Starting phenix.real_space_refine on Fri Jul 3 20:55:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0r_22610/07_2026/7k0r_22610.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.144 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 60 5.16 5 C 10290 2.51 5 N 2580 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "E" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2647 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 330} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'PO4': 1, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.20 Number of scatterers: 16038 At special positions: 0 Unit cell: (107.63, 106.485, 124.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 12 15.00 O 3096 8.00 N 2580 7.00 C 10290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 620.8 milliseconds 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3876 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 48 sheets defined 27.0% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.516A pdb=" N GLU A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 308 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 51 through 61 Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 218 through 226 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 308 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 69 through 76 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 208 through 217 Processing helix chain 'D' and resid 218 through 226 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 308 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 69 through 76 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 226 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 69 through 76 Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 208 through 217 Processing helix chain 'F' and resid 218 through 226 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 251 through 262 removed outlier: 3.515A pdb=" N GLU F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL A 32 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.900A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.900A pdb=" N ILE A 80 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP A 125 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR A 99 " --> pdb=" O ILE A 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE A 281 " --> pdb=" O CYS A 291 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS A 291 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP A 283 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER A 289 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER A 329 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET A 331 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 342 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP A 333 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.675A pdb=" N VAL B 32 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE B 80 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR B 99 " --> pdb=" O ILE B 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 163 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 267 removed outlier: 4.793A pdb=" N ILE B 281 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS B 291 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 283 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 289 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER B 329 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET B 331 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 342 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP B 333 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL C 32 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE C 80 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP C 125 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC3, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.862A pdb=" N THR C 99 " --> pdb=" O ILE C 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 163 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE C 281 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS C 291 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP C 283 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER C 289 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER C 329 " --> pdb=" O PRO C 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET C 331 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 342 " --> pdb=" O MET C 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 333 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.677A pdb=" N VAL D 32 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE D 80 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP D 125 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'D' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR D 99 " --> pdb=" O ILE D 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 163 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE D 281 " --> pdb=" O CYS D 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS D 291 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP D 283 " --> pdb=" O SER D 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER D 289 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 316 through 323 removed outlier: 7.553A pdb=" N SER D 329 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET D 331 " --> pdb=" O PHE D 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 342 " --> pdb=" O MET D 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP D 333 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL E 32 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE E 80 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ASP E 125 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'E' and resid 99 through 100 removed outlier: 7.861A pdb=" N THR E 99 " --> pdb=" O ILE E 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 163 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE E 281 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N CYS E 291 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP E 283 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER E 289 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER E 329 " --> pdb=" O PRO E 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET E 331 " --> pdb=" O PHE E 342 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE E 342 " --> pdb=" O MET E 331 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP E 333 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.676A pdb=" N VAL F 32 " --> pdb=" O LEU F 43 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.899A pdb=" N ILE F 80 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP F 125 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'F' and resid 99 through 100 removed outlier: 7.860A pdb=" N THR F 99 " --> pdb=" O ILE F 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 163 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 267 removed outlier: 4.794A pdb=" N ILE F 281 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N CYS F 291 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP F 283 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER F 289 " --> pdb=" O ASP F 283 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 316 through 323 removed outlier: 7.554A pdb=" N SER F 329 " --> pdb=" O PRO F 344 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET F 331 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE F 342 " --> pdb=" O MET F 331 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP F 333 " --> pdb=" O GLU F 340 " (cutoff:3.500A) 660 hydrogen bonds defined for protein. 1710 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: 2.91 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5106 1.33 - 1.45: 2192 1.45 - 1.57: 8980 1.57 - 1.68: 6 1.68 - 1.80: 90 Bond restraints: 16374 Sorted by residual: bond pdb=" O5' U5P B 401 " pdb=" P U5P B 401 " ideal model delta sigma weight residual 1.711 1.590 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" O5' U5P E 401 " pdb=" P U5P E 401 " ideal model delta sigma weight residual 1.711 1.590 0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" O5' U5P C 401 " pdb=" P U5P C 401 " ideal model delta sigma weight residual 1.711 1.591 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" O5' U5P A 401 " pdb=" P U5P A 401 " ideal model delta sigma weight residual 1.711 1.591 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" O5' U5P D 401 " pdb=" P U5P D 401 " ideal model delta sigma weight residual 1.711 1.591 0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 16369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 21240 1.67 - 3.34: 955 3.34 - 5.01: 125 5.01 - 6.68: 15 6.68 - 8.35: 3 Bond angle restraints: 22338 Sorted by residual: angle pdb=" O1P U5P B 401 " pdb=" P U5P B 401 " pdb=" O2P U5P B 401 " ideal model delta sigma weight residual 119.60 111.25 8.35 3.00e+00 1.11e-01 7.75e+00 angle pdb=" O1P U5P C 401 " pdb=" P U5P C 401 " pdb=" O2P U5P C 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" O1P U5P A 401 " pdb=" P U5P A 401 " pdb=" O2P U5P A 401 " ideal model delta sigma weight residual 119.60 111.29 8.31 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CA TYR A 231 " pdb=" CB TYR A 231 " pdb=" CG TYR A 231 " ideal model delta sigma weight residual 113.90 109.32 4.58 1.80e+00 3.09e-01 6.46e+00 angle pdb=" CA TYR B 231 " pdb=" CB TYR B 231 " pdb=" CG TYR B 231 " ideal model delta sigma weight residual 113.90 109.35 4.55 1.80e+00 3.09e-01 6.38e+00 ... (remaining 22333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8916 17.06 - 34.12: 504 34.12 - 51.19: 114 51.19 - 68.25: 30 68.25 - 85.31: 30 Dihedral angle restraints: 9594 sinusoidal: 3588 harmonic: 6006 Sorted by residual: dihedral pdb=" CA PHE A 177 " pdb=" C PHE A 177 " pdb=" N ASN A 178 " pdb=" CA ASN A 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE E 177 " pdb=" C PHE E 177 " pdb=" N ASN E 178 " pdb=" CA ASN E 178 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE D 177 " pdb=" C PHE D 177 " pdb=" N ASN D 178 " pdb=" CA ASN D 178 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1543 0.041 - 0.082: 720 0.082 - 0.123: 261 0.123 - 0.164: 86 0.164 - 0.205: 12 Chirality restraints: 2622 Sorted by residual: chirality pdb=" C2' U5P F 401 " pdb=" C1' U5P F 401 " pdb=" C3' U5P F 401 " pdb=" O2' U5P F 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' U5P D 401 " pdb=" C1' U5P D 401 " pdb=" C3' U5P D 401 " pdb=" O2' U5P D 401 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C1' U5P C 401 " pdb=" C2' U5P C 401 " pdb=" N1 U5P C 401 " pdb=" O4' U5P C 401 " both_signs ideal model delta sigma weight residual False 2.24 2.44 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2619 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.78e+00 pdb=" CG TRP C 59 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP C 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 59 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 59 " -0.010 2.00e-02 2.50e+03 1.05e-02 2.73e+00 pdb=" CG TRP B 59 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 59 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 59 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 59 " 0.010 2.00e-02 2.50e+03 1.04e-02 2.72e+00 pdb=" CG TRP D 59 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP D 59 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 59 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 59 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 355 2.68 - 3.23: 15668 3.23 - 3.79: 26538 3.79 - 4.34: 35240 4.34 - 4.90: 58713 Nonbonded interactions: 136514 Sorted by model distance: nonbonded pdb=" NE2 HIS A 235 " pdb=" O1 PO4 A 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS E 235 " pdb=" O3 PO4 E 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS D 235 " pdb=" O3 PO4 D 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS B 235 " pdb=" O1 PO4 B 402 " model vdw 2.122 3.120 nonbonded pdb=" NE2 HIS C 235 " pdb=" O1 PO4 C 402 " model vdw 2.122 3.120 ... (remaining 136509 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.120 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.010 0.121 16374 Z= 0.443 Angle : 0.792 8.353 22338 Z= 0.433 Chirality : 0.056 0.205 2622 Planarity : 0.004 0.030 2856 Dihedral : 13.366 85.311 5718 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.05 % Allowed : 4.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2058 helix: -1.17 (0.19), residues: 534 sheet: -0.50 (0.26), residues: 336 loop : -0.46 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 136 TYR 0.025 0.003 TYR B 231 PHE 0.026 0.003 PHE D 177 TRP 0.029 0.003 TRP C 59 HIS 0.008 0.002 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00999 / 0.44 (16374) covalent geometry : angle 0.79180 / 0.43 (22338) hydrogen bonds : bond 0.18669 / 12.56 ( 606) hydrogen bonds : angle 8.09397 / 5.87 ( 1710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.442 Fit side-chains REVERT: A 68 PRO cc_start: 0.8223 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: B 245 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7645 (tp40) REVERT: B 331 MET cc_start: 0.6147 (mmm) cc_final: 0.5912 (tpt) REVERT: C 219 MET cc_start: 0.8251 (ttp) cc_final: 0.7654 (ttm) REVERT: E 245 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7183 (tp40) outliers start: 18 outliers final: 2 residues processed: 137 average time/residue: 0.1223 time to fit residues: 25.5976 Evaluate side-chains 60 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 245 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 29 ASN F 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.066240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.057979 restraints weight = 60344.364| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.55 r_work: 0.3312 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16374 Z= 0.133 Angle : 0.496 4.556 22338 Z= 0.271 Chirality : 0.045 0.162 2622 Planarity : 0.003 0.036 2856 Dihedral : 5.224 40.758 2198 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.05 % Allowed : 7.31 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2058 helix: 0.25 (0.22), residues: 534 sheet: 0.87 (0.26), residues: 318 loop : -0.17 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 136 TYR 0.008 0.001 TYR E 238 PHE 0.013 0.001 PHE A 330 TRP 0.011 0.001 TRP B 59 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16374) covalent geometry : angle 0.49559 / 0.27 (22338) hydrogen bonds : bond 0.04091 / 2.74 ( 606) hydrogen bonds : angle 5.63443 / 4.10 ( 1710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.457 Fit side-chains REVERT: B 105 MET cc_start: 0.8166 (mmm) cc_final: 0.7906 (tpt) REVERT: B 331 MET cc_start: 0.6884 (mmm) cc_final: 0.6632 (tpp) REVERT: C 105 MET cc_start: 0.8447 (tpt) cc_final: 0.7974 (tpt) REVERT: C 219 MET cc_start: 0.7873 (ttp) cc_final: 0.7612 (ttm) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.1203 time to fit residues: 16.4947 Evaluate side-chains 68 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 2 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 chunk 167 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN B 29 ASN D 29 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.064711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056415 restraints weight = 61354.383| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.52 r_work: 0.3264 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16374 Z= 0.200 Angle : 0.562 10.376 22338 Z= 0.302 Chirality : 0.047 0.168 2622 Planarity : 0.004 0.031 2856 Dihedral : 4.835 21.108 2192 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.75 % Allowed : 7.43 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2058 helix: 0.51 (0.23), residues: 534 sheet: 0.27 (0.25), residues: 354 loop : -0.09 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 136 TYR 0.018 0.002 TYR D 231 PHE 0.012 0.002 PHE E 269 TRP 0.013 0.002 TRP E 333 HIS 0.006 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (16374) covalent geometry : angle 0.56180 / 0.30 (22338) hydrogen bonds : bond 0.04540 / 3.09 ( 606) hydrogen bonds : angle 5.49923 / 4.00 ( 1710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.419 Fit side-chains REVERT: B 105 MET cc_start: 0.8424 (mmm) cc_final: 0.8119 (tpt) REVERT: B 331 MET cc_start: 0.7536 (mmm) cc_final: 0.7148 (tpp) REVERT: C 219 MET cc_start: 0.8038 (ttp) cc_final: 0.7804 (ttm) outliers start: 30 outliers final: 14 residues processed: 80 average time/residue: 0.0954 time to fit residues: 12.8644 Evaluate side-chains 63 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 243 HIS Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.063831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055260 restraints weight = 61242.070| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.65 r_work: 0.3220 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16374 Z= 0.112 Angle : 0.440 5.414 22338 Z= 0.239 Chirality : 0.044 0.159 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.445 18.041 2190 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.05 % Allowed : 8.42 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2058 helix: 0.72 (0.23), residues: 534 sheet: 1.04 (0.28), residues: 318 loop : -0.09 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 139 TYR 0.009 0.001 TYR E 226 PHE 0.006 0.001 PHE F 222 TRP 0.009 0.001 TRP E 333 HIS 0.003 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (16374) covalent geometry : angle 0.43972 / 0.24 (22338) hydrogen bonds : bond 0.03172 / 2.15 ( 606) hydrogen bonds : angle 4.99507 / 3.63 ( 1710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8569 (mmm) cc_final: 0.8195 (tpt) REVERT: B 331 MET cc_start: 0.7683 (mmm) cc_final: 0.7196 (tpt) REVERT: C 219 MET cc_start: 0.8048 (ttp) cc_final: 0.7760 (ttm) REVERT: C 331 MET cc_start: 0.7571 (tpp) cc_final: 0.7367 (tpt) outliers start: 18 outliers final: 11 residues processed: 66 average time/residue: 0.1014 time to fit residues: 11.3079 Evaluate side-chains 57 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 95 optimal weight: 0.3980 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.062742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054133 restraints weight = 61625.171| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.65 r_work: 0.3204 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.6101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16374 Z= 0.156 Angle : 0.469 6.011 22338 Z= 0.253 Chirality : 0.045 0.160 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.442 16.172 2190 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.05 % Allowed : 9.12 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.18), residues: 2058 helix: 0.75 (0.23), residues: 534 sheet: 1.02 (0.29), residues: 318 loop : -0.11 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.012 0.001 TYR D 231 PHE 0.008 0.001 PHE E 123 TRP 0.011 0.001 TRP E 333 HIS 0.004 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (16374) covalent geometry : angle 0.46948 / 0.25 (22338) hydrogen bonds : bond 0.03339 / 2.27 ( 606) hydrogen bonds : angle 5.04051 / 3.65 ( 1710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8626 (mmm) cc_final: 0.8172 (tpp) REVERT: B 331 MET cc_start: 0.7867 (mmm) cc_final: 0.7258 (tpt) REVERT: F 331 MET cc_start: 0.7899 (mmm) cc_final: 0.6880 (tpt) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 0.1034 time to fit residues: 11.2416 Evaluate side-chains 58 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.061640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.053032 restraints weight = 61958.388| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.66 r_work: 0.3173 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16374 Z= 0.195 Angle : 0.495 5.266 22338 Z= 0.265 Chirality : 0.046 0.156 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.584 15.745 2190 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.46 % Allowed : 9.24 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2058 helix: 0.71 (0.23), residues: 534 sheet: 0.79 (0.29), residues: 336 loop : -0.14 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 207 TYR 0.013 0.001 TYR D 231 PHE 0.010 0.001 PHE D 269 TRP 0.009 0.001 TRP E 333 HIS 0.005 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (16374) covalent geometry : angle 0.49473 / 0.27 (22338) hydrogen bonds : bond 0.03495 / 2.36 ( 606) hydrogen bonds : angle 5.18583 / 3.77 ( 1710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 0.573 Fit side-chains REVERT: B 331 MET cc_start: 0.7982 (mmm) cc_final: 0.7326 (tpt) REVERT: C 210 MET cc_start: 0.8203 (ttm) cc_final: 0.7999 (ttm) REVERT: F 201 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8365 (tp) REVERT: F 331 MET cc_start: 0.7954 (mmm) cc_final: 0.7043 (tpt) outliers start: 25 outliers final: 16 residues processed: 66 average time/residue: 0.0955 time to fit residues: 11.2799 Evaluate side-chains 59 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 201 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.062246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053682 restraints weight = 61511.035| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.63 r_work: 0.3190 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.6843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16374 Z= 0.146 Angle : 0.451 5.684 22338 Z= 0.244 Chirality : 0.045 0.153 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.438 15.811 2190 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.40 % Allowed : 9.36 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2058 helix: 0.74 (0.23), residues: 534 sheet: 1.06 (0.30), residues: 318 loop : -0.18 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.009 0.001 TYR D 226 PHE 0.008 0.001 PHE A 269 TRP 0.008 0.001 TRP E 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16374) covalent geometry : angle 0.45052 / 0.24 (22338) hydrogen bonds : bond 0.03215 / 2.17 ( 606) hydrogen bonds : angle 5.00002 / 3.63 ( 1710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.522 Fit side-chains REVERT: B 219 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (mmm) REVERT: B 331 MET cc_start: 0.7986 (mmm) cc_final: 0.7332 (tpt) REVERT: F 331 MET cc_start: 0.7962 (mmm) cc_final: 0.7049 (tpt) outliers start: 24 outliers final: 19 residues processed: 63 average time/residue: 0.0854 time to fit residues: 9.6429 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.062006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053460 restraints weight = 61930.993| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.65 r_work: 0.3181 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16374 Z= 0.156 Angle : 0.458 6.054 22338 Z= 0.247 Chirality : 0.045 0.152 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.416 15.767 2190 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 9.47 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 2058 helix: 0.82 (0.23), residues: 528 sheet: 1.05 (0.31), residues: 318 loop : -0.21 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.010 0.001 TYR E 231 PHE 0.009 0.001 PHE A 269 TRP 0.008 0.001 TRP E 333 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (16374) covalent geometry : angle 0.45783 / 0.25 (22338) hydrogen bonds : bond 0.03243 / 2.20 ( 606) hydrogen bonds : angle 4.99701 / 3.63 ( 1710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.633 Fit side-chains REVERT: B 219 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8527 (mmm) REVERT: B 331 MET cc_start: 0.8036 (mmm) cc_final: 0.7369 (tpt) REVERT: F 331 MET cc_start: 0.7933 (mmm) cc_final: 0.7064 (tpt) outliers start: 24 outliers final: 20 residues processed: 63 average time/residue: 0.0775 time to fit residues: 9.0359 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 203 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.062594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054119 restraints weight = 61577.524| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.62 r_work: 0.3208 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.7105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16374 Z= 0.110 Angle : 0.426 6.463 22338 Z= 0.232 Chirality : 0.044 0.148 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.273 15.616 2190 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.40 % Allowed : 9.47 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2058 helix: 0.87 (0.23), residues: 528 sheet: 1.18 (0.31), residues: 318 loop : -0.14 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 139 TYR 0.009 0.001 TYR D 226 PHE 0.007 0.001 PHE A 269 TRP 0.005 0.001 TRP E 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (16374) covalent geometry : angle 0.42606 / 0.23 (22338) hydrogen bonds : bond 0.02958 / 2.00 ( 606) hydrogen bonds : angle 4.84429 / 3.51 ( 1710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: B 219 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8556 (mmm) REVERT: B 331 MET cc_start: 0.8022 (mmm) cc_final: 0.7487 (tpt) REVERT: F 331 MET cc_start: 0.7918 (mmm) cc_final: 0.7092 (tpt) outliers start: 24 outliers final: 18 residues processed: 67 average time/residue: 0.1168 time to fit residues: 12.9062 Evaluate side-chains 61 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 170 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053720 restraints weight = 61661.729| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.65 r_work: 0.3194 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16374 Z= 0.145 Angle : 0.448 7.239 22338 Z= 0.242 Chirality : 0.045 0.152 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.316 15.499 2190 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 9.71 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2058 helix: 0.86 (0.23), residues: 528 sheet: 1.20 (0.31), residues: 318 loop : -0.13 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.009 0.001 TYR E 33 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP E 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (16374) covalent geometry : angle 0.44798 / 0.24 (22338) hydrogen bonds : bond 0.03134 / 2.12 ( 606) hydrogen bonds : angle 4.93019 / 3.57 ( 1710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4116 Ramachandran restraints generated. 2058 Oldfield, 0 Emsley, 2058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: B 219 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8598 (mmm) REVERT: B 331 MET cc_start: 0.8029 (mmm) cc_final: 0.7476 (tpt) REVERT: F 331 MET cc_start: 0.7947 (mmm) cc_final: 0.7117 (tpt) outliers start: 21 outliers final: 19 residues processed: 61 average time/residue: 0.0913 time to fit residues: 9.9839 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 219 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 3 optimal weight: 0.5980 chunk 200 optimal weight: 0.0970 chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.063823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055395 restraints weight = 60876.798| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.62 r_work: 0.3220 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16374 Z= 0.072 Angle : 0.403 6.242 22338 Z= 0.220 Chirality : 0.043 0.144 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.077 15.551 2190 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.99 % Allowed : 9.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2058 helix: 0.83 (0.23), residues: 540 sheet: 1.41 (0.31), residues: 318 loop : 0.05 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.009 0.001 TYR D 226 PHE 0.007 0.001 PHE E 330 TRP 0.006 0.001 TRP E 87 HIS 0.002 0.000 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.07 (16374) covalent geometry : angle 0.40305 / 0.22 (22338) hydrogen bonds : bond 0.02630 / 1.79 ( 606) hydrogen bonds : angle 4.62718 / 3.35 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2476.52 seconds wall clock time: 43 minutes 45.42 seconds (2625.42 seconds total)