Starting phenix.real_space_refine on Mon Mar 18 16:56:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6val_21142/03_2024/6val_21142.pdb" } resolution = 3.87 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= 0.072 sd= 0.561 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 165 5.16 5 C 14047 2.51 5 N 3663 2.21 5 O 3740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21615 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "I" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "J" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1965 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 11.29, per 1000 atoms: 0.52 Number of scatterers: 21615 At special positions: 0 Unit cell: (145.22, 147.34, 99.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 165 16.00 O 3740 8.00 N 3663 7.00 C 14047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 126 " distance=2.03 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: 8.44 Conformation dependent library (CDL) restraints added in 4.0 seconds 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 107 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.671A pdb=" N VAL A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR A 280 " --> pdb=" O TRP A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 107 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.636A pdb=" N THR B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 107 Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 265 Processing helix chain 'C' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR C 280 " --> pdb=" O TRP C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 265 Processing helix chain 'D' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR D 280 " --> pdb=" O TRP D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 107 Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE E 248 " --> pdb=" O ASN E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 265 Processing helix chain 'E' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR E 280 " --> pdb=" O TRP E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.944A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA F 174 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE F 248 " --> pdb=" O ASN F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 265 Processing helix chain 'F' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR F 280 " --> pdb=" O TRP F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU F 304 " --> pdb=" O TRP F 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 107 Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE G 248 " --> pdb=" O ASN G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 265 Processing helix chain 'G' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR G 280 " --> pdb=" O TRP G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU G 304 " --> pdb=" O TRP G 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 107 Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA H 174 " --> pdb=" O ALA H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE H 248 " --> pdb=" O ASN H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 Processing helix chain 'H' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR H 280 " --> pdb=" O TRP H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU H 304 " --> pdb=" O TRP H 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY I 54 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET I 76 " --> pdb=" O ASN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 107 Processing helix chain 'I' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 128 Processing helix chain 'I' and resid 147 through 157 Processing helix chain 'I' and resid 170 through 208 removed outlier: 4.059A pdb=" N ALA I 174 " --> pdb=" O ALA I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 249 removed outlier: 3.519A pdb=" N PHE I 248 " --> pdb=" O ASN I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 265 Processing helix chain 'I' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR I 280 " --> pdb=" O TRP I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU I 304 " --> pdb=" O TRP I 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.946A pdb=" N LEU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY J 54 " --> pdb=" O ALA J 50 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 72 through 83 removed outlier: 4.024A pdb=" N MET J 76 " --> pdb=" O ASN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 107 Processing helix chain 'J' and resid 107 through 121 removed outlier: 3.670A pdb=" N VAL J 112 " --> pdb=" O ILE J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 128 Processing helix chain 'J' and resid 147 through 157 Processing helix chain 'J' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA J 174 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE J 248 " --> pdb=" O ASN J 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 265 Processing helix chain 'J' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR J 280 " --> pdb=" O TRP J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 304 removed outlier: 3.535A pdb=" N LEU J 304 " --> pdb=" O TRP J 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.945A pdb=" N LEU K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY K 54 " --> pdb=" O ALA K 50 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 72 through 83 removed outlier: 4.023A pdb=" N MET K 76 " --> pdb=" O ASN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 107 Processing helix chain 'K' and resid 107 through 121 removed outlier: 3.669A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 147 through 157 Processing helix chain 'K' and resid 170 through 208 removed outlier: 4.060A pdb=" N ALA K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 249 removed outlier: 3.518A pdb=" N PHE K 248 " --> pdb=" O ASN K 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 265 Processing helix chain 'K' and resid 272 through 280 removed outlier: 3.637A pdb=" N THR K 280 " --> pdb=" O TRP K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 304 removed outlier: 3.536A pdb=" N LEU K 304 " --> pdb=" O TRP K 300 " (cutoff:3.500A) 1529 hydrogen bonds defined for protein. 4587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 9.14 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: 6952 1.34 - 1.46: 5054 1.46 - 1.58: 9917 1.58 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 22143 Sorted by residual: bond pdb=" N ILE K 162 " pdb=" CA ILE K 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.50e+00 bond pdb=" N ILE C 162 " pdb=" CA ILE C 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.49e+00 bond pdb=" N ILE H 162 " pdb=" CA ILE H 162 " ideal model delta sigma weight residual 1.462 1.449 0.013 1.06e-02 8.90e+03 1.48e+00 bond pdb=" N ILE G 162 " pdb=" CA ILE G 162 " ideal model delta sigma weight residual 1.462 1.450 0.013 1.06e-02 8.90e+03 1.46e+00 bond pdb=" N ILE F 162 " pdb=" CA ILE F 162 " ideal model delta sigma weight residual 1.462 1.450 0.013 1.06e-02 8.90e+03 1.45e+00 ... (remaining 22138 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.21: 581 106.21 - 113.18: 12046 113.18 - 120.15: 8356 120.15 - 127.11: 8980 127.11 - 134.08: 298 Bond angle restraints: 30261 Sorted by residual: angle pdb=" N ARG G 46 " pdb=" CA ARG G 46 " pdb=" C ARG G 46 " ideal model delta sigma weight residual 114.56 111.24 3.32 1.27e+00 6.20e-01 6.84e+00 angle pdb=" N ARG D 46 " pdb=" CA ARG D 46 " pdb=" C ARG D 46 " ideal model delta sigma weight residual 114.56 111.24 3.32 1.27e+00 6.20e-01 6.84e+00 angle pdb=" N ARG B 46 " pdb=" CA ARG B 46 " pdb=" C ARG B 46 " ideal model delta sigma weight residual 114.56 111.25 3.31 1.27e+00 6.20e-01 6.80e+00 angle pdb=" N ARG K 46 " pdb=" CA ARG K 46 " pdb=" C ARG K 46 " ideal model delta sigma weight residual 114.56 111.26 3.30 1.27e+00 6.20e-01 6.76e+00 angle pdb=" N ARG I 46 " pdb=" CA ARG I 46 " pdb=" C ARG I 46 " ideal model delta sigma weight residual 114.56 111.27 3.29 1.27e+00 6.20e-01 6.72e+00 ... (remaining 30256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 11253 15.65 - 31.30: 1245 31.30 - 46.95: 449 46.95 - 62.60: 22 62.60 - 78.26: 22 Dihedral angle restraints: 12991 sinusoidal: 4686 harmonic: 8305 Sorted by residual: dihedral pdb=" CB CYS J 41 " pdb=" SG CYS J 41 " pdb=" SG CYS J 126 " pdb=" CB CYS J 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.26 78.26 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS F 41 " pdb=" SG CYS F 41 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " pdb=" CB CYS G 126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 12988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2360 0.036 - 0.071: 932 0.071 - 0.107: 153 0.107 - 0.143: 31 0.143 - 0.178: 11 Chirality restraints: 3487 Sorted by residual: chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ILE G 169 " pdb=" N ILE G 169 " pdb=" C ILE G 169 " pdb=" CB ILE G 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE C 169 " pdb=" N ILE C 169 " pdb=" C ILE C 169 " pdb=" CB ILE C 169 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3484 not shown) Planarity restraints: 3850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO E 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO C 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO F 60 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.028 5.00e-02 4.00e+02 ... (remaining 3847 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 137 2.62 - 3.19: 21082 3.19 - 3.76: 32928 3.76 - 4.33: 40664 4.33 - 4.90: 66759 Nonbonded interactions: 161570 Sorted by model distance: nonbonded pdb=" OH TYR K 97 " pdb=" OE2 GLU K 215 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR E 97 " pdb=" OE2 GLU E 215 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR F 97 " pdb=" OE2 GLU F 215 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR I 97 " pdb=" OE2 GLU I 215 " model vdw 2.052 2.440 nonbonded pdb=" OH TYR H 97 " pdb=" OE2 GLU H 215 " model vdw 2.052 2.440 ... (remaining 161565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.980 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 54.410 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 0.044 22143 Z= 0.326 Angle : 0.738 6.992 30261 Z= 0.426 Chirality : 0.038 0.178 3487 Planarity : 0.005 0.050 3850 Dihedral : 14.395 63.578 7568 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.02 % Allowed : 4.96 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.13), residues: 2761 helix: -1.41 (0.09), residues: 1969 sheet: None (None), residues: 0 loop : -4.11 (0.16), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 300 HIS 0.005 0.001 HIS K 236 PHE 0.011 0.001 PHE B 198 TYR 0.017 0.001 TYR J 97 ARG 0.002 0.000 ARG H 246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 477 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7889 (tp40) cc_final: 0.7322 (tm-30) REVERT: A 234 GLU cc_start: 0.8524 (tt0) cc_final: 0.8241 (tp30) REVERT: B 102 MET cc_start: 0.8879 (mmp) cc_final: 0.8596 (tpp) REVERT: B 104 GLN cc_start: 0.8008 (tp40) cc_final: 0.7423 (tm-30) REVERT: B 234 GLU cc_start: 0.8665 (tt0) cc_final: 0.8379 (tp30) REVERT: C 102 MET cc_start: 0.8904 (mmp) cc_final: 0.8424 (tpp) REVERT: C 104 GLN cc_start: 0.8075 (tp40) cc_final: 0.7323 (tm-30) REVERT: C 259 GLU cc_start: 0.6735 (tm-30) cc_final: 0.6359 (tp30) REVERT: D 104 GLN cc_start: 0.7823 (tp40) cc_final: 0.7429 (tm-30) REVERT: D 287 GLU cc_start: 0.8118 (tt0) cc_final: 0.7669 (tt0) REVERT: E 102 MET cc_start: 0.8954 (mmp) cc_final: 0.8484 (tpp) REVERT: E 104 GLN cc_start: 0.7892 (tp40) cc_final: 0.7231 (tm-30) REVERT: E 210 LEU cc_start: 0.8672 (mt) cc_final: 0.8337 (mp) REVERT: F 104 GLN cc_start: 0.7993 (tp40) cc_final: 0.7457 (tm-30) REVERT: F 234 GLU cc_start: 0.8481 (tt0) cc_final: 0.8269 (tp30) REVERT: G 102 MET cc_start: 0.8774 (mmp) cc_final: 0.8358 (tpp) REVERT: G 104 GLN cc_start: 0.8162 (tp40) cc_final: 0.7599 (tm-30) REVERT: H 41 CYS cc_start: 0.6574 (m) cc_final: 0.6361 (m) REVERT: H 104 GLN cc_start: 0.7956 (tp40) cc_final: 0.7470 (tm-30) REVERT: I 102 MET cc_start: 0.8832 (mmp) cc_final: 0.8517 (tpp) REVERT: I 104 GLN cc_start: 0.7934 (tp40) cc_final: 0.7302 (tm-30) REVERT: I 163 TYR cc_start: 0.6920 (t80) cc_final: 0.6549 (t80) REVERT: I 259 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6265 (tp30) REVERT: J 41 CYS cc_start: 0.6529 (m) cc_final: 0.6294 (m) REVERT: J 102 MET cc_start: 0.8917 (mmp) cc_final: 0.8645 (tpp) REVERT: J 104 GLN cc_start: 0.8036 (tp40) cc_final: 0.7648 (tm-30) REVERT: J 234 GLU cc_start: 0.8582 (tt0) cc_final: 0.8347 (tp30) REVERT: K 102 MET cc_start: 0.8937 (mmp) cc_final: 0.8572 (tpp) REVERT: K 104 GLN cc_start: 0.7637 (tp40) cc_final: 0.6983 (tm-30) outliers start: 22 outliers final: 3 residues processed: 499 average time/residue: 0.2579 time to fit residues: 214.9952 Evaluate side-chains 318 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 315 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain K residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 298 HIS B 227 GLN B 230 GLN B 298 HIS C 227 GLN C 230 GLN C 298 HIS D 227 GLN D 230 GLN D 298 HIS E 214 GLN E 227 GLN E 230 GLN E 298 HIS F 214 GLN F 227 GLN F 230 GLN F 298 HIS G 230 GLN G 298 HIS H 230 GLN H 298 HIS I 214 GLN I 230 GLN I 298 HIS J 214 GLN J 227 GLN J 230 GLN J 298 HIS K 214 GLN K 227 GLN K 230 GLN K 298 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22143 Z= 0.259 Angle : 0.664 6.111 30261 Z= 0.344 Chirality : 0.039 0.176 3487 Planarity : 0.005 0.053 3850 Dihedral : 4.843 22.013 3061 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.68 % Allowed : 14.42 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2761 helix: 0.17 (0.11), residues: 1958 sheet: None (None), residues: 0 loop : -3.21 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 300 HIS 0.006 0.001 HIS A 236 PHE 0.010 0.001 PHE G 198 TYR 0.023 0.001 TYR C 285 ARG 0.002 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 371 time to evaluate : 2.546 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: A 104 GLN cc_start: 0.7669 (tp40) cc_final: 0.7066 (tm-30) REVERT: A 234 GLU cc_start: 0.8517 (tt0) cc_final: 0.8314 (tp30) REVERT: B 104 GLN cc_start: 0.7837 (tp40) cc_final: 0.7320 (tm-30) REVERT: B 193 MET cc_start: 0.6414 (tpp) cc_final: 0.5818 (tpt) REVERT: B 234 GLU cc_start: 0.8705 (tt0) cc_final: 0.8370 (tp30) REVERT: C 104 GLN cc_start: 0.7728 (tp40) cc_final: 0.7063 (tm-30) REVERT: C 234 GLU cc_start: 0.8775 (tp30) cc_final: 0.8351 (tp30) REVERT: D 104 GLN cc_start: 0.7913 (tp40) cc_final: 0.7480 (tm-30) REVERT: D 234 GLU cc_start: 0.8627 (tp30) cc_final: 0.8400 (tp30) REVERT: D 287 GLU cc_start: 0.8127 (tt0) cc_final: 0.7750 (tt0) REVERT: E 104 GLN cc_start: 0.7792 (tp40) cc_final: 0.7146 (tm-30) REVERT: E 193 MET cc_start: 0.6583 (tpp) cc_final: 0.6043 (tpt) REVERT: E 275 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7689 (mm-40) REVERT: F 104 GLN cc_start: 0.7878 (tp40) cc_final: 0.7436 (tm-30) REVERT: F 193 MET cc_start: 0.6838 (tpp) cc_final: 0.6103 (tmm) REVERT: F 234 GLU cc_start: 0.8534 (tt0) cc_final: 0.8257 (tp30) REVERT: G 104 GLN cc_start: 0.8146 (tp40) cc_final: 0.7562 (tm-30) REVERT: G 119 LEU cc_start: 0.8282 (mt) cc_final: 0.8013 (mm) REVERT: G 193 MET cc_start: 0.6618 (tpp) cc_final: 0.6091 (tmm) REVERT: G 234 GLU cc_start: 0.8668 (tp30) cc_final: 0.8437 (tp30) REVERT: H 104 GLN cc_start: 0.7837 (tp40) cc_final: 0.7409 (tm-30) REVERT: H 193 MET cc_start: 0.6582 (tpp) cc_final: 0.5967 (tmm) REVERT: I 234 GLU cc_start: 0.8562 (tp30) cc_final: 0.8304 (tp30) REVERT: I 259 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6448 (tp30) REVERT: J 104 GLN cc_start: 0.7936 (tp40) cc_final: 0.7525 (tm-30) REVERT: J 234 GLU cc_start: 0.8555 (tt0) cc_final: 0.8345 (tp30) REVERT: K 104 GLN cc_start: 0.7610 (tp40) cc_final: 0.6952 (tm-30) REVERT: K 193 MET cc_start: 0.5377 (tpt) cc_final: 0.5052 (tpp) outliers start: 101 outliers final: 68 residues processed: 407 average time/residue: 0.2484 time to fit residues: 172.2063 Evaluate side-chains 405 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 337 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 85 optimal weight: 0.0470 chunk 200 optimal weight: 10.0000 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS G 227 GLN ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22143 Z= 0.181 Angle : 0.589 5.845 30261 Z= 0.299 Chirality : 0.036 0.163 3487 Planarity : 0.005 0.051 3850 Dihedral : 4.296 19.323 3058 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.29 % Allowed : 18.41 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2761 helix: 1.02 (0.11), residues: 2057 sheet: None (None), residues: 0 loop : -3.70 (0.18), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 300 HIS 0.006 0.001 HIS B 236 PHE 0.006 0.001 PHE H 198 TYR 0.010 0.001 TYR J 97 ARG 0.002 0.000 ARG H 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 381 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7635 (tp40) cc_final: 0.7062 (tm-30) REVERT: B 104 GLN cc_start: 0.7832 (tp40) cc_final: 0.7271 (tm-30) REVERT: B 119 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8007 (mm) REVERT: B 259 GLU cc_start: 0.6522 (tp30) cc_final: 0.6186 (tp30) REVERT: C 104 GLN cc_start: 0.7632 (tp40) cc_final: 0.6929 (tm-30) REVERT: C 119 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (mm) REVERT: C 196 LEU cc_start: 0.8177 (tp) cc_final: 0.7797 (tp) REVERT: C 234 GLU cc_start: 0.8800 (tp30) cc_final: 0.8495 (tp30) REVERT: C 259 GLU cc_start: 0.6558 (tp30) cc_final: 0.6262 (tp30) REVERT: D 104 GLN cc_start: 0.7812 (tp40) cc_final: 0.7420 (tm-30) REVERT: D 193 MET cc_start: 0.6900 (tpp) cc_final: 0.6290 (tmm) REVERT: D 234 GLU cc_start: 0.8716 (tp30) cc_final: 0.8381 (tp30) REVERT: D 287 GLU cc_start: 0.8077 (tt0) cc_final: 0.7761 (tt0) REVERT: E 98 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8125 (mtp) REVERT: E 104 GLN cc_start: 0.7691 (tp40) cc_final: 0.7332 (tm-30) REVERT: E 275 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7448 (mm-40) REVERT: F 104 GLN cc_start: 0.7838 (tp40) cc_final: 0.7052 (tm-30) REVERT: F 193 MET cc_start: 0.6886 (tpp) cc_final: 0.6054 (tmm) REVERT: G 104 GLN cc_start: 0.8077 (tp40) cc_final: 0.7540 (tm-30) REVERT: G 259 GLU cc_start: 0.6493 (tp30) cc_final: 0.6226 (tp30) REVERT: H 104 GLN cc_start: 0.7764 (tp40) cc_final: 0.7335 (tm-30) REVERT: H 115 SER cc_start: 0.8484 (t) cc_final: 0.8194 (t) REVERT: H 193 MET cc_start: 0.6669 (tpp) cc_final: 0.6091 (tmm) REVERT: H 259 GLU cc_start: 0.6517 (tp30) cc_final: 0.6235 (tp30) REVERT: I 196 LEU cc_start: 0.8400 (tp) cc_final: 0.8133 (tt) REVERT: I 234 GLU cc_start: 0.8672 (tp30) cc_final: 0.8330 (tp30) REVERT: I 258 ASP cc_start: 0.5837 (m-30) cc_final: 0.5624 (m-30) REVERT: I 259 GLU cc_start: 0.6615 (tm-30) cc_final: 0.6296 (tp30) REVERT: J 104 GLN cc_start: 0.7827 (tp40) cc_final: 0.7457 (tm-30) REVERT: K 104 GLN cc_start: 0.7559 (tp40) cc_final: 0.6964 (tm-30) REVERT: K 193 MET cc_start: 0.5618 (tpt) cc_final: 0.5239 (tpp) REVERT: K 287 GLU cc_start: 0.7894 (tt0) cc_final: 0.7663 (tt0) outliers start: 71 outliers final: 32 residues processed: 417 average time/residue: 0.2462 time to fit residues: 174.1326 Evaluate side-chains 371 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain K residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 129 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS C 205 HIS D 205 HIS F 205 HIS G 205 HIS H 205 HIS ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 HIS K 205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22143 Z= 0.202 Angle : 0.593 8.194 30261 Z= 0.300 Chirality : 0.037 0.158 3487 Planarity : 0.005 0.054 3850 Dihedral : 4.171 18.638 3058 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.57 % Allowed : 20.83 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 2761 helix: 1.27 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.50 (0.17), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 276 HIS 0.006 0.002 HIS F 236 PHE 0.008 0.001 PHE B 198 TYR 0.009 0.001 TYR F 97 ARG 0.001 0.000 ARG K 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7648 (tp40) cc_final: 0.7129 (tm-30) REVERT: A 234 GLU cc_start: 0.8719 (tp30) cc_final: 0.8508 (tp30) REVERT: A 259 GLU cc_start: 0.6439 (tp30) cc_final: 0.6038 (tp30) REVERT: B 104 GLN cc_start: 0.7754 (tp40) cc_final: 0.7260 (tm-30) REVERT: B 119 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (mm) REVERT: B 234 GLU cc_start: 0.8728 (tp30) cc_final: 0.8219 (tp30) REVERT: B 259 GLU cc_start: 0.6482 (tp30) cc_final: 0.6145 (tp30) REVERT: C 104 GLN cc_start: 0.7630 (tp40) cc_final: 0.6943 (tm-30) REVERT: C 196 LEU cc_start: 0.8186 (tp) cc_final: 0.7810 (tp) REVERT: C 234 GLU cc_start: 0.8809 (tp30) cc_final: 0.8462 (tp30) REVERT: C 259 GLU cc_start: 0.6544 (tp30) cc_final: 0.6189 (tp30) REVERT: D 104 GLN cc_start: 0.7846 (tp40) cc_final: 0.7447 (tm-30) REVERT: D 193 MET cc_start: 0.6896 (tpp) cc_final: 0.6295 (tmm) REVERT: D 234 GLU cc_start: 0.8737 (tp30) cc_final: 0.8384 (tp30) REVERT: D 287 GLU cc_start: 0.8091 (tt0) cc_final: 0.7789 (tt0) REVERT: E 275 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7444 (mm-40) REVERT: F 104 GLN cc_start: 0.7809 (tp40) cc_final: 0.6999 (tm-30) REVERT: F 193 MET cc_start: 0.6990 (tpp) cc_final: 0.6179 (tmm) REVERT: F 234 GLU cc_start: 0.8678 (tp30) cc_final: 0.8426 (tp30) REVERT: G 104 GLN cc_start: 0.7983 (tp40) cc_final: 0.7463 (tm-30) REVERT: G 259 GLU cc_start: 0.6498 (tp30) cc_final: 0.6185 (tp30) REVERT: H 104 GLN cc_start: 0.7773 (tp40) cc_final: 0.7355 (tm-30) REVERT: H 115 SER cc_start: 0.8424 (t) cc_final: 0.8109 (t) REVERT: H 119 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7913 (mm) REVERT: H 193 MET cc_start: 0.6707 (tpp) cc_final: 0.6116 (tmm) REVERT: H 259 GLU cc_start: 0.6499 (tp30) cc_final: 0.6281 (tp30) REVERT: I 193 MET cc_start: 0.6733 (tpp) cc_final: 0.5826 (tmm) REVERT: I 196 LEU cc_start: 0.8454 (tp) cc_final: 0.8177 (tt) REVERT: I 234 GLU cc_start: 0.8705 (tp30) cc_final: 0.8322 (tp30) REVERT: J 104 GLN cc_start: 0.7776 (tp40) cc_final: 0.7440 (tm-30) REVERT: K 104 GLN cc_start: 0.7448 (tp40) cc_final: 0.6956 (tm-30) REVERT: K 193 MET cc_start: 0.5623 (tpt) cc_final: 0.5231 (tpp) REVERT: K 287 GLU cc_start: 0.7875 (tt0) cc_final: 0.7610 (tt0) outliers start: 77 outliers final: 64 residues processed: 400 average time/residue: 0.2529 time to fit residues: 169.9368 Evaluate side-chains 403 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 337 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 238 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS F 205 HIS G 205 HIS H 205 HIS ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22143 Z= 0.212 Angle : 0.594 8.026 30261 Z= 0.301 Chirality : 0.037 0.154 3487 Planarity : 0.005 0.052 3850 Dihedral : 4.122 18.421 3058 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.22 % Allowed : 22.40 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2761 helix: 1.40 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.36 (0.17), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 300 HIS 0.006 0.001 HIS B 236 PHE 0.009 0.001 PHE B 198 TYR 0.010 0.001 TYR F 97 ARG 0.001 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 345 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7654 (tp40) cc_final: 0.7140 (tm-30) REVERT: A 234 GLU cc_start: 0.8694 (tp30) cc_final: 0.8445 (tp30) REVERT: A 259 GLU cc_start: 0.6385 (tp30) cc_final: 0.6006 (tp30) REVERT: B 104 GLN cc_start: 0.7778 (tp40) cc_final: 0.7307 (tm-30) REVERT: B 119 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7991 (mm) REVERT: B 234 GLU cc_start: 0.8780 (tp30) cc_final: 0.8247 (tp30) REVERT: C 104 GLN cc_start: 0.7751 (tp40) cc_final: 0.7054 (tm-30) REVERT: C 196 LEU cc_start: 0.8176 (tp) cc_final: 0.7781 (tp) REVERT: C 234 GLU cc_start: 0.8822 (tp30) cc_final: 0.8461 (tp30) REVERT: C 259 GLU cc_start: 0.6634 (tp30) cc_final: 0.6284 (tp30) REVERT: D 104 GLN cc_start: 0.7867 (tp40) cc_final: 0.7455 (tm-30) REVERT: D 193 MET cc_start: 0.6872 (tpp) cc_final: 0.6306 (tmm) REVERT: D 234 GLU cc_start: 0.8811 (tp30) cc_final: 0.8408 (tp30) REVERT: D 287 GLU cc_start: 0.8104 (tt0) cc_final: 0.7860 (tt0) REVERT: E 275 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7567 (mm-40) REVERT: F 104 GLN cc_start: 0.7705 (tp40) cc_final: 0.6928 (tm-30) REVERT: F 193 MET cc_start: 0.6999 (tpp) cc_final: 0.6139 (tmm) REVERT: F 234 GLU cc_start: 0.8729 (tp30) cc_final: 0.8456 (tp30) REVERT: F 259 GLU cc_start: 0.6256 (tp30) cc_final: 0.5925 (tp30) REVERT: G 104 GLN cc_start: 0.7966 (tp40) cc_final: 0.7487 (tm-30) REVERT: G 234 GLU cc_start: 0.8788 (tp30) cc_final: 0.8389 (tp30) REVERT: G 259 GLU cc_start: 0.6498 (tp30) cc_final: 0.6159 (tp30) REVERT: H 104 GLN cc_start: 0.7799 (tp40) cc_final: 0.7377 (tm-30) REVERT: H 193 MET cc_start: 0.6688 (tpp) cc_final: 0.6061 (tmm) REVERT: H 234 GLU cc_start: 0.8844 (tp30) cc_final: 0.8473 (tp30) REVERT: H 259 GLU cc_start: 0.6518 (tp30) cc_final: 0.6275 (tp30) REVERT: I 193 MET cc_start: 0.6795 (tpp) cc_final: 0.5985 (tmm) REVERT: I 196 LEU cc_start: 0.8405 (tp) cc_final: 0.8108 (tt) REVERT: I 234 GLU cc_start: 0.8706 (tp30) cc_final: 0.8312 (tp30) REVERT: J 104 GLN cc_start: 0.7849 (tp40) cc_final: 0.7463 (tm-30) REVERT: J 107 MET cc_start: 0.7848 (ttm) cc_final: 0.7583 (ttm) REVERT: K 104 GLN cc_start: 0.7440 (tp40) cc_final: 0.6942 (tm-30) REVERT: K 193 MET cc_start: 0.5606 (tpt) cc_final: 0.5213 (tpp) REVERT: K 287 GLU cc_start: 0.7806 (tt0) cc_final: 0.7457 (tt0) outliers start: 91 outliers final: 77 residues processed: 399 average time/residue: 0.2524 time to fit residues: 171.0175 Evaluate side-chains 416 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 338 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS E 227 GLN F 205 HIS G 205 HIS H 205 HIS ** H 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22143 Z= 0.298 Angle : 0.656 9.069 30261 Z= 0.335 Chirality : 0.039 0.155 3487 Planarity : 0.005 0.052 3850 Dihedral : 4.298 19.629 3058 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.24 % Allowed : 22.50 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.15), residues: 2761 helix: 1.28 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.29 (0.18), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.006 0.002 HIS B 236 PHE 0.012 0.001 PHE B 198 TYR 0.013 0.001 TYR G 97 ARG 0.002 0.000 ARG I 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 344 time to evaluate : 2.590 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: A 104 GLN cc_start: 0.7756 (tp40) cc_final: 0.7248 (tm-30) REVERT: A 234 GLU cc_start: 0.8661 (tp30) cc_final: 0.8355 (tp30) REVERT: B 104 GLN cc_start: 0.7911 (tp40) cc_final: 0.7417 (tm-30) REVERT: B 119 LEU cc_start: 0.8193 (mt) cc_final: 0.7949 (mm) REVERT: B 234 GLU cc_start: 0.8783 (tp30) cc_final: 0.8238 (tp30) REVERT: B 259 GLU cc_start: 0.6507 (tp30) cc_final: 0.6170 (tp30) REVERT: C 104 GLN cc_start: 0.7836 (tp40) cc_final: 0.7151 (tm-30) REVERT: C 196 LEU cc_start: 0.8147 (tp) cc_final: 0.7817 (tp) REVERT: C 234 GLU cc_start: 0.8838 (tp30) cc_final: 0.8476 (tp30) REVERT: C 259 GLU cc_start: 0.6638 (tp30) cc_final: 0.6282 (tp30) REVERT: D 104 GLN cc_start: 0.7858 (tp40) cc_final: 0.7643 (tm-30) REVERT: D 193 MET cc_start: 0.6814 (tpp) cc_final: 0.6246 (tmm) REVERT: D 234 GLU cc_start: 0.8797 (tp30) cc_final: 0.8370 (tp30) REVERT: F 104 GLN cc_start: 0.7771 (tp40) cc_final: 0.7051 (tm-30) REVERT: F 193 MET cc_start: 0.6897 (tpp) cc_final: 0.6302 (tmm) REVERT: F 234 GLU cc_start: 0.8785 (tp30) cc_final: 0.8467 (tp30) REVERT: F 259 GLU cc_start: 0.6278 (tp30) cc_final: 0.5899 (tp30) REVERT: G 104 GLN cc_start: 0.8162 (tp40) cc_final: 0.7680 (tm-30) REVERT: G 119 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7933 (mm) REVERT: G 193 MET cc_start: 0.6571 (tpp) cc_final: 0.6230 (tmm) REVERT: G 234 GLU cc_start: 0.8762 (tp30) cc_final: 0.8300 (tp30) REVERT: G 259 GLU cc_start: 0.6716 (tp30) cc_final: 0.6299 (tp30) REVERT: H 104 GLN cc_start: 0.7950 (tp40) cc_final: 0.7749 (tm-30) REVERT: H 193 MET cc_start: 0.6666 (tpp) cc_final: 0.6047 (tmm) REVERT: H 234 GLU cc_start: 0.8824 (tp30) cc_final: 0.8342 (tp30) REVERT: H 259 GLU cc_start: 0.6582 (tp30) cc_final: 0.6354 (tp30) REVERT: H 287 GLU cc_start: 0.7634 (tt0) cc_final: 0.7037 (tt0) REVERT: I 193 MET cc_start: 0.6742 (tpp) cc_final: 0.5945 (tmm) REVERT: I 234 GLU cc_start: 0.8704 (tp30) cc_final: 0.8288 (tp30) REVERT: I 259 GLU cc_start: 0.6379 (tp30) cc_final: 0.5932 (tp30) REVERT: J 104 GLN cc_start: 0.7914 (tp40) cc_final: 0.7489 (tm-30) REVERT: K 104 GLN cc_start: 0.7594 (tp40) cc_final: 0.7052 (tm-30) REVERT: K 149 GLU cc_start: 0.5632 (mm-30) cc_final: 0.5378 (mm-30) REVERT: K 193 MET cc_start: 0.5479 (tpt) cc_final: 0.5081 (tpp) REVERT: K 275 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7612 (mm-40) outliers start: 113 outliers final: 104 residues processed: 411 average time/residue: 0.2549 time to fit residues: 179.2109 Evaluate side-chains 442 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 337 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 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 205 HIS B 205 HIS C 205 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS E 205 HIS ** F 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22143 Z= 0.290 Angle : 0.656 8.367 30261 Z= 0.334 Chirality : 0.039 0.154 3487 Planarity : 0.005 0.050 3850 Dihedral : 4.280 20.320 3058 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 6.03 % Allowed : 22.63 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2761 helix: 1.34 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.20 (0.18), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 276 HIS 0.006 0.002 HIS B 236 PHE 0.011 0.001 PHE B 198 TYR 0.012 0.001 TYR I 97 ARG 0.002 0.000 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 343 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7883 (tp40) cc_final: 0.7386 (tm-30) REVERT: A 234 GLU cc_start: 0.8670 (tp30) cc_final: 0.8363 (tp30) REVERT: A 259 GLU cc_start: 0.6425 (tp30) cc_final: 0.6129 (tp30) REVERT: B 104 GLN cc_start: 0.7984 (tp40) cc_final: 0.7459 (tm-30) REVERT: B 119 LEU cc_start: 0.8211 (mt) cc_final: 0.7990 (mm) REVERT: B 193 MET cc_start: 0.6655 (tpp) cc_final: 0.6170 (tpt) REVERT: B 234 GLU cc_start: 0.8781 (tp30) cc_final: 0.8210 (tp30) REVERT: B 259 GLU cc_start: 0.6498 (tp30) cc_final: 0.6167 (tp30) REVERT: C 104 GLN cc_start: 0.7827 (tp40) cc_final: 0.7153 (tm-30) REVERT: C 196 LEU cc_start: 0.8160 (tp) cc_final: 0.7804 (tp) REVERT: C 234 GLU cc_start: 0.8846 (tp30) cc_final: 0.8482 (tp30) REVERT: C 259 GLU cc_start: 0.6669 (tp30) cc_final: 0.6313 (tp30) REVERT: D 104 GLN cc_start: 0.7898 (tp40) cc_final: 0.7685 (tm-30) REVERT: D 193 MET cc_start: 0.6815 (tpp) cc_final: 0.6268 (tmm) REVERT: D 234 GLU cc_start: 0.8772 (tp30) cc_final: 0.8351 (tp30) REVERT: E 234 GLU cc_start: 0.8845 (tp30) cc_final: 0.8615 (tp30) REVERT: F 193 MET cc_start: 0.6939 (tpp) cc_final: 0.6340 (tmm) REVERT: F 234 GLU cc_start: 0.8811 (tp30) cc_final: 0.8417 (tp30) REVERT: F 259 GLU cc_start: 0.6261 (tp30) cc_final: 0.5847 (tp30) REVERT: G 104 GLN cc_start: 0.8237 (tp40) cc_final: 0.7823 (tm-30) REVERT: G 119 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7924 (mm) REVERT: G 234 GLU cc_start: 0.8767 (tp30) cc_final: 0.8243 (tp30) REVERT: G 259 GLU cc_start: 0.6629 (tp30) cc_final: 0.6249 (tp30) REVERT: H 104 GLN cc_start: 0.8010 (tp40) cc_final: 0.7803 (tm-30) REVERT: H 120 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7344 (t0) REVERT: H 193 MET cc_start: 0.6640 (tpp) cc_final: 0.6004 (tmm) REVERT: H 234 GLU cc_start: 0.8841 (tp30) cc_final: 0.8366 (tp30) REVERT: H 259 GLU cc_start: 0.6576 (tp30) cc_final: 0.6326 (tp30) REVERT: H 287 GLU cc_start: 0.7643 (tt0) cc_final: 0.7253 (tt0) REVERT: I 193 MET cc_start: 0.6785 (tpp) cc_final: 0.5966 (tmm) REVERT: I 234 GLU cc_start: 0.8731 (tp30) cc_final: 0.8293 (tp30) REVERT: I 259 GLU cc_start: 0.6391 (tp30) cc_final: 0.5932 (tp30) REVERT: J 104 GLN cc_start: 0.7978 (tp40) cc_final: 0.7508 (tm-30) REVERT: K 104 GLN cc_start: 0.7751 (tp40) cc_final: 0.7236 (tm-30) REVERT: K 275 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7518 (mm-40) REVERT: K 287 GLU cc_start: 0.7888 (tt0) cc_final: 0.7660 (tt0) outliers start: 130 outliers final: 105 residues processed: 422 average time/residue: 0.2541 time to fit residues: 183.9899 Evaluate side-chains 446 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 339 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 270 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS ** F 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22143 Z= 0.233 Angle : 0.627 9.409 30261 Z= 0.315 Chirality : 0.038 0.163 3487 Planarity : 0.005 0.050 3850 Dihedral : 4.065 19.364 3058 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.75 % Allowed : 23.14 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2761 helix: 1.59 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -3.03 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 300 HIS 0.006 0.001 HIS B 236 PHE 0.009 0.001 PHE B 198 TYR 0.011 0.001 TYR H 97 ARG 0.002 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 349 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8335 (mtt) cc_final: 0.8036 (ttm) REVERT: A 104 GLN cc_start: 0.7931 (tp40) cc_final: 0.7390 (tm-30) REVERT: A 234 GLU cc_start: 0.8660 (tp30) cc_final: 0.8370 (tp30) REVERT: A 259 GLU cc_start: 0.6314 (tp30) cc_final: 0.5980 (tp30) REVERT: B 104 GLN cc_start: 0.7996 (tp40) cc_final: 0.7461 (tm-30) REVERT: B 119 LEU cc_start: 0.8214 (mt) cc_final: 0.7991 (mm) REVERT: B 234 GLU cc_start: 0.8780 (tp30) cc_final: 0.8198 (tp30) REVERT: B 259 GLU cc_start: 0.6416 (tp30) cc_final: 0.6044 (tp30) REVERT: C 104 GLN cc_start: 0.7933 (tp40) cc_final: 0.7215 (tm-30) REVERT: C 196 LEU cc_start: 0.8139 (tp) cc_final: 0.7787 (tp) REVERT: C 234 GLU cc_start: 0.8852 (tp30) cc_final: 0.8515 (tp30) REVERT: C 259 GLU cc_start: 0.6593 (tp30) cc_final: 0.6270 (tp30) REVERT: D 104 GLN cc_start: 0.7967 (tp40) cc_final: 0.7733 (tm-30) REVERT: D 193 MET cc_start: 0.6809 (tpp) cc_final: 0.6281 (tmm) REVERT: D 234 GLU cc_start: 0.8840 (tp30) cc_final: 0.8392 (tp30) REVERT: F 193 MET cc_start: 0.7009 (tpp) cc_final: 0.6420 (tmm) REVERT: F 234 GLU cc_start: 0.8788 (tp30) cc_final: 0.8477 (tp30) REVERT: F 257 ASP cc_start: 0.7138 (p0) cc_final: 0.6894 (p0) REVERT: F 259 GLU cc_start: 0.6251 (tp30) cc_final: 0.5860 (tp30) REVERT: G 104 GLN cc_start: 0.8193 (tp40) cc_final: 0.7784 (tm-30) REVERT: G 119 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7973 (mm) REVERT: G 234 GLU cc_start: 0.8730 (tp30) cc_final: 0.8286 (tp30) REVERT: G 259 GLU cc_start: 0.6647 (tp30) cc_final: 0.6262 (tp30) REVERT: G 275 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7602 (mm-40) REVERT: H 193 MET cc_start: 0.6677 (tpp) cc_final: 0.6040 (tmm) REVERT: H 234 GLU cc_start: 0.8836 (tp30) cc_final: 0.8366 (tp30) REVERT: H 259 GLU cc_start: 0.6444 (tp30) cc_final: 0.6200 (tp30) REVERT: H 287 GLU cc_start: 0.7502 (tt0) cc_final: 0.7091 (tt0) REVERT: I 193 MET cc_start: 0.6776 (tpp) cc_final: 0.5976 (tmm) REVERT: I 196 LEU cc_start: 0.8258 (tp) cc_final: 0.7890 (tt) REVERT: I 234 GLU cc_start: 0.8736 (tp30) cc_final: 0.8285 (tp30) REVERT: I 259 GLU cc_start: 0.6353 (tp30) cc_final: 0.6145 (tp30) REVERT: J 104 GLN cc_start: 0.7991 (tp40) cc_final: 0.7521 (tm-30) REVERT: J 234 GLU cc_start: 0.8676 (tp30) cc_final: 0.8349 (tp30) REVERT: K 104 GLN cc_start: 0.7776 (tp40) cc_final: 0.7219 (tm-30) REVERT: K 120 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7608 (t70) REVERT: K 275 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7415 (mm-40) REVERT: K 287 GLU cc_start: 0.7850 (tt0) cc_final: 0.7565 (tt0) outliers start: 124 outliers final: 107 residues processed: 416 average time/residue: 0.2451 time to fit residues: 174.2087 Evaluate side-chains 451 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 342 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 THR Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 270 THR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 180 CYS Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 270 THR Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 117 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 180 CYS Chi-restraints excluded: chain K residue 206 TYR Chi-restraints excluded: chain K residue 270 THR Chi-restraints excluded: chain K residue 279 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 223 optimal weight: 0.1980 chunk 233 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS E 205 HIS G 205 HIS H 205 HIS J 205 HIS K 205 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22143 Z= 0.171 Angle : 0.601 8.924 30261 Z= 0.295 Chirality : 0.036 0.142 3487 Planarity : 0.005 0.051 3850 Dihedral : 3.813 17.247 3058 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.25 % Allowed : 26.07 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 2761 helix: 1.89 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.77 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 300 HIS 0.006 0.001 HIS B 236 PHE 0.005 0.001 PHE H 198 TYR 0.006 0.001 TYR H 163 ARG 0.006 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 389 time to evaluate : 2.348 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: A 104 GLN cc_start: 0.7843 (tp40) cc_final: 0.7340 (tm-30) REVERT: A 119 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8014 (mm) REVERT: A 193 MET cc_start: 0.6555 (tpp) cc_final: 0.6153 (tpt) REVERT: A 234 GLU cc_start: 0.8653 (tp30) cc_final: 0.8138 (tp30) REVERT: A 259 GLU cc_start: 0.6251 (tp30) cc_final: 0.5924 (tp30) REVERT: B 104 GLN cc_start: 0.7913 (tp40) cc_final: 0.7427 (tm-30) REVERT: B 119 LEU cc_start: 0.8161 (mt) cc_final: 0.7921 (mm) REVERT: B 234 GLU cc_start: 0.8841 (tp30) cc_final: 0.8261 (tp30) REVERT: B 259 GLU cc_start: 0.6357 (tp30) cc_final: 0.5988 (tp30) REVERT: B 287 GLU cc_start: 0.7781 (tt0) cc_final: 0.7379 (tt0) REVERT: C 104 GLN cc_start: 0.7850 (tp40) cc_final: 0.7142 (tm-30) REVERT: C 120 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7296 (t0) REVERT: C 196 LEU cc_start: 0.8046 (tp) cc_final: 0.7692 (tp) REVERT: C 234 GLU cc_start: 0.8875 (tp30) cc_final: 0.8500 (tp30) REVERT: C 259 GLU cc_start: 0.6483 (tp30) cc_final: 0.6132 (tp30) REVERT: D 104 GLN cc_start: 0.7958 (tp40) cc_final: 0.7712 (tm-30) REVERT: D 193 MET cc_start: 0.6773 (tpp) cc_final: 0.6253 (tmm) REVERT: D 234 GLU cc_start: 0.8851 (tp30) cc_final: 0.8572 (tp30) REVERT: E 215 GLU cc_start: 0.8778 (tp30) cc_final: 0.8511 (tp30) REVERT: F 193 MET cc_start: 0.6887 (tpp) cc_final: 0.6308 (tmm) REVERT: F 234 GLU cc_start: 0.8825 (tp30) cc_final: 0.8593 (tp30) REVERT: F 259 GLU cc_start: 0.6147 (tp30) cc_final: 0.5866 (tp30) REVERT: G 104 GLN cc_start: 0.8178 (tp40) cc_final: 0.7656 (tm-30) REVERT: G 215 GLU cc_start: 0.8763 (tp30) cc_final: 0.8485 (tp30) REVERT: G 234 GLU cc_start: 0.8811 (tp30) cc_final: 0.8384 (tp30) REVERT: G 259 GLU cc_start: 0.6423 (tp30) cc_final: 0.6077 (tp30) REVERT: H 119 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7917 (mm) REVERT: H 193 MET cc_start: 0.6818 (tpp) cc_final: 0.6224 (tmm) REVERT: H 234 GLU cc_start: 0.8821 (tp30) cc_final: 0.7618 (tp30) REVERT: H 259 GLU cc_start: 0.6243 (tp30) cc_final: 0.6008 (tp30) REVERT: H 287 GLU cc_start: 0.7781 (tt0) cc_final: 0.7524 (tt0) REVERT: I 193 MET cc_start: 0.6819 (tpp) cc_final: 0.6058 (tmm) REVERT: I 196 LEU cc_start: 0.8205 (tp) cc_final: 0.7846 (tt) REVERT: I 220 GLN cc_start: 0.8229 (mt0) cc_final: 0.8010 (mt0) REVERT: I 234 GLU cc_start: 0.8748 (tp30) cc_final: 0.8462 (tp30) REVERT: I 259 GLU cc_start: 0.6347 (tp30) cc_final: 0.5867 (tp30) REVERT: J 104 GLN cc_start: 0.7959 (tp40) cc_final: 0.7499 (tm-30) REVERT: J 215 GLU cc_start: 0.8771 (tp30) cc_final: 0.8480 (tp30) REVERT: J 234 GLU cc_start: 0.8691 (tp30) cc_final: 0.8015 (tp30) REVERT: K 98 MET cc_start: 0.8156 (mtt) cc_final: 0.7857 (ttm) REVERT: K 104 GLN cc_start: 0.7612 (tp40) cc_final: 0.7103 (tm-30) REVERT: K 120 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7417 (t70) REVERT: K 193 MET cc_start: 0.5987 (tmm) cc_final: 0.5630 (tpp) REVERT: K 275 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7323 (mm-40) REVERT: K 287 GLU cc_start: 0.7788 (tt0) cc_final: 0.7269 (tt0) outliers start: 70 outliers final: 49 residues processed: 433 average time/residue: 0.2674 time to fit residues: 192.2385 Evaluate side-chains 409 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 356 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 252 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS B 205 HIS C 205 HIS D 205 HIS G 205 HIS H 205 HIS K 40 ASN K 205 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22143 Z= 0.202 Angle : 0.624 8.403 30261 Z= 0.313 Chirality : 0.038 0.222 3487 Planarity : 0.005 0.051 3850 Dihedral : 3.842 18.068 3058 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.06 % Allowed : 26.72 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.16), residues: 2761 helix: 1.91 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.64 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 276 HIS 0.006 0.001 HIS B 236 PHE 0.007 0.001 PHE H 198 TYR 0.007 0.001 TYR B 97 ARG 0.002 0.000 ARG G 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 354 time to evaluate : 2.572 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: A 104 GLN cc_start: 0.7901 (tp40) cc_final: 0.7384 (tm-30) REVERT: A 193 MET cc_start: 0.6537 (tpp) cc_final: 0.6275 (tmm) REVERT: A 234 GLU cc_start: 0.8637 (tp30) cc_final: 0.8317 (tp30) REVERT: A 259 GLU cc_start: 0.6289 (tp30) cc_final: 0.5937 (tp30) REVERT: B 104 GLN cc_start: 0.7942 (tp40) cc_final: 0.7441 (tm-30) REVERT: B 119 LEU cc_start: 0.8158 (mt) cc_final: 0.7897 (mm) REVERT: B 234 GLU cc_start: 0.8811 (tp30) cc_final: 0.8215 (tp30) REVERT: B 259 GLU cc_start: 0.6377 (tp30) cc_final: 0.5995 (tp30) REVERT: B 287 GLU cc_start: 0.7710 (tt0) cc_final: 0.7286 (tt0) REVERT: C 104 GLN cc_start: 0.7861 (tp40) cc_final: 0.7131 (tm-30) REVERT: C 196 LEU cc_start: 0.8032 (tp) cc_final: 0.7678 (tp) REVERT: C 234 GLU cc_start: 0.8817 (tp30) cc_final: 0.8536 (tp30) REVERT: C 259 GLU cc_start: 0.6544 (tp30) cc_final: 0.6237 (tp30) REVERT: D 104 GLN cc_start: 0.8000 (tp40) cc_final: 0.7760 (tm-30) REVERT: D 193 MET cc_start: 0.6944 (tpp) cc_final: 0.6383 (tmm) REVERT: D 234 GLU cc_start: 0.8849 (tp30) cc_final: 0.8540 (tp30) REVERT: D 275 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7441 (mm-40) REVERT: E 193 MET cc_start: 0.6614 (tpp) cc_final: 0.6210 (tpt) REVERT: F 193 MET cc_start: 0.6823 (tpp) cc_final: 0.6305 (tmm) REVERT: F 234 GLU cc_start: 0.8825 (tp30) cc_final: 0.8419 (tp30) REVERT: F 259 GLU cc_start: 0.6169 (tp30) cc_final: 0.5877 (tp30) REVERT: G 104 GLN cc_start: 0.8151 (tp40) cc_final: 0.7705 (tm-30) REVERT: G 119 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7956 (mm) REVERT: G 234 GLU cc_start: 0.8770 (tp30) cc_final: 0.8316 (tp30) REVERT: G 259 GLU cc_start: 0.6609 (tp30) cc_final: 0.6226 (tp30) REVERT: G 275 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7499 (mm-40) REVERT: H 193 MET cc_start: 0.6767 (tpp) cc_final: 0.6194 (tmm) REVERT: H 234 GLU cc_start: 0.8834 (tp30) cc_final: 0.8349 (tp30) REVERT: H 259 GLU cc_start: 0.6356 (tp30) cc_final: 0.6135 (tp30) REVERT: H 287 GLU cc_start: 0.7737 (tt0) cc_final: 0.7418 (tt0) REVERT: I 193 MET cc_start: 0.6766 (tpp) cc_final: 0.6065 (tmm) REVERT: I 196 LEU cc_start: 0.8249 (tp) cc_final: 0.7897 (tt) REVERT: I 234 GLU cc_start: 0.8741 (tp30) cc_final: 0.8436 (tp30) REVERT: I 259 GLU cc_start: 0.6399 (tp30) cc_final: 0.5908 (tp30) REVERT: J 104 GLN cc_start: 0.7911 (tp40) cc_final: 0.7468 (tm-30) REVERT: J 234 GLU cc_start: 0.8676 (tp30) cc_final: 0.8300 (tp30) REVERT: K 98 MET cc_start: 0.8104 (mtt) cc_final: 0.7791 (ttm) REVERT: K 104 GLN cc_start: 0.7605 (tp40) cc_final: 0.7081 (tm-30) REVERT: K 120 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7389 (t70) REVERT: K 275 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7395 (mm-40) outliers start: 66 outliers final: 56 residues processed: 401 average time/residue: 0.2480 time to fit residues: 168.9559 Evaluate side-chains 403 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 345 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 206 TYR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 206 TYR Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain E residue 68 PHE Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 206 TYR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain G residue 68 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 206 TYR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 159 CYS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 206 TYR Chi-restraints excluded: chain J residue 68 PHE Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 206 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 218 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS C 227 GLN D 205 HIS F 227 GLN G 205 HIS H 205 HIS J 205 HIS K 205 HIS K 227 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.114774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.092453 restraints weight = 48032.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095528 restraints weight = 27437.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097665 restraints weight = 18900.095| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22143 Z= 0.261 Angle : 0.669 9.513 30261 Z= 0.335 Chirality : 0.039 0.243 3487 Planarity : 0.005 0.049 3850 Dihedral : 3.969 18.440 3058 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.76 % Allowed : 26.21 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.16), residues: 2761 helix: 1.82 (0.11), residues: 2046 sheet: None (None), residues: 0 loop : -2.63 (0.19), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 276 HIS 0.006 0.002 HIS C 236 PHE 0.011 0.001 PHE H 198 TYR 0.011 0.001 TYR E 97 ARG 0.003 0.000 ARG I 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3973.97 seconds wall clock time: 72 minutes 38.08 seconds (4358.08 seconds total)