Starting phenix.real_space_refine on Thu May 29 20:52:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w9x_37384/05_2025/8w9x_37384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w9x_37384/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w9x_37384/05_2025/8w9x_37384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w9x_37384/05_2025/8w9x_37384.map" model { file = "/net/cci-nas-00/data/ceres_data/8w9x_37384/05_2025/8w9x_37384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w9x_37384/05_2025/8w9x_37384.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} 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: {'GLN:plan1': 4, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 18.98, per 1000 atoms: 0.58 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: 8.88 Conformation dependent library (CDL) restraints added in 4.7 seconds 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: 4.71 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: 11.52 Time building geometry restraints manager: 10.18 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: 0.03 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: 4.130 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: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 72.510 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.460 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.013 0.002 TRP K 205 HIS 0.011 0.002 HIS L 21 PHE 0.033 0.002 PHE D 367 TYR 0.014 0.002 TYR C 94 ARG 0.012 0.001 ARG I 320 Details of bonding type rmsd hydrogen bonds : bond 0.18053 ( 1491) hydrogen bonds : angle 6.38555 ( 4218) covalent geometry : bond 0.00555 (33264) covalent geometry : angle 0.66095 (45288) *********************** 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 : 3.832 Fit side-chains REVERT: A 257 MET cc_start: 0.7619 (mmt) cc_final: 0.7338 (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: 0.7490 (tpp) REVERT: H 88 ILE cc_start: 0.8882 (tp) cc_final: 0.8672 (mm) REVERT: H 118 LEU cc_start: 0.8241 (tt) cc_final: 0.7891 (tp) REVERT: H 257 MET cc_start: 0.7590 (mmt) cc_final: 0.7293 (mmt) REVERT: H 316 MET cc_start: 0.7935 (mmp) cc_final: 0.7526 (ttm) REVERT: L 76 ILE cc_start: 0.7539 (mt) cc_final: 0.7282 (mt) REVERT: L 87 THR cc_start: 0.6707 (m) cc_final: 0.6506 (t) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.4636 time to fit residues: 252.7368 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 : 3.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 181 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 338 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 205 optimal weight: 0.4980 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 218 GLN B 218 GLN C 77 GLN D 21 HIS D 218 GLN H 21 HIS H 218 GLN J 21 HIS K 15 GLN 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 = 0.3857 r_free = 0.3857 target = 0.125787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112252 restraints weight = 66661.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.111034 restraints weight = 116227.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111379 restraints weight = 109808.367| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33264 Z= 0.168 Angle : 0.546 6.487 45288 Z= 0.281 Chirality : 0.042 0.160 5292 Planarity : 0.004 0.076 5868 Dihedral : 4.041 17.059 4512 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4272 helix: 1.41 (0.12), residues: 1944 sheet: -1.98 (0.22), residues: 552 loop : -1.32 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 147 HIS 0.008 0.002 HIS L 21 PHE 0.016 0.002 PHE E 367 TYR 0.015 0.001 TYR L 141 ARG 0.006 0.001 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 1491) hydrogen bonds : angle 4.92850 ( 4218) covalent geometry : bond 0.00394 (33264) covalent geometry : angle 0.54572 (45288) *********************** 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 320 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 4.094 Fit side-chains REVERT: A 73 MET cc_start: 0.6545 (mmm) cc_final: 0.6320 (tpt) REVERT: A 257 MET cc_start: 0.7510 (mmt) cc_final: 0.7211 (mmt) REVERT: A 356 PHE cc_start: 0.5740 (t80) cc_final: 0.3251 (m-10) REVERT: B 356 PHE cc_start: 0.4904 (t80) cc_final: 0.3060 (m-10) REVERT: D 257 MET cc_start: 0.7543 (mmt) cc_final: 0.7302 (mmt) REVERT: E 237 LEU cc_start: 0.7365 (mm) cc_final: 0.7161 (mm) REVERT: H 257 MET cc_start: 0.7569 (mmt) cc_final: 0.7184 (mmt) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.4563 time to fit residues: 234.3497 Evaluate side-chains 227 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 136 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 418 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 416 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 E 85 ASN E 218 GLN E 282 HIS F 218 GLN H 21 HIS H 85 ASN I 218 GLN J 15 GLN J 21 HIS J 218 GLN K 21 HIS L 21 HIS L 218 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.126700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112829 restraints weight = 66684.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111643 restraints weight = 116695.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.111989 restraints weight = 112146.763| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33264 Z= 0.128 Angle : 0.511 6.659 45288 Z= 0.258 Chirality : 0.041 0.155 5292 Planarity : 0.004 0.064 5868 Dihedral : 3.783 16.201 4512 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 4272 helix: 1.62 (0.12), residues: 1944 sheet: -2.02 (0.21), residues: 552 loop : -1.26 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 147 HIS 0.007 0.001 HIS L 21 PHE 0.018 0.002 PHE B 361 TYR 0.012 0.001 TYR K 94 ARG 0.008 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 1491) hydrogen bonds : angle 4.60931 ( 4218) covalent geometry : bond 0.00299 (33264) covalent geometry : angle 0.51113 (45288) *********************** 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 339 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.7540 (mp) cc_final: 0.7308 (mp) REVERT: A 73 MET cc_start: 0.6772 (mmm) cc_final: 0.6429 (tpt) REVERT: A 257 MET cc_start: 0.7441 (mmt) cc_final: 0.7213 (mmt) REVERT: A 356 PHE cc_start: 0.5772 (t80) cc_final: 0.3256 (m-10) REVERT: D 168 MET cc_start: 0.7408 (tpt) cc_final: 0.6939 (tpp) REVERT: G 73 MET cc_start: 0.6646 (mmm) cc_final: 0.6303 (tpt) REVERT: H 99 GLN cc_start: 0.8090 (pp30) cc_final: 0.7743 (tm-30) REVERT: H 168 MET cc_start: 0.7259 (tpt) cc_final: 0.6995 (tpp) REVERT: H 257 MET cc_start: 0.7548 (mmt) cc_final: 0.7241 (mmt) REVERT: I 99 GLN cc_start: 0.8092 (pp30) cc_final: 0.7743 (tm-30) REVERT: L 316 MET cc_start: 0.6161 (ttm) cc_final: 0.5920 (ttm) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.4552 time to fit residues: 244.4928 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 : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 45 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 402 optimal weight: 0.9980 chunk 255 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 218 GLN B 282 HIS C 282 HIS D 21 HIS D 218 GLN E 15 GLN E 176 ASN F 218 GLN G 282 HIS H 21 HIS H 176 ASN I 218 GLN I 282 HIS J 21 HIS J 282 HIS K 21 HIS K 282 HIS L 15 GLN L 21 HIS L 282 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110571 restraints weight = 66904.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109880 restraints weight = 135575.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110236 restraints weight = 123149.309| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33264 Z= 0.165 Angle : 0.546 6.945 45288 Z= 0.278 Chirality : 0.042 0.145 5292 Planarity : 0.004 0.058 5868 Dihedral : 3.947 16.995 4512 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4272 helix: 1.53 (0.12), residues: 1956 sheet: -2.13 (0.21), residues: 552 loop : -1.45 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 147 HIS 0.007 0.001 HIS J 21 PHE 0.019 0.002 PHE B 361 TYR 0.020 0.001 TYR E 141 ARG 0.007 0.001 ARG J 58 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 1491) hydrogen bonds : angle 4.65748 ( 4218) covalent geometry : bond 0.00388 (33264) covalent geometry : angle 0.54566 (45288) *********************** 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 322 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6849 (mmm) cc_final: 0.6507 (tpt) REVERT: A 168 MET cc_start: 0.7437 (tpt) cc_final: 0.7088 (tpp) REVERT: A 356 PHE cc_start: 0.5577 (t80) cc_final: 0.3007 (m-10) REVERT: B 168 MET cc_start: 0.7301 (mmm) cc_final: 0.7074 (tmm) REVERT: D 168 MET cc_start: 0.7583 (tpt) cc_final: 0.7097 (tpp) REVERT: D 257 MET cc_start: 0.7586 (mmt) cc_final: 0.7236 (mmt) REVERT: G 73 MET cc_start: 0.6886 (mmm) cc_final: 0.6479 (tpt) REVERT: H 168 MET cc_start: 0.7382 (tpt) cc_final: 0.7005 (tpp) REVERT: I 99 GLN cc_start: 0.8161 (pp30) cc_final: 0.7873 (tm-30) REVERT: K 168 MET cc_start: 0.7592 (tpt) cc_final: 0.7278 (tpp) REVERT: L 168 MET cc_start: 0.7679 (tpt) cc_final: 0.7337 (tpp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.4704 time to fit residues: 236.9777 Evaluate side-chains 234 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 3.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 298 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 313 optimal weight: 0.9990 chunk 320 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 181 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 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 A 85 ASN D 21 HIS F 282 HIS H 21 HIS J 21 HIS K 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 = 0.3861 r_free = 0.3861 target = 0.126187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112270 restraints weight = 66722.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111345 restraints weight = 114719.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111609 restraints weight = 114935.135| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33264 Z= 0.125 Angle : 0.518 6.833 45288 Z= 0.258 Chirality : 0.041 0.137 5292 Planarity : 0.004 0.055 5868 Dihedral : 3.741 16.244 4512 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4272 helix: 1.76 (0.12), residues: 1956 sheet: -1.91 (0.21), residues: 528 loop : -1.42 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 147 HIS 0.007 0.001 HIS L 21 PHE 0.020 0.001 PHE E 367 TYR 0.011 0.001 TYR J 94 ARG 0.009 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03004 ( 1491) hydrogen bonds : angle 4.47678 ( 4218) covalent geometry : bond 0.00296 (33264) covalent geometry : angle 0.51781 (45288) *********************** 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 335 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 4.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6817 (mmm) cc_final: 0.6493 (tpt) REVERT: A 168 MET cc_start: 0.7515 (tpt) cc_final: 0.7101 (tpp) REVERT: B 168 MET cc_start: 0.7282 (mmm) cc_final: 0.6946 (tmm) REVERT: D 168 MET cc_start: 0.7630 (tpt) cc_final: 0.7081 (tpp) REVERT: D 257 MET cc_start: 0.7676 (mmt) cc_final: 0.7465 (mmt) REVERT: H 99 GLN cc_start: 0.8124 (pp30) cc_final: 0.7713 (tm-30) REVERT: H 168 MET cc_start: 0.7415 (tpt) cc_final: 0.6995 (tpp) REVERT: I 99 GLN cc_start: 0.8126 (pp30) cc_final: 0.7865 (tm-30) REVERT: K 168 MET cc_start: 0.7668 (tpt) cc_final: 0.7306 (tpp) REVERT: L 168 MET cc_start: 0.7648 (tpt) cc_final: 0.7288 (tpp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.4501 time to fit residues: 241.5178 Evaluate side-chains 249 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 310 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 332 optimal weight: 0.9980 chunk 334 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 341 optimal weight: 0.5980 chunk 278 optimal weight: 0.7980 chunk 114 optimal weight: 0.0020 chunk 359 optimal weight: 3.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 H 21 HIS I 85 ASN J 21 HIS K 21 HIS L 21 HIS L 85 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113565 restraints weight = 66378.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112048 restraints weight = 110720.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.112315 restraints weight = 112962.451| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33264 Z= 0.099 Angle : 0.504 7.130 45288 Z= 0.252 Chirality : 0.041 0.150 5292 Planarity : 0.004 0.051 5868 Dihedral : 3.542 14.911 4512 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4272 helix: 1.97 (0.12), residues: 1956 sheet: -1.82 (0.21), residues: 528 loop : -1.36 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 147 HIS 0.007 0.001 HIS L 21 PHE 0.021 0.001 PHE E 367 TYR 0.019 0.001 TYR F 94 ARG 0.009 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 1491) hydrogen bonds : angle 4.36762 ( 4218) covalent geometry : bond 0.00231 (33264) covalent geometry : angle 0.50360 (45288) *********************** 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 348 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 3.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6773 (mmm) cc_final: 0.6425 (tpt) REVERT: A 168 MET cc_start: 0.7501 (tpt) cc_final: 0.7050 (tpp) REVERT: A 257 MET cc_start: 0.7485 (mmt) cc_final: 0.7234 (mmt) REVERT: B 58 ARG cc_start: 0.7014 (ptp90) cc_final: 0.6735 (mtm-85) REVERT: B 168 MET cc_start: 0.7279 (mmm) cc_final: 0.6965 (tmm) REVERT: C 168 MET cc_start: 0.7573 (mmm) cc_final: 0.7355 (mmm) REVERT: D 168 MET cc_start: 0.7599 (tpt) cc_final: 0.6989 (tpp) REVERT: H 99 GLN cc_start: 0.8008 (pp30) cc_final: 0.7698 (tm-30) REVERT: H 168 MET cc_start: 0.7346 (tpt) cc_final: 0.6907 (tpp) REVERT: H 257 MET cc_start: 0.7619 (mmt) cc_final: 0.7288 (mmt) REVERT: I 99 GLN cc_start: 0.8075 (pp30) cc_final: 0.7754 (tm-30) REVERT: J 56 LEU cc_start: 0.7838 (mm) cc_final: 0.7341 (mm) REVERT: K 168 MET cc_start: 0.7630 (tpt) cc_final: 0.7271 (tpp) REVERT: L 168 MET cc_start: 0.7662 (tpt) cc_final: 0.7297 (tmm) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.4547 time to fit residues: 252.1321 Evaluate side-chains 260 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 422 optimal weight: 5.9990 chunk 309 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 347 optimal weight: 0.0670 chunk 80 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 194 optimal weight: 0.4980 chunk 384 optimal weight: 2.9990 chunk 393 optimal weight: 30.0000 overall best weight: 1.3124 ------------------------------------------------------------------------------- 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 F 85 ASN H 21 HIS I 176 ASN J 21 HIS K 21 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 = 0.3851 r_free = 0.3851 target = 0.125392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110980 restraints weight = 67010.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.110693 restraints weight = 137493.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110929 restraints weight = 125231.898| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33264 Z= 0.149 Angle : 0.548 8.406 45288 Z= 0.273 Chirality : 0.042 0.159 5292 Planarity : 0.004 0.050 5868 Dihedral : 3.761 16.201 4512 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4272 helix: 1.87 (0.12), residues: 1956 sheet: -1.96 (0.21), residues: 528 loop : -1.44 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 147 HIS 0.008 0.001 HIS J 21 PHE 0.024 0.002 PHE K 367 TYR 0.032 0.002 TYR E 253 ARG 0.011 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 1491) hydrogen bonds : angle 4.51270 ( 4218) covalent geometry : bond 0.00355 (33264) covalent geometry : angle 0.54847 (45288) *********************** 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 326 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 4.146 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.6778 (mmm) cc_final: 0.6482 (tpt) REVERT: A 168 MET cc_start: 0.7551 (tpt) cc_final: 0.7074 (tpp) REVERT: A 257 MET cc_start: 0.7535 (mmt) cc_final: 0.7232 (mmt) REVERT: A 356 PHE cc_start: 0.5839 (t80) cc_final: 0.3063 (m-10) REVERT: B 50 ILE cc_start: 0.7901 (mm) cc_final: 0.7571 (mm) REVERT: B 58 ARG cc_start: 0.6893 (ptp90) cc_final: 0.6596 (mtm-85) REVERT: B 168 MET cc_start: 0.7270 (mmm) cc_final: 0.6815 (tmm) REVERT: D 168 MET cc_start: 0.7612 (tpt) cc_final: 0.7090 (tpp) REVERT: D 257 MET cc_start: 0.7607 (mmt) cc_final: 0.7294 (mmt) REVERT: D 358 LEU cc_start: 0.4963 (pt) cc_final: 0.4581 (tt) REVERT: H 99 GLN cc_start: 0.8091 (pp30) cc_final: 0.7738 (tm-30) REVERT: H 168 MET cc_start: 0.7448 (tpt) cc_final: 0.7024 (tpp) REVERT: H 257 MET cc_start: 0.7579 (mmt) cc_final: 0.7214 (mmt) REVERT: I 99 GLN cc_start: 0.8124 (pp30) cc_final: 0.7896 (tm-30) REVERT: I 130 VAL cc_start: 0.9014 (t) cc_final: 0.8732 (m) REVERT: J 56 LEU cc_start: 0.7846 (mm) cc_final: 0.7424 (mm) REVERT: K 168 MET cc_start: 0.7641 (tpt) cc_final: 0.7264 (tpp) REVERT: L 168 MET cc_start: 0.7650 (tpt) cc_final: 0.7320 (tmm) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.4532 time to fit residues: 235.3078 Evaluate side-chains 252 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 90 optimal weight: 1.9990 chunk 364 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 428 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 212 HIS D 21 HIS D 282 HIS E 218 GLN G 78 ASN H 21 HIS H 212 HIS H 218 GLN J 21 HIS J 85 ASN J 218 GLN K 21 HIS K 218 GLN L 21 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.122545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108804 restraints weight = 67644.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.109106 restraints weight = 147487.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.108716 restraints weight = 118836.360| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 33264 Z= 0.243 Angle : 0.636 8.003 45288 Z= 0.323 Chirality : 0.044 0.160 5292 Planarity : 0.005 0.049 5868 Dihedral : 4.349 19.512 4512 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4272 helix: 1.47 (0.12), residues: 1956 sheet: -2.34 (0.20), residues: 528 loop : -1.67 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 205 HIS 0.009 0.002 HIS L 21 PHE 0.025 0.002 PHE I 367 TYR 0.019 0.002 TYR E 253 ARG 0.012 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 1491) hydrogen bonds : angle 4.88054 ( 4218) covalent geometry : bond 0.00573 (33264) covalent geometry : angle 0.63584 (45288) *********************** 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 304 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6755 (mmm) cc_final: 0.6461 (tpt) REVERT: A 168 MET cc_start: 0.7624 (tpt) cc_final: 0.7214 (tpp) REVERT: A 257 MET cc_start: 0.7587 (mmt) cc_final: 0.7244 (mmt) REVERT: A 356 PHE cc_start: 0.5959 (t80) cc_final: 0.3018 (m-10) REVERT: B 50 ILE cc_start: 0.7960 (mm) cc_final: 0.7700 (mm) REVERT: B 58 ARG cc_start: 0.6955 (ptp90) cc_final: 0.6685 (mtm-85) REVERT: B 168 MET cc_start: 0.7352 (mmm) cc_final: 0.6815 (tmm) REVERT: C 50 ILE cc_start: 0.8033 (mm) cc_final: 0.7830 (mm) REVERT: D 168 MET cc_start: 0.7659 (tpt) cc_final: 0.7386 (tpp) REVERT: D 257 MET cc_start: 0.7706 (mmt) cc_final: 0.7369 (mmt) REVERT: D 358 LEU cc_start: 0.5129 (pt) cc_final: 0.4826 (tt) REVERT: H 168 MET cc_start: 0.7541 (tpt) cc_final: 0.7328 (tpp) REVERT: I 99 GLN cc_start: 0.8234 (pp30) cc_final: 0.7984 (tm-30) REVERT: K 168 MET cc_start: 0.7759 (tpt) cc_final: 0.7483 (tpp) REVERT: L 168 MET cc_start: 0.7693 (tpt) cc_final: 0.7283 (tmm) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.4565 time to fit residues: 220.2986 Evaluate side-chains 234 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 25 optimal weight: 0.0970 chunk 341 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 346 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 314 optimal weight: 3.9990 chunk 362 optimal weight: 0.2980 chunk 420 optimal weight: 0.9990 chunk 33 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 E 218 GLN F 284 ASN H 21 HIS J 21 HIS K 21 HIS K 218 GLN L 21 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112215 restraints weight = 66568.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110845 restraints weight = 114862.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111150 restraints weight = 113359.268| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 33264 Z= 0.105 Angle : 0.557 8.967 45288 Z= 0.275 Chirality : 0.042 0.155 5292 Planarity : 0.004 0.050 5868 Dihedral : 3.699 15.687 4512 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 4272 helix: 1.88 (0.12), residues: 1956 sheet: -2.26 (0.20), residues: 528 loop : -1.49 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 PHE 0.022 0.001 PHE I 367 TYR 0.012 0.001 TYR E 164 ARG 0.012 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 1491) hydrogen bonds : angle 4.53971 ( 4218) covalent geometry : bond 0.00245 (33264) covalent geometry : angle 0.55727 (45288) *********************** 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 345 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 4.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.7743 (mm) cc_final: 0.7540 (mm) REVERT: A 73 MET cc_start: 0.6701 (mmm) cc_final: 0.6126 (tpt) REVERT: A 168 MET cc_start: 0.7543 (tpt) cc_final: 0.7036 (tpp) REVERT: A 257 MET cc_start: 0.7402 (mmt) cc_final: 0.7183 (mmt) REVERT: A 356 PHE cc_start: 0.5875 (t80) cc_final: 0.2986 (m-10) REVERT: B 50 ILE cc_start: 0.7912 (mm) cc_final: 0.7667 (mm) REVERT: B 58 ARG cc_start: 0.6893 (ptp90) cc_final: 0.6652 (mtm-85) REVERT: B 168 MET cc_start: 0.7310 (mmm) cc_final: 0.6949 (tmm) REVERT: D 168 MET cc_start: 0.7495 (tpt) cc_final: 0.7264 (mmm) REVERT: D 358 LEU cc_start: 0.4927 (pt) cc_final: 0.4684 (tt) REVERT: H 99 GLN cc_start: 0.8081 (pp30) cc_final: 0.7652 (tm-30) REVERT: H 168 MET cc_start: 0.7345 (tpt) cc_final: 0.6886 (tpp) REVERT: I 99 GLN cc_start: 0.8125 (pp30) cc_final: 0.7876 (tm-30) REVERT: I 130 VAL cc_start: 0.8923 (t) cc_final: 0.8616 (m) REVERT: J 56 LEU cc_start: 0.7809 (mm) cc_final: 0.7235 (mm) REVERT: K 168 MET cc_start: 0.7698 (tpt) cc_final: 0.7269 (tpp) REVERT: L 168 MET cc_start: 0.7637 (tpt) cc_final: 0.7278 (tmm) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.4525 time to fit residues: 249.9378 Evaluate side-chains 256 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 228 optimal weight: 5.9990 chunk 389 optimal weight: 0.0770 chunk 349 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 394 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 310 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 H 21 HIS J 21 HIS ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.112474 restraints weight = 66145.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.111047 restraints weight = 109992.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111330 restraints weight = 115827.040| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33264 Z= 0.111 Angle : 0.561 10.198 45288 Z= 0.276 Chirality : 0.042 0.170 5292 Planarity : 0.004 0.049 5868 Dihedral : 3.592 15.130 4512 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4272 helix: 1.99 (0.12), residues: 1944 sheet: -2.39 (0.19), residues: 552 loop : -1.39 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 147 HIS 0.008 0.001 HIS L 21 PHE 0.029 0.002 PHE H 367 TYR 0.023 0.001 TYR G 94 ARG 0.014 0.001 ARG G 58 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 1491) hydrogen bonds : angle 4.50213 ( 4218) covalent geometry : bond 0.00262 (33264) covalent geometry : angle 0.56143 (45288) ********************** 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 343 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.7673 (mm) cc_final: 0.7472 (mm) REVERT: A 73 MET cc_start: 0.6600 (mmm) cc_final: 0.6316 (tpt) REVERT: A 168 MET cc_start: 0.7565 (tpt) cc_final: 0.7092 (tpp) REVERT: A 356 PHE cc_start: 0.5863 (t80) cc_final: 0.2777 (m-10) REVERT: B 50 ILE cc_start: 0.7873 (mm) cc_final: 0.7621 (mm) REVERT: B 58 ARG cc_start: 0.6809 (ptp90) cc_final: 0.6586 (mtm-85) REVERT: B 168 MET cc_start: 0.7333 (mmm) cc_final: 0.6980 (tmm) REVERT: D 168 MET cc_start: 0.7568 (tpt) cc_final: 0.7005 (tpp) REVERT: D 257 MET cc_start: 0.7699 (mmt) cc_final: 0.7376 (mmt) REVERT: D 358 LEU cc_start: 0.4922 (pt) cc_final: 0.4672 (tt) REVERT: G 168 MET cc_start: 0.7135 (tpt) cc_final: 0.6815 (tmm) REVERT: H 99 GLN cc_start: 0.8073 (pp30) cc_final: 0.7644 (tm-30) REVERT: H 168 MET cc_start: 0.7326 (tpt) cc_final: 0.6861 (tpp) REVERT: H 257 MET cc_start: 0.7614 (mmt) cc_final: 0.7219 (mmt) REVERT: I 99 GLN cc_start: 0.8113 (pp30) cc_final: 0.7748 (tm-30) REVERT: I 130 VAL cc_start: 0.8765 (t) cc_final: 0.8477 (m) REVERT: K 168 MET cc_start: 0.7720 (tpt) cc_final: 0.7298 (tpp) REVERT: L 168 MET cc_start: 0.7638 (tpt) cc_final: 0.7247 (tpp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.4505 time to fit residues: 247.6727 Evaluate side-chains 260 residues out of total 3900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 3.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 3 optimal weight: 7.9990 chunk 259 optimal weight: 0.9980 chunk 370 optimal weight: 0.1980 chunk 293 optimal weight: 0.0040 chunk 373 optimal weight: 0.9990 chunk 342 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 59 optimal weight: 0.0570 chunk 51 optimal weight: 0.7980 chunk 374 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 21 HIS B 218 GLN D 21 HIS H 21 HIS H 218 GLN I 218 GLN J 21 HIS ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 GLN K 21 HIS L 21 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113795 restraints weight = 66208.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.112467 restraints weight = 121570.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112742 restraints weight = 109939.412| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33264 Z= 0.097 Angle : 0.546 9.535 45288 Z= 0.266 Chirality : 0.041 0.160 5292 Planarity : 0.004 0.048 5868 Dihedral : 3.423 13.836 4512 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 4272 helix: 2.10 (0.12), residues: 1944 sheet: -2.31 (0.20), residues: 552 loop : -1.33 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 147 HIS 0.008 0.001 HIS L 21 PHE 0.029 0.002 PHE D 367 TYR 0.025 0.001 TYR H 94 ARG 0.015 0.001 ARG D 58 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 1491) hydrogen bonds : angle 4.40177 ( 4218) covalent geometry : bond 0.00226 (33264) covalent geometry : angle 0.54588 (45288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7978.58 seconds wall clock time: 142 minutes 10.85 seconds (8530.85 seconds total)