Starting phenix.real_space_refine on Tue Aug 26 02:22:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9x_37384/08_2025/8w9x_37384.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.045 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 108 5.16 5 C 20796 2.51 5 N 5568 2.21 5 O 6144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32616 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "E" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "F" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "G" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "H" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "I" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "J" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "K" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2718 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 20, 'TRANS': 339} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 3, 'GLN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 6.63, per 1000 atoms: 0.20 Number of scatterers: 32616 At special positions: 0 Unit cell: (178.02, 188.899, 121.647, 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 108 16.00 O 6144 8.00 N 5568 7.00 C 20796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8232 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 49.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 11 through 25 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.897A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.532A pdb=" N THR A 81 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.657A pdb=" N ILE A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 114 through 131 Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.100A pdb=" N ILE A 151 " --> pdb=" O TRP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.638A pdb=" N GLU A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 309 Processing helix chain 'A' and resid 310 through 320 Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 51 through 64 removed outlier: 4.223A pdb=" N ILE B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.662A pdb=" N THR B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.930A pdb=" N ILE B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 113 through 131 removed outlier: 4.286A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 removed outlier: 4.074A pdb=" N ILE B 151 " --> pdb=" O TRP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.678A pdb=" N GLU B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 265 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 309 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'C' and resid 12 through 25 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 51 through 64 removed outlier: 4.282A pdb=" N ILE C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.654A pdb=" N THR C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 99 Processing helix chain 'C' and resid 105 through 109 Processing helix chain 'C' and resid 113 through 131 removed outlier: 4.248A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 3.560A pdb=" N LYS C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE C 151 " --> pdb=" O TRP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 3.520A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.647A pdb=" N GLU C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 265 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 309 Processing helix chain 'C' and resid 310 through 320 Processing helix chain 'C' and resid 356 through 359 Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 51 through 64 removed outlier: 3.887A pdb=" N ILE D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.574A pdb=" N THR D 81 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 101 removed outlier: 3.959A pdb=" N ILE D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 Processing helix chain 'D' and resid 113 through 130 removed outlier: 4.252A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.543A pdb=" N LYS D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.643A pdb=" N GLU D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 356 through 359 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'E' and resid 12 through 25 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 51 through 64 removed outlier: 3.783A pdb=" N ILE E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.540A pdb=" N LYS E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.727A pdb=" N ILE E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 109 Processing helix chain 'E' and resid 114 through 131 Processing helix chain 'E' and resid 139 through 151 removed outlier: 4.122A pdb=" N ILE E 151 " --> pdb=" O TRP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 193 through 199 removed outlier: 3.708A pdb=" N GLU E 197 " --> pdb=" O ILE E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 356 through 359 Processing helix chain 'E' and resid 360 through 373 Processing helix chain 'F' and resid 12 through 25 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 51 through 64 removed outlier: 3.771A pdb=" N ILE F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.856A pdb=" N THR F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.871A pdb=" N ILE F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 113 through 131 removed outlier: 4.390A pdb=" N ALA F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 151 removed outlier: 3.511A pdb=" N LYS F 143 " --> pdb=" O THR F 139 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE F 151 " --> pdb=" O TRP F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.501A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.639A pdb=" N GLU F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 265 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 356 through 359 Processing helix chain 'F' and resid 360 through 373 Processing helix chain 'G' and resid 12 through 25 Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 51 through 64 removed outlier: 3.547A pdb=" N PHE G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 83 removed outlier: 3.634A pdb=" N THR G 81 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.834A pdb=" N ILE G 101 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 109 Processing helix chain 'G' and resid 113 through 131 removed outlier: 4.274A pdb=" N ALA G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 151 removed outlier: 4.055A pdb=" N ILE G 151 " --> pdb=" O TRP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 Processing helix chain 'G' and resid 193 through 199 removed outlier: 3.635A pdb=" N GLU G 197 " --> pdb=" O ILE G 193 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN G 199 " --> pdb=" O THR G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 265 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 309 Processing helix chain 'G' and resid 310 through 320 Processing helix chain 'G' and resid 356 through 359 Processing helix chain 'G' and resid 360 through 373 Processing helix chain 'H' and resid 12 through 25 Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 51 through 64 removed outlier: 3.876A pdb=" N ILE H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 83 removed outlier: 3.524A pdb=" N LYS H 74 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 114 through 131 Processing helix chain 'H' and resid 139 through 151 removed outlier: 3.513A pdb=" N LYS H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE H 151 " --> pdb=" O TRP H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 175 Processing helix chain 'H' and resid 193 through 199 removed outlier: 3.676A pdb=" N GLU H 197 " --> pdb=" O ILE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 265 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 356 through 359 Processing helix chain 'H' and resid 360 through 373 Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 51 through 64 removed outlier: 3.971A pdb=" N ILE I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.686A pdb=" N THR I 81 " --> pdb=" O GLN I 77 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.797A pdb=" N ILE I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 109 Processing helix chain 'I' and resid 113 through 131 removed outlier: 4.296A pdb=" N ALA I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 151 removed outlier: 3.508A pdb=" N LYS I 143 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE I 151 " --> pdb=" O TRP I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 175 removed outlier: 3.554A pdb=" N LEU I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 199 removed outlier: 3.675A pdb=" N GLU I 197 " --> pdb=" O ILE I 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 265 Processing helix chain 'I' and resid 280 through 294 Processing helix chain 'I' and resid 306 through 309 Processing helix chain 'I' and resid 310 through 320 Processing helix chain 'I' and resid 356 through 359 Processing helix chain 'I' and resid 360 through 373 Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 51 through 64 removed outlier: 3.668A pdb=" N ILE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.623A pdb=" N THR J 81 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.979A pdb=" N ILE J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 109 Processing helix chain 'J' and resid 113 through 131 removed outlier: 4.307A pdb=" N ALA J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 151 removed outlier: 3.524A pdb=" N LYS J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE J 151 " --> pdb=" O TRP J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.502A pdb=" N LEU J 175 " --> pdb=" O ALA J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 199 removed outlier: 3.636A pdb=" N GLU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 265 Processing helix chain 'J' and resid 280 through 294 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 356 through 359 Processing helix chain 'J' and resid 360 through 373 Processing helix chain 'K' and resid 12 through 25 Processing helix chain 'K' and resid 36 through 41 Processing helix chain 'K' and resid 51 through 64 removed outlier: 3.714A pdb=" N ILE K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.555A pdb=" N LYS K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 81 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.995A pdb=" N ILE K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 109 Processing helix chain 'K' and resid 114 through 131 Processing helix chain 'K' and resid 139 through 151 removed outlier: 4.176A pdb=" N ILE K 151 " --> pdb=" O TRP K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 193 through 199 removed outlier: 3.695A pdb=" N GLU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 265 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 356 through 359 Processing helix chain 'K' and resid 360 through 373 Processing helix chain 'L' and resid 12 through 25 Processing helix chain 'L' and resid 36 through 41 Processing helix chain 'L' and resid 51 through 64 removed outlier: 3.878A pdb=" N ILE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.550A pdb=" N LYS L 74 " --> pdb=" O SER L 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR L 82 " --> pdb=" O ASN L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 101 removed outlier: 4.002A pdb=" N ILE L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 109 Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 139 through 151 removed outlier: 4.168A pdb=" N ILE L 151 " --> pdb=" O TRP L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 175 removed outlier: 3.511A pdb=" N LEU L 175 " --> pdb=" O ALA L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 199 removed outlier: 3.685A pdb=" N GLU L 197 " --> pdb=" O ILE L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 265 Processing helix chain 'L' and resid 280 through 294 Processing helix chain 'L' and resid 306 through 309 Processing helix chain 'L' and resid 310 through 320 Processing helix chain 'L' and resid 356 through 359 Processing helix chain 'L' and resid 360 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180 removed outlier: 6.089A pdb=" N PHE A 180 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LYS A 210 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 159 " --> pdb=" O TRP A 209 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 33 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 184 removed outlier: 3.747A pdb=" N PHE A 190 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 189 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 191 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 226 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 324 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 179 through 180 removed outlier: 6.106A pdb=" N PHE B 180 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYS B 210 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE B 159 " --> pdb=" O TRP B 209 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE B 33 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 184 removed outlier: 3.636A pdb=" N PHE B 190 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 189 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE B 191 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE B 226 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'C' and resid 179 through 180 removed outlier: 6.117A pdb=" N PHE C 180 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LYS C 210 " --> pdb=" O PHE C 180 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE C 33 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 183 through 184 removed outlier: 3.750A pdb=" N PHE C 190 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 189 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE C 191 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE C 226 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB4, first strand: chain 'D' and resid 179 through 180 removed outlier: 6.132A pdb=" N PHE D 180 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LYS D 210 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE D 33 " --> pdb=" O CYS D 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'D' and resid 183 through 184 removed outlier: 3.753A pdb=" N PHE D 190 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 189 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N PHE D 191 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE D 226 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 324 through 326 Processing sheet with id=AB8, first strand: chain 'E' and resid 179 through 180 removed outlier: 6.126A pdb=" N PHE E 180 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LYS E 210 " --> pdb=" O PHE E 180 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE E 33 " --> pdb=" O CYS E 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'E' and resid 183 through 184 removed outlier: 3.646A pdb=" N PHE E 190 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 189 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE E 191 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE E 226 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AC3, first strand: chain 'F' and resid 179 through 180 removed outlier: 6.108A pdb=" N PHE F 180 " --> pdb=" O LEU F 208 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS F 210 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE F 33 " --> pdb=" O CYS F 274 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'F' and resid 183 through 184 removed outlier: 3.757A pdb=" N PHE F 190 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 189 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE F 191 " --> pdb=" O ILE F 226 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE F 226 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 325 through 326 Processing sheet with id=AC7, first strand: chain 'G' and resid 179 through 180 removed outlier: 6.116A pdb=" N PHE G 180 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LYS G 210 " --> pdb=" O PHE G 180 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE G 159 " --> pdb=" O TRP G 209 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE G 33 " --> pdb=" O CYS G 274 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'G' and resid 183 through 184 removed outlier: 3.713A pdb=" N PHE G 190 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE G 191 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE G 226 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 324 through 326 Processing sheet with id=AD2, first strand: chain 'H' and resid 179 through 180 removed outlier: 6.157A pdb=" N PHE H 180 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS H 210 " --> pdb=" O PHE H 180 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE H 159 " --> pdb=" O TRP H 209 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE H 33 " --> pdb=" O CYS H 274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'H' and resid 183 through 184 removed outlier: 3.666A pdb=" N PHE H 190 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 189 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE H 191 " --> pdb=" O ILE H 226 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE H 226 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 325 through 326 Processing sheet with id=AD6, first strand: chain 'I' and resid 179 through 180 removed outlier: 6.083A pdb=" N PHE I 180 " --> pdb=" O LEU I 208 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS I 210 " --> pdb=" O PHE I 180 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE I 159 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE I 33 " --> pdb=" O CYS I 274 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'I' and resid 183 through 184 removed outlier: 3.642A pdb=" N PHE I 190 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE I 191 " --> pdb=" O ILE I 226 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ILE I 226 " --> pdb=" O PHE I 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 324 through 326 Processing sheet with id=AE1, first strand: chain 'J' and resid 179 through 180 removed outlier: 6.114A pdb=" N PHE J 180 " --> pdb=" O LEU J 208 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LYS J 210 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE J 33 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'J' and resid 183 through 184 removed outlier: 3.687A pdb=" N PHE J 190 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE J 191 " --> pdb=" O ILE J 226 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE J 226 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'K' and resid 179 through 180 removed outlier: 6.086A pdb=" N PHE K 180 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS K 210 " --> pdb=" O PHE K 180 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE K 159 " --> pdb=" O TRP K 209 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE K 33 " --> pdb=" O CYS K 274 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AE7, first strand: chain 'K' and resid 183 through 184 removed outlier: 3.710A pdb=" N PHE K 190 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA K 189 " --> pdb=" O ARG K 228 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE K 191 " --> pdb=" O ILE K 226 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE K 226 " --> pdb=" O PHE K 191 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 325 through 326 Processing sheet with id=AE9, first strand: chain 'L' and resid 179 through 180 removed outlier: 6.138A pdb=" N PHE L 180 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LYS L 210 " --> pdb=" O PHE L 180 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE L 159 " --> pdb=" O TRP L 209 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE L 33 " --> pdb=" O CYS L 274 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'L' and resid 183 through 184 removed outlier: 3.611A pdb=" N PHE L 190 " --> pdb=" O VAL L 184 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA L 189 " --> pdb=" O ARG L 228 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE L 191 " --> pdb=" O ILE L 226 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE L 226 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 325 through 326 1491 hydrogen bonds defined for protein. 4218 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: 5.78 Time building geometry restraints manager: 2.56 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: 10840 1.34 - 1.46: 4765 1.46 - 1.57: 17491 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 33264 Sorted by residual: bond pdb=" N PRO L 252 " pdb=" CA PRO L 252 " ideal model delta sigma weight residual 1.474 1.461 0.013 7.40e-03 1.83e+04 2.90e+00 bond pdb=" N PRO E 252 " pdb=" CA PRO E 252 " ideal model delta sigma weight residual 1.474 1.462 0.012 7.40e-03 1.83e+04 2.70e+00 bond pdb=" N PRO I 252 " pdb=" CA PRO I 252 " ideal model delta sigma weight residual 1.474 1.462 0.012 7.40e-03 1.83e+04 2.61e+00 bond pdb=" N PRO B 252 " pdb=" CA PRO B 252 " ideal model delta sigma weight residual 1.474 1.462 0.012 7.40e-03 1.83e+04 2.56e+00 bond pdb=" N PRO F 252 " pdb=" CA PRO F 252 " ideal model delta sigma weight residual 1.474 1.462 0.012 7.40e-03 1.83e+04 2.55e+00 ... (remaining 33259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 43908 1.60 - 3.20: 1164 3.20 - 4.79: 149 4.79 - 6.39: 49 6.39 - 7.99: 18 Bond angle restraints: 45288 Sorted by residual: angle pdb=" N ILE E 238 " pdb=" CA ILE E 238 " pdb=" C ILE E 238 " ideal model delta sigma weight residual 112.80 107.00 5.80 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 112.80 107.36 5.44 1.15e+00 7.56e-01 2.24e+01 angle pdb=" N ILE L 238 " pdb=" CA ILE L 238 " pdb=" C ILE L 238 " ideal model delta sigma weight residual 112.80 107.38 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" N ILE C 238 " pdb=" CA ILE C 238 " pdb=" C ILE C 238 " ideal model delta sigma weight residual 112.80 107.47 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 112.80 107.52 5.28 1.15e+00 7.56e-01 2.11e+01 ... (remaining 45283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 18512 17.89 - 35.77: 1337 35.77 - 53.66: 299 53.66 - 71.54: 60 71.54 - 89.43: 12 Dihedral angle restraints: 20220 sinusoidal: 7596 harmonic: 12624 Sorted by residual: dihedral pdb=" CA TRP J 205 " pdb=" C TRP J 205 " pdb=" N SER J 206 " pdb=" CA SER J 206 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TRP H 205 " pdb=" C TRP H 205 " pdb=" N SER H 206 " pdb=" CA SER H 206 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TRP D 205 " pdb=" C TRP D 205 " pdb=" N SER D 206 " pdb=" CA SER D 206 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 20217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3703 0.044 - 0.087: 1236 0.087 - 0.131: 339 0.131 - 0.174: 9 0.174 - 0.218: 5 Chirality restraints: 5292 Sorted by residual: chirality pdb=" CG LEU B 125 " pdb=" CB LEU B 125 " pdb=" CD1 LEU B 125 " pdb=" CD2 LEU B 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE L 238 " pdb=" N ILE L 238 " pdb=" C ILE L 238 " pdb=" CB ILE L 238 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CG LEU I 125 " pdb=" CB LEU I 125 " pdb=" CD1 LEU I 125 " pdb=" CD2 LEU I 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 5289 not shown) Planarity restraints: 5868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN J 294 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO J 295 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO J 295 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO J 295 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 294 " -0.049 5.00e-02 4.00e+02 7.50e-02 9.01e+00 pdb=" N PRO A 295 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 294 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO K 295 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 295 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 295 " 0.037 5.00e-02 4.00e+02 ... (remaining 5865 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 778 2.69 - 3.24: 33197 3.24 - 3.79: 49356 3.79 - 4.35: 61853 4.35 - 4.90: 105656 Nonbonded interactions: 250840 Sorted by model distance: nonbonded pdb=" OG SER C 186 " pdb=" OH TYR J 179 " model vdw 2.137 3.040 nonbonded pdb=" OG SER F 186 " pdb=" OH TYR G 179 " model vdw 2.142 3.040 nonbonded pdb=" OH TYR F 179 " pdb=" OG SER G 186 " model vdw 2.147 3.040 nonbonded pdb=" OG SER E 186 " pdb=" OH TYR H 179 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR E 179 " pdb=" OG SER H 186 " model vdw 2.167 3.040 ... (remaining 250835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5.120 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: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.340 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.006 0.077 33264 Z= 0.241 Angle : 0.661 7.992 45288 Z= 0.355 Chirality : 0.044 0.218 5292 Planarity : 0.005 0.112 5868 Dihedral : 13.722 89.430 11988 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.13), residues: 4272 helix: 1.36 (0.12), residues: 1908 sheet: -1.64 (0.23), residues: 528 loop : -1.23 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 320 TYR 0.014 0.002 TYR C 94 PHE 0.033 0.002 PHE D 367 TRP 0.013 0.002 TRP K 205 HIS 0.011 0.002 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00555 (33264) covalent geometry : angle 0.66095 (45288) hydrogen bonds : bond 0.18053 ( 1491) hydrogen bonds : angle 6.38555 ( 4218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.099 Fit side-chains REVERT: A 257 MET cc_start: 0.7619 (mmt) cc_final: 0.7342 (mmt) REVERT: E 58 ARG cc_start: 0.8565 (ptt180) cc_final: 0.8363 (ttp80) REVERT: E 76 ILE cc_start: 0.7445 (mt) cc_final: 0.7237 (mt) REVERT: E 168 MET cc_start: 0.7823 (tpt) cc_final: 0.7492 (tpp) REVERT: H 88 ILE cc_start: 0.8882 (tp) cc_final: 0.8674 (mm) REVERT: H 118 LEU cc_start: 0.8241 (tt) cc_final: 0.7890 (tp) REVERT: H 257 MET cc_start: 0.7590 (mmt) cc_final: 0.7290 (mmt) REVERT: H 316 MET cc_start: 0.7935 (mmp) cc_final: 0.7484 (ttm) REVERT: L 76 ILE cc_start: 0.7539 (mt) cc_final: 0.7280 (mt) REVERT: L 87 THR cc_start: 0.6707 (m) cc_final: 0.6507 (t) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2012 time to fit residues: 110.7281 Evaluate side-chains 246 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS C 77 GLN D 21 HIS H 21 HIS J 21 HIS K 15 GLN L 21 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.126929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113237 restraints weight = 66944.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112113 restraints weight = 114282.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112254 restraints weight = 115369.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111950 restraints weight = 86282.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112202 restraints weight = 83899.258| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.134 Angle : 0.519 6.542 45288 Z= 0.266 Chirality : 0.042 0.162 5292 Planarity : 0.004 0.076 5868 Dihedral : 3.882 16.177 4512 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.13), residues: 4272 helix: 1.56 (0.12), residues: 1944 sheet: -1.92 (0.22), residues: 552 loop : -1.25 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 43 TYR 0.019 0.001 TYR L 141 PHE 0.015 0.002 PHE E 367 TRP 0.013 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00309 (33264) covalent geometry : angle 0.51878 (45288) hydrogen bonds : bond 0.03834 ( 1491) hydrogen bonds : angle 4.83259 ( 4218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6646 (mmm) cc_final: 0.6404 (tpt) REVERT: A 257 MET cc_start: 0.7435 (mmt) cc_final: 0.7159 (mmt) REVERT: A 356 PHE cc_start: 0.5716 (t80) cc_final: 0.3268 (m-10) REVERT: B 356 PHE cc_start: 0.4771 (t80) cc_final: 0.2988 (m-10) REVERT: H 257 MET cc_start: 0.7499 (mmt) cc_final: 0.7187 (mmt) REVERT: I 99 GLN cc_start: 0.8126 (pp30) cc_final: 0.7747 (tm-30) REVERT: J 73 MET cc_start: 0.6489 (mmm) cc_final: 0.6277 (tpt) REVERT: K 316 MET cc_start: 0.6193 (tpp) cc_final: 0.5917 (tpp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1816 time to fit residues: 95.0733 Evaluate side-chains 236 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 373 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 131 optimal weight: 0.0970 chunk 298 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 364 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 85 ASN D 21 HIS F 218 GLN H 21 HIS H 85 ASN J 15 GLN J 21 HIS J 218 GLN K 21 HIS K 218 GLN L 21 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.127275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114059 restraints weight = 66585.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112647 restraints weight = 121602.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.112087 restraints weight = 120478.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110936 restraints weight = 110473.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111258 restraints weight = 105750.407| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33264 Z= 0.124 Angle : 0.504 6.719 45288 Z= 0.255 Chirality : 0.041 0.153 5292 Planarity : 0.004 0.064 5868 Dihedral : 3.725 15.813 4512 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.13), residues: 4272 helix: 1.70 (0.12), residues: 1944 sheet: -1.98 (0.21), residues: 552 loop : -1.22 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 43 TYR 0.011 0.001 TYR K 94 PHE 0.021 0.002 PHE B 361 TRP 0.012 0.001 TRP G 147 HIS 0.007 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00289 (33264) covalent geometry : angle 0.50406 (45288) hydrogen bonds : bond 0.03311 ( 1491) hydrogen bonds : angle 4.58596 ( 4218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6785 (mmm) cc_final: 0.6490 (tpt) REVERT: A 257 MET cc_start: 0.7458 (mmt) cc_final: 0.7253 (mmt) REVERT: A 356 PHE cc_start: 0.5777 (t80) cc_final: 0.3298 (m-10) REVERT: C 168 MET cc_start: 0.7493 (tpt) cc_final: 0.7205 (mmm) REVERT: D 168 MET cc_start: 0.7537 (tpt) cc_final: 0.7069 (tpp) REVERT: D 257 MET cc_start: 0.7644 (mmt) cc_final: 0.7401 (mmt) REVERT: E 237 LEU cc_start: 0.7317 (mm) cc_final: 0.7073 (mm) REVERT: H 99 GLN cc_start: 0.8149 (pp30) cc_final: 0.7783 (tm-30) REVERT: H 168 MET cc_start: 0.7320 (tpt) cc_final: 0.7044 (tpp) REVERT: H 257 MET cc_start: 0.7532 (mmt) cc_final: 0.7199 (mmt) REVERT: I 99 GLN cc_start: 0.8122 (pp30) cc_final: 0.7815 (tm-30) REVERT: J 73 MET cc_start: 0.6754 (mmm) cc_final: 0.6437 (tpt) REVERT: K 257 MET cc_start: 0.7471 (mmt) cc_final: 0.7125 (mmt) REVERT: K 316 MET cc_start: 0.6123 (tpp) cc_final: 0.5851 (tpp) REVERT: L 237 LEU cc_start: 0.7554 (mm) cc_final: 0.7339 (mm) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1891 time to fit residues: 102.5980 Evaluate side-chains 248 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 327 optimal weight: 5.9990 chunk 423 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 40.0000 chunk 337 optimal weight: 0.9990 chunk 321 optimal weight: 50.0000 chunk 172 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS B 266 GLN B 282 HIS D 21 HIS E 15 GLN E 85 ASN E 176 ASN E 218 GLN E 282 HIS F 218 GLN H 21 HIS H 176 ASN I 282 HIS J 21 HIS J 282 HIS K 21 HIS L 15 GLN L 21 HIS L 266 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109841 restraints weight = 66994.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109211 restraints weight = 141125.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109570 restraints weight = 125639.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110236 restraints weight = 90704.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110176 restraints weight = 91459.096| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33264 Z= 0.205 Angle : 0.577 6.761 45288 Z= 0.295 Chirality : 0.043 0.139 5292 Planarity : 0.004 0.063 5868 Dihedral : 4.131 17.492 4512 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.13), residues: 4272 helix: 1.46 (0.12), residues: 1944 sheet: -1.97 (0.21), residues: 528 loop : -1.45 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 58 TYR 0.019 0.002 TYR E 141 PHE 0.019 0.002 PHE B 361 TRP 0.011 0.002 TRP G 147 HIS 0.008 0.002 HIS J 21 Details of bonding type rmsd covalent geometry : bond 0.00484 (33264) covalent geometry : angle 0.57719 (45288) hydrogen bonds : bond 0.03633 ( 1491) hydrogen bonds : angle 4.76694 ( 4218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6866 (mmm) cc_final: 0.6535 (tpt) REVERT: A 168 MET cc_start: 0.7465 (tpt) cc_final: 0.7129 (tpp) REVERT: A 356 PHE cc_start: 0.5590 (t80) cc_final: 0.2965 (m-10) REVERT: D 168 MET cc_start: 0.7630 (tpt) cc_final: 0.7143 (tpp) REVERT: H 168 MET cc_start: 0.7429 (tpt) cc_final: 0.7046 (tpp) REVERT: I 99 GLN cc_start: 0.8189 (pp30) cc_final: 0.7881 (tm-30) REVERT: J 73 MET cc_start: 0.6800 (mmm) cc_final: 0.6590 (tpt) REVERT: L 168 MET cc_start: 0.7733 (tpt) cc_final: 0.7389 (tpp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1893 time to fit residues: 95.3191 Evaluate side-chains 235 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 337 optimal weight: 1.9990 chunk 405 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 203 optimal weight: 0.0060 chunk 324 optimal weight: 10.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS B 218 GLN C 282 HIS D 21 HIS H 21 HIS I 85 ASN I 292 GLN J 21 HIS K 21 HIS L 21 HIS L 218 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.126961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112406 restraints weight = 66795.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110469 restraints weight = 117941.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110760 restraints weight = 127732.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110318 restraints weight = 95480.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110625 restraints weight = 94891.939| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.108 Angle : 0.504 6.811 45288 Z= 0.251 Chirality : 0.041 0.139 5292 Planarity : 0.004 0.054 5868 Dihedral : 3.691 15.775 4512 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.13), residues: 4272 helix: 1.85 (0.12), residues: 1956 sheet: -2.11 (0.21), residues: 552 loop : -1.37 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.013 0.001 TYR C 94 PHE 0.019 0.001 PHE I 367 TRP 0.011 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00253 (33264) covalent geometry : angle 0.50391 (45288) hydrogen bonds : bond 0.02895 ( 1491) hydrogen bonds : angle 4.40328 ( 4218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6926 (mmm) cc_final: 0.6584 (tpt) REVERT: A 168 MET cc_start: 0.7443 (tpt) cc_final: 0.7036 (tpp) REVERT: C 168 MET cc_start: 0.7476 (tpt) cc_final: 0.6903 (tmm) REVERT: D 168 MET cc_start: 0.7600 (tpt) cc_final: 0.7056 (tpp) REVERT: H 99 GLN cc_start: 0.8055 (pp30) cc_final: 0.7673 (tm-30) REVERT: H 168 MET cc_start: 0.7371 (tpt) cc_final: 0.6971 (tpp) REVERT: I 99 GLN cc_start: 0.8143 (pp30) cc_final: 0.7877 (tm-30) REVERT: L 168 MET cc_start: 0.7670 (tpt) cc_final: 0.7289 (tpp) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1855 time to fit residues: 101.2786 Evaluate side-chains 250 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 20 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 358 optimal weight: 9.9990 chunk 405 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 282 HIS B 218 GLN D 21 HIS D 282 HIS G 282 HIS H 21 HIS I 176 ASN I 292 GLN J 21 HIS K 21 HIS L 21 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109769 restraints weight = 67237.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109245 restraints weight = 141491.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109434 restraints weight = 125933.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.109034 restraints weight = 97736.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.109405 restraints weight = 85793.159| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33264 Z= 0.199 Angle : 0.579 7.866 45288 Z= 0.293 Chirality : 0.042 0.135 5292 Planarity : 0.004 0.053 5868 Dihedral : 4.095 17.471 4512 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.13), residues: 4272 helix: 1.60 (0.12), residues: 1956 sheet: -2.12 (0.21), residues: 528 loop : -1.58 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.013 0.002 TYR H 164 PHE 0.021 0.002 PHE E 367 TRP 0.010 0.002 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00473 (33264) covalent geometry : angle 0.57887 (45288) hydrogen bonds : bond 0.03442 ( 1491) hydrogen bonds : angle 4.70458 ( 4218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6867 (mmm) cc_final: 0.6541 (tpt) REVERT: A 168 MET cc_start: 0.7544 (tpt) cc_final: 0.7185 (tpp) REVERT: A 257 MET cc_start: 0.7547 (mmt) cc_final: 0.7131 (mmt) REVERT: A 356 PHE cc_start: 0.5913 (t80) cc_final: 0.3113 (m-10) REVERT: B 168 MET cc_start: 0.7410 (tpt) cc_final: 0.7202 (tpp) REVERT: D 168 MET cc_start: 0.7706 (tpt) cc_final: 0.7166 (tpp) REVERT: D 257 MET cc_start: 0.7661 (mmt) cc_final: 0.7347 (mmt) REVERT: D 358 LEU cc_start: 0.4981 (pt) cc_final: 0.4579 (tt) REVERT: E 168 MET cc_start: 0.7661 (tpt) cc_final: 0.7339 (tpp) REVERT: H 168 MET cc_start: 0.7540 (tpt) cc_final: 0.7124 (tpp) REVERT: H 257 MET cc_start: 0.7646 (mmt) cc_final: 0.7198 (mmt) REVERT: I 99 GLN cc_start: 0.8181 (pp30) cc_final: 0.7919 (tm-30) REVERT: J 56 LEU cc_start: 0.7956 (mm) cc_final: 0.7472 (mm) REVERT: K 257 MET cc_start: 0.7565 (mmt) cc_final: 0.7137 (mmt) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2279 time to fit residues: 114.3615 Evaluate side-chains 238 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 109 optimal weight: 0.7980 chunk 350 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 299 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 412 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 403 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS D 21 HIS F 282 HIS H 21 HIS J 21 HIS J 85 ASN K 21 HIS L 21 HIS L 282 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.126113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111837 restraints weight = 66794.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110745 restraints weight = 119829.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111083 restraints weight = 120190.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111453 restraints weight = 83204.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111481 restraints weight = 85168.419| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33264 Z= 0.116 Angle : 0.525 7.754 45288 Z= 0.261 Chirality : 0.041 0.166 5292 Planarity : 0.004 0.050 5868 Dihedral : 3.737 16.057 4512 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.13), residues: 4272 helix: 1.92 (0.12), residues: 1956 sheet: -2.09 (0.21), residues: 528 loop : -1.48 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 58 TYR 0.013 0.001 TYR G 94 PHE 0.022 0.002 PHE I 367 TRP 0.011 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00274 (33264) covalent geometry : angle 0.52471 (45288) hydrogen bonds : bond 0.02891 ( 1491) hydrogen bonds : angle 4.45612 ( 4218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6847 (mmm) cc_final: 0.6508 (tpt) REVERT: A 168 MET cc_start: 0.7510 (tpt) cc_final: 0.7064 (tpp) REVERT: A 257 MET cc_start: 0.7235 (mmt) cc_final: 0.7027 (mmt) REVERT: A 356 PHE cc_start: 0.5920 (t80) cc_final: 0.3126 (m-10) REVERT: B 58 ARG cc_start: 0.7066 (ptp90) cc_final: 0.6772 (mtm-85) REVERT: B 168 MET cc_start: 0.7341 (tpt) cc_final: 0.7084 (tpp) REVERT: D 168 MET cc_start: 0.7632 (tpt) cc_final: 0.7064 (tpp) REVERT: D 257 MET cc_start: 0.7457 (mmt) cc_final: 0.7249 (mmt) REVERT: H 99 GLN cc_start: 0.8046 (pp30) cc_final: 0.7659 (tm-30) REVERT: H 168 MET cc_start: 0.7417 (tpt) cc_final: 0.6977 (tpp) REVERT: H 257 MET cc_start: 0.7570 (mmt) cc_final: 0.7215 (mmt) REVERT: I 99 GLN cc_start: 0.8098 (pp30) cc_final: 0.7851 (tm-30) REVERT: K 168 MET cc_start: 0.7453 (tpt) cc_final: 0.7177 (tpp) REVERT: K 257 MET cc_start: 0.7480 (mmt) cc_final: 0.7165 (mmt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2257 time to fit residues: 121.2441 Evaluate side-chains 251 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 191 optimal weight: 2.9990 chunk 281 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 321 optimal weight: 40.0000 chunk 227 optimal weight: 4.9990 chunk 367 optimal weight: 8.9990 chunk 172 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS D 21 HIS ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN H 21 HIS H 212 HIS J 21 HIS J 218 GLN K 21 HIS K 218 GLN L 21 HIS L 85 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.123299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.109821 restraints weight = 67505.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109489 restraints weight = 141954.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109379 restraints weight = 124287.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109122 restraints weight = 94061.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109444 restraints weight = 80719.330| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33264 Z= 0.204 Angle : 0.605 8.047 45288 Z= 0.304 Chirality : 0.043 0.153 5292 Planarity : 0.004 0.050 5868 Dihedral : 4.175 17.536 4512 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.13), residues: 4272 helix: 1.65 (0.12), residues: 1956 sheet: -2.31 (0.20), residues: 528 loop : -1.65 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 58 TYR 0.022 0.002 TYR F 94 PHE 0.025 0.002 PHE E 367 TRP 0.010 0.002 TRP E 205 HIS 0.009 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00485 (33264) covalent geometry : angle 0.60540 (45288) hydrogen bonds : bond 0.03509 ( 1491) hydrogen bonds : angle 4.77066 ( 4218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6750 (mmm) cc_final: 0.6411 (tpt) REVERT: A 168 MET cc_start: 0.7583 (tpt) cc_final: 0.7191 (tpp) REVERT: A 257 MET cc_start: 0.7488 (mmt) cc_final: 0.7187 (mmt) REVERT: A 356 PHE cc_start: 0.5972 (t80) cc_final: 0.3030 (m-10) REVERT: B 50 ILE cc_start: 0.8009 (mm) cc_final: 0.7698 (mm) REVERT: B 168 MET cc_start: 0.7468 (tpt) cc_final: 0.7165 (tpp) REVERT: D 257 MET cc_start: 0.7517 (mmt) cc_final: 0.7199 (mmt) REVERT: D 358 LEU cc_start: 0.5046 (pt) cc_final: 0.4705 (tt) REVERT: H 168 MET cc_start: 0.7487 (tpt) cc_final: 0.7268 (tpp) REVERT: H 257 MET cc_start: 0.7673 (mmt) cc_final: 0.7254 (mmt) REVERT: I 99 GLN cc_start: 0.8160 (pp30) cc_final: 0.7937 (tm-30) REVERT: J 56 LEU cc_start: 0.7932 (mm) cc_final: 0.7404 (mm) REVERT: K 168 MET cc_start: 0.7688 (tpt) cc_final: 0.7356 (tpp) REVERT: K 257 MET cc_start: 0.7630 (mmt) cc_final: 0.7295 (mmt) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2267 time to fit residues: 115.3567 Evaluate side-chains 243 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 342 optimal weight: 0.7980 chunk 337 optimal weight: 0.8980 chunk 364 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 242 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS D 21 HIS ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 GLN G 292 GLN H 21 HIS J 21 HIS K 21 HIS K 218 GLN K 282 HIS L 21 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.126104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112510 restraints weight = 66736.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111211 restraints weight = 112498.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111338 restraints weight = 117332.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110829 restraints weight = 91882.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111056 restraints weight = 97943.085| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.113 Angle : 0.557 9.253 45288 Z= 0.275 Chirality : 0.042 0.160 5292 Planarity : 0.004 0.065 5868 Dihedral : 3.740 15.765 4512 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.13), residues: 4272 helix: 1.94 (0.12), residues: 1956 sheet: -2.30 (0.20), residues: 528 loop : -1.50 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 58 TYR 0.013 0.001 TYR E 164 PHE 0.024 0.002 PHE E 367 TRP 0.010 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00266 (33264) covalent geometry : angle 0.55653 (45288) hydrogen bonds : bond 0.02908 ( 1491) hydrogen bonds : angle 4.54013 ( 4218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6717 (mmm) cc_final: 0.6395 (tpt) REVERT: A 168 MET cc_start: 0.7528 (tpt) cc_final: 0.7021 (tpp) REVERT: A 257 MET cc_start: 0.7350 (mmt) cc_final: 0.7144 (mmt) REVERT: A 356 PHE cc_start: 0.5950 (t80) cc_final: 0.3051 (m-10) REVERT: B 50 ILE cc_start: 0.7898 (mm) cc_final: 0.7642 (mm) REVERT: B 58 ARG cc_start: 0.6904 (ptp90) cc_final: 0.6652 (mtm-85) REVERT: B 168 MET cc_start: 0.7399 (tpt) cc_final: 0.7104 (tpp) REVERT: C 168 MET cc_start: 0.7521 (tpt) cc_final: 0.7258 (mmm) REVERT: D 257 MET cc_start: 0.7460 (mmt) cc_final: 0.7205 (mmt) REVERT: D 358 LEU cc_start: 0.5080 (pt) cc_final: 0.4772 (tt) REVERT: H 99 GLN cc_start: 0.8073 (pp30) cc_final: 0.7670 (tm-30) REVERT: H 155 HIS cc_start: 0.7967 (m170) cc_final: 0.7634 (m170) REVERT: H 257 MET cc_start: 0.7612 (mmt) cc_final: 0.7277 (mmt) REVERT: I 99 GLN cc_start: 0.8090 (pp30) cc_final: 0.7847 (tm-30) REVERT: J 56 LEU cc_start: 0.7878 (mm) cc_final: 0.7440 (mm) REVERT: K 168 MET cc_start: 0.7608 (tpt) cc_final: 0.7258 (tpp) REVERT: K 257 MET cc_start: 0.7500 (mmt) cc_final: 0.7206 (mmt) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.2262 time to fit residues: 123.3368 Evaluate side-chains 259 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 260 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 chunk 378 optimal weight: 0.5980 chunk 327 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 333 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 401 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 292 GLN C 239 HIS D 21 HIS ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 HIS I 77 GLN J 21 HIS L 21 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.125969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.111169 restraints weight = 66862.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109886 restraints weight = 118727.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110232 restraints weight = 119970.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110646 restraints weight = 85445.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110698 restraints weight = 84637.151| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.119 Angle : 0.568 8.932 45288 Z= 0.279 Chirality : 0.042 0.164 5292 Planarity : 0.004 0.056 5868 Dihedral : 3.681 15.469 4512 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.13), residues: 4272 helix: 2.03 (0.12), residues: 1956 sheet: -2.46 (0.19), residues: 552 loop : -1.42 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 58 TYR 0.022 0.002 TYR G 94 PHE 0.028 0.002 PHE E 367 TRP 0.010 0.001 TRP H 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00284 (33264) covalent geometry : angle 0.56760 (45288) hydrogen bonds : bond 0.02909 ( 1491) hydrogen bonds : angle 4.51628 ( 4218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8544 Ramachandran restraints generated. 4272 Oldfield, 0 Emsley, 4272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6743 (mmm) cc_final: 0.6408 (tpt) REVERT: A 168 MET cc_start: 0.7584 (tpt) cc_final: 0.7113 (tpp) REVERT: A 356 PHE cc_start: 0.5960 (t80) cc_final: 0.3033 (m-10) REVERT: B 50 ILE cc_start: 0.7914 (mm) cc_final: 0.7668 (mm) REVERT: B 58 ARG cc_start: 0.6994 (ptp90) cc_final: 0.6669 (mtm-85) REVERT: B 168 MET cc_start: 0.7366 (tpt) cc_final: 0.7071 (tpp) REVERT: C 168 MET cc_start: 0.7530 (tpt) cc_final: 0.7174 (tmm) REVERT: C 200 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7970 (mtmt) REVERT: D 168 MET cc_start: 0.7398 (tpt) cc_final: 0.7196 (tpp) REVERT: D 257 MET cc_start: 0.7436 (mmt) cc_final: 0.7209 (mmt) REVERT: D 358 LEU cc_start: 0.5200 (pt) cc_final: 0.4945 (tt) REVERT: H 99 GLN cc_start: 0.8074 (pp30) cc_final: 0.7661 (tm-30) REVERT: H 155 HIS cc_start: 0.7990 (m170) cc_final: 0.7667 (m170) REVERT: H 168 MET cc_start: 0.7137 (tpt) cc_final: 0.6790 (tpp) REVERT: H 257 MET cc_start: 0.7608 (mmt) cc_final: 0.7320 (mmt) REVERT: I 99 GLN cc_start: 0.8096 (pp30) cc_final: 0.7875 (tm-30) REVERT: J 56 LEU cc_start: 0.7961 (mm) cc_final: 0.7481 (mm) REVERT: K 168 MET cc_start: 0.7668 (tpt) cc_final: 0.7326 (tpp) REVERT: K 257 MET cc_start: 0.7317 (mmt) cc_final: 0.7093 (mmt) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2191 time to fit residues: 121.7525 Evaluate side-chains 263 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 261 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 375 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 228 optimal weight: 0.3980 chunk 379 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS D 21 HIS ** D 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 HIS J 21 HIS K 21 HIS L 21 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.125557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.111458 restraints weight = 66377.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110228 restraints weight = 122012.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.110591 restraints weight = 119214.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110809 restraints weight = 82980.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110993 restraints weight = 84796.306| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.130 Angle : 0.569 8.844 45288 Z= 0.281 Chirality : 0.042 0.223 5292 Planarity : 0.004 0.049 5868 Dihedral : 3.706 15.563 4512 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.13), residues: 4272 helix: 2.06 (0.12), residues: 1956 sheet: -2.28 (0.20), residues: 528 loop : -1.44 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 58 TYR 0.017 0.001 TYR J 276 PHE 0.030 0.002 PHE I 367 TRP 0.009 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 Details of bonding type rmsd covalent geometry : bond 0.00311 (33264) covalent geometry : angle 0.56901 (45288) hydrogen bonds : bond 0.02963 ( 1491) hydrogen bonds : angle 4.53395 ( 4218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3835.42 seconds wall clock time: 68 minutes 15.76 seconds (4095.76 seconds total)