: 0.8972 (pttm) cc_final: 0.8654 (ptmm) REVERT: F 166 THR cc_start: 0.8819 (m) cc_final: 0.8167 (p) REVERT: F 213 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.7437 (ttp-110) REVERT: F 226 ASN cc_start: 0.9121 (m-40) cc_final: 0.8641 (m-40) REVERT: F 251 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8406 (mtp85) REVERT: F 406 MET cc_start: 0.8604 (tpp) cc_final: 0.7729 (tpp) REVERT: F 410 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8084 (mt-10) REVERT: F 422 TYR cc_start: 0.8888 (OUTLIER) cc_final: 0.7962 (t80) REVERT: D 99 ASN cc_start: 0.8359 (t0) cc_final: 0.7927 (t0) REVERT: D 122 LYS cc_start: 0.8857 (pttp) cc_final: 0.8576 (ptmm) REVERT: D 257 MET cc_start: 0.8398 (mmm) cc_final: 0.8042 (mmp) REVERT: D 279 GLN cc_start: 0.8483 (pt0) cc_final: 0.8257 (pt0) REVERT: D 323 MET cc_start: 0.7802 (mpp) cc_final: 0.7307 (mpp) REVERT: D 329 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8978 (tp40) REVERT: D 344 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.8071 (p-90) REVERT: D 364 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8619 (m) REVERT: D 375 GLN cc_start: 0.8294 (pp30) cc_final: 0.7087 (pp30) REVERT: D 376 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 379 LYS cc_start: 0.9234 (mtpt) cc_final: 0.8664 (mtpt) REVERT: D 405 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 422 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7842 (t80) REVERT: G 14 ASN cc_start: 0.8861 (m-40) cc_final: 0.8611 (m-40) REVERT: G 31 ASP cc_start: 0.8929 (m-30) cc_final: 0.8472 (m-30) REVERT: G 50 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: G 67 ASP cc_start: 0.8498 (t0) cc_final: 0.8274 (t70) REVERT: G 121 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8457 (mtm180) REVERT: G 164 MET cc_start: 0.8500 (mtm) cc_final: 0.8201 (mtt) REVERT: G 226 ASN cc_start: 0.9049 (m-40) cc_final: 0.8763 (m-40) REVERT: G 291 GLN cc_start: 0.8721 (mp10) cc_final: 0.8476 (mp10) REVERT: G 297 LYS cc_start: 0.9060 (tppt) cc_final: 0.8787 (tppt) REVERT: G 310 TYR cc_start: 0.9174 (m-10) cc_final: 0.8910 (m-80) REVERT: G 375 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7838 (pp30) REVERT: G 403 MET cc_start: 0.7831 (mtp) cc_final: 0.7199 (ttp) REVERT: G 404 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8088 (p0) REVERT: G 405 GLU cc_start: 0.7977 (pp20) cc_final: 0.7735 (pp20) REVERT: G 410 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8698 (mt-10) REVERT: H 31 ASP cc_start: 0.8778 (m-30) cc_final: 0.8535 (m-30) REVERT: H 67 ASP cc_start: 0.8383 (t0) cc_final: 0.8063 (t0) REVERT: H 121 ARG cc_start: 0.8810 (ttm110) cc_final: 0.8544 (mtm180) REVERT: H 198 GLU cc_start: 0.8747 (pt0) cc_final: 0.8248 (pt0) REVERT: H 208 TYR cc_start: 0.9091 (m-10) cc_final: 0.8608 (m-80) REVERT: H 282 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7916 (ttp80) REVERT: H 291 GLN cc_start: 0.8937 (mp10) cc_final: 0.8720 (mp10) REVERT: H 337 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7396 (t0) REVERT: H 344 TRP cc_start: 0.9046 (OUTLIER) cc_final: 0.8283 (p-90) REVERT: H 370 ASN cc_start: 0.8401 (t0) cc_final: 0.7999 (t0) REVERT: H 375 GLN cc_start: 0.8230 (pp30) cc_final: 0.6471 (pp30) REVERT: H 379 LYS cc_start: 0.9530 (ttmt) cc_final: 0.8867 (mtmm) REVERT: H 406 MET cc_start: 0.8019 (mmm) cc_final: 0.7531 (mmm) REVERT: H 426 GLN cc_start: 0.7868 (tt0) cc_final: 0.7551 (tm-30) REVERT: I 73 MET cc_start: 0.8854 (mmm) cc_final: 0.8479 (mtm) REVERT: I 121 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8505 (mtm180) REVERT: I 195 ASN cc_start: 0.9233 (m-40) cc_final: 0.8992 (m-40) REVERT: I 198 GLU cc_start: 0.8735 (pt0) cc_final: 0.8408 (pt0) REVERT: I 363 MET cc_start: 0.8383 (ptp) cc_final: 0.7843 (ptt) REVERT: I 375 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7644 (pp30) REVERT: I 410 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8322 (mp0) REVERT: B 50 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: B 122 LYS cc_start: 0.8837 (pttp) cc_final: 0.8466 (ptmm) REVERT: B 284 LEU cc_start: 0.7740 (pt) cc_final: 0.7425 (pt) REVERT: B 325 GLU cc_start: 0.8488 (pt0) cc_final: 0.8246 (pt0) REVERT: B 406 MET cc_start: 0.8346 (tpp) cc_final: 0.7611 (tpp) REVERT: B 410 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8014 (mt-10) outliers start: 289 outliers final: 240 residues processed: 1588 average time/residue: 0.5750 time to fit residues: 1505.8967 Evaluate side-chains 1646 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1380 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 9.9990 chunk 484 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 336 optimal weight: 9.9990 chunk 508 optimal weight: 6.9990 chunk 467 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 393 HIS L 8 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN D 307 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 423 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 41998 Z= 0.350 Angle : 0.750 12.626 57035 Z= 0.384 Chirality : 0.048 0.291 6240 Planarity : 0.005 0.055 7411 Dihedral : 10.037 147.036 5850 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 6.66 % Allowed : 28.71 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 5136 helix: 0.99 (0.10), residues: 2424 sheet: -1.01 (0.19), residues: 732 loop : -1.70 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 388 HIS 0.011 0.001 HIS D 190 PHE 0.045 0.002 PHE L 255 TYR 0.074 0.002 TYR C 210 ARG 0.011 0.001 ARG J 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1671 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1377 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8438 (p0) REVERT: A 69 ASP cc_start: 0.8266 (t0) cc_final: 0.8032 (t0) REVERT: A 90 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7874 (tp30) REVERT: A 96 LYS cc_start: 0.8856 (tppt) cc_final: 0.8606 (tppp) REVERT: A 120 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8302 (t70) REVERT: A 121 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8087 (tpt170) REVERT: A 153 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9317 (mp) REVERT: A 224 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: A 357 TYR cc_start: 0.8734 (m-80) cc_final: 0.8427 (m-80) REVERT: A 430 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9200 (tptt) REVERT: C 90 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8045 (tp30) REVERT: C 123 ARG cc_start: 0.8705 (ttm170) cc_final: 0.8490 (tpp80) REVERT: C 138 PHE cc_start: 0.8516 (m-80) cc_final: 0.7946 (m-80) REVERT: C 269 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8524 (pp) REVERT: C 309 HIS cc_start: 0.8260 (m90) cc_final: 0.7704 (m90) REVERT: C 417 GLU cc_start: 0.8619 (mp0) cc_final: 0.8316 (mp0) REVERT: E 76 ASP cc_start: 0.8694 (m-30) cc_final: 0.8486 (m-30) REVERT: E 90 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7829 (tm-30) REVERT: E 214 ARG cc_start: 0.8900 (tmm-80) cc_final: 0.8272 (tmm-80) REVERT: E 248 LEU cc_start: 0.9260 (tp) cc_final: 0.9005 (tt) REVERT: E 313 MET cc_start: 0.8491 (mtm) cc_final: 0.8170 (mtm) REVERT: E 357 TYR cc_start: 0.8626 (m-80) cc_final: 0.8397 (m-80) REVERT: E 430 LYS cc_start: 0.9585 (ttmt) cc_final: 0.9299 (tptt) REVERT: J 33 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8553 (p0) REVERT: J 88 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.4980 (t70) REVERT: J 176 GLN cc_start: 0.9126 (mp10) cc_final: 0.8654 (mp10) REVERT: J 300 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8781 (t0) REVERT: J 339 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7301 (ptm160) REVERT: J 346 TRP cc_start: 0.8648 (p-90) cc_final: 0.4563 (t-100) REVERT: J 381 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7614 (p) REVERT: J 430 LYS cc_start: 0.9561 (ttmt) cc_final: 0.9238 (tptt) REVERT: J 432 TYR cc_start: 0.8557 (m-80) cc_final: 0.8045 (t80) REVERT: K 90 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: K 251 ASP cc_start: 0.8322 (t70) cc_final: 0.7986 (p0) REVERT: K 256 GLN cc_start: 0.9219 (pt0) cc_final: 0.8867 (tm-30) REVERT: K 300 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8756 (t0) REVERT: K 346 TRP cc_start: 0.8600 (p-90) cc_final: 0.4252 (t-100) REVERT: K 357 TYR cc_start: 0.8452 (m-80) cc_final: 0.8125 (m-80) REVERT: K 430 LYS cc_start: 0.9511 (ttmt) cc_final: 0.9156 (tptt) REVERT: K 432 TYR cc_start: 0.8544 (m-80) cc_final: 0.7922 (t80) REVERT: K 433 GLU cc_start: 0.9039 (tt0) cc_final: 0.8809 (tp30) REVERT: L 109 THR cc_start: 0.8645 (m) cc_final: 0.8328 (p) REVERT: L 224 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: L 232 SER cc_start: 0.9165 (m) cc_final: 0.8727 (p) REVERT: L 259 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9232 (mm) REVERT: L 346 TRP cc_start: 0.8428 (p-90) cc_final: 0.4654 (t-100) REVERT: L 352 LYS cc_start: 0.3220 (mmtt) cc_final: 0.2900 (mptt) REVERT: L 372 GLN cc_start: 0.8658 (mp10) cc_final: 0.8437 (pm20) REVERT: L 394 LYS cc_start: 0.9415 (mppt) cc_final: 0.9034 (mppt) REVERT: F 122 LYS cc_start: 0.8982 (pttm) cc_final: 0.8674 (ptmm) REVERT: F 166 THR cc_start: 0.8862 (m) cc_final: 0.8210 (p) REVERT: F 226 ASN cc_start: 0.9102 (m-40) cc_final: 0.8685 (m-40) REVERT: F 251 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8414 (mtp85) REVERT: F 406 MET cc_start: 0.8590 (tpp) cc_final: 0.7707 (tpp) REVERT: F 410 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 422 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7991 (t80) REVERT: D 99 ASN cc_start: 0.8383 (t0) cc_final: 0.8022 (t0) REVERT: D 123 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8561 (mm-30) REVERT: D 257 MET cc_start: 0.8488 (mmm) cc_final: 0.8130 (mmp) REVERT: D 279 GLN cc_start: 0.8538 (pt0) cc_final: 0.8287 (pt0) REVERT: D 323 MET cc_start: 0.7829 (mpp) cc_final: 0.7545 (mpp) REVERT: D 328 GLU cc_start: 0.8588 (pp20) cc_final: 0.8207 (pp20) REVERT: D 329 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8748 (tp40) REVERT: D 344 TRP cc_start: 0.8928 (OUTLIER) cc_final: 0.8001 (p-90) REVERT: D 364 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8648 (m) REVERT: D 375 GLN cc_start: 0.8253 (pp30) cc_final: 0.7006 (pp30) REVERT: D 376 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7853 (mt-10) REVERT: D 379 LYS cc_start: 0.9206 (mtpt) cc_final: 0.8527 (mtpt) REVERT: D 405 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 422 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7905 (t80) REVERT: G 14 ASN cc_start: 0.8877 (m-40) cc_final: 0.8620 (m-40) REVERT: G 31 ASP cc_start: 0.8905 (m-30) cc_final: 0.8457 (m-30) REVERT: G 50 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: G 67 ASP cc_start: 0.8562 (t0) cc_final: 0.8230 (t70) REVERT: G 121 ARG cc_start: 0.8892 (ttm110) cc_final: 0.8476 (mtm180) REVERT: G 164 MET cc_start: 0.8557 (mtm) cc_final: 0.8239 (mtt) REVERT: G 194 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8690 (mt-10) REVERT: G 226 ASN cc_start: 0.9042 (m-40) cc_final: 0.8759 (m-40) REVERT: G 232 THR cc_start: 0.8743 (m) cc_final: 0.8522 (m) REVERT: G 291 GLN cc_start: 0.8744 (mp10) cc_final: 0.8515 (mp10) REVERT: G 310 TYR cc_start: 0.9227 (m-10) cc_final: 0.8922 (m-80) REVERT: G 375 GLN cc_start: 0.8461 (pp30) cc_final: 0.8002 (pp30) REVERT: G 403 MET cc_start: 0.7862 (mtp) cc_final: 0.7097 (ttp) REVERT: G 404 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7670 (p0) REVERT: G 410 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8704 (mt-10) REVERT: H 31 ASP cc_start: 0.8784 (m-30) cc_final: 0.8580 (m-30) REVERT: H 45 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7925 (mt-10) REVERT: H 67 ASP cc_start: 0.8391 (t0) cc_final: 0.7975 (t0) REVERT: H 121 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8498 (mtm180) REVERT: H 198 GLU cc_start: 0.8822 (pt0) cc_final: 0.8254 (pt0) REVERT: H 208 TYR cc_start: 0.9123 (m-10) cc_final: 0.8626 (m-80) REVERT: H 282 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7938 (ttp80) REVERT: H 291 GLN cc_start: 0.8956 (mp10) cc_final: 0.8724 (mp10) REVERT: H 337 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7416 (t0) REVERT: H 344 TRP cc_start: 0.9074 (OUTLIER) cc_final: 0.8345 (p-90) REVERT: H 370 ASN cc_start: 0.8415 (t0) cc_final: 0.8029 (t0) REVERT: H 375 GLN cc_start: 0.8232 (pp30) cc_final: 0.7604 (pp30) REVERT: H 426 GLN cc_start: 0.7917 (tt0) cc_final: 0.7630 (tp40) REVERT: I 73 MET cc_start: 0.8866 (mmm) cc_final: 0.8534 (mtm) REVERT: I 121 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8562 (mtm180) REVERT: I 198 GLU cc_start: 0.8826 (pt0) cc_final: 0.8429 (pt0) REVERT: I 299 MET cc_start: 0.8037 (mmp) cc_final: 0.7725 (mmp) REVERT: I 329 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8683 (mm-40) REVERT: I 363 MET cc_start: 0.8379 (ptp) cc_final: 0.7835 (ptt) REVERT: I 410 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8373 (mp0) REVERT: B 50 TYR cc_start: 0.8288 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: B 122 LYS cc_start: 0.8883 (pttp) cc_final: 0.8557 (ptmm) REVERT: B 226 ASN cc_start: 0.9064 (m-40) cc_final: 0.8651 (m-40) REVERT: B 406 MET cc_start: 0.8338 (tpp) cc_final: 0.7589 (tpp) REVERT: B 410 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8063 (mt-10) outliers start: 294 outliers final: 250 residues processed: 1551 average time/residue: 0.5281 time to fit residues: 1337.8064 Evaluate side-chains 1640 residues out of total 4428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1365 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 129 CYS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 304 LYS Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 338 LYS Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 338 LYS Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 197 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 41 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 165 ASN Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 404 ASP Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 165 ASN Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 202 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 335 SER Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 364 SER Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 10.0000 chunk 430 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 373 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 405 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 416 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN C 285 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN K 393 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 298 ASN D 307 HIS D 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.107571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090835 restraints weight = 89506.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094095 restraints weight = 44921.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.096322 restraints weight = 27415.567| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 41998 Z= 0.205 Angle : 0.732 12.932 57035 Z= 0.370 Chirality : 0.046 0.292 6240 Planarity : 0.005 0.053 7411 Dihedral : 9.746 144.654 5848 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.09 % Rotamer: Outliers : 4.55 % Allowed : 31.20 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 5136 helix: 1.09 (0.10), residues: 2442 sheet: -0.63 (0.20), residues: 690 loop : -1.70 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 21 HIS 0.009 0.001 HIS B 6 PHE 0.046 0.002 PHE D 20 TYR 0.072 0.001 TYR L 210 ARG 0.011 0.001 ARG J 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19595.89 seconds wall clock time: 348 minutes 2.67 seconds (20882.67 seconds total)