Starting phenix.real_space_refine on Sat Sep 12 13:45:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0r_22610/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0r_22610/09_2026/7k0r_22610.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.82, per 1000 atoms: 0.24 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: 1.49 Conformation dependent library (CDL) restraints added in 740.9 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: 0.59 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: 2.92 Time building geometry restraints manager: 1.91 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=" O3 PO4 D 402 " pdb=" P PO4 D 402 " ideal model delta sigma weight residual 1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" O3 PO4 F 402 " pdb=" P PO4 F 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 E 402 " pdb=" P PO4 E 402 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" O3 PO4 A 402 " pdb=" P PO4 A 402 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 16369 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 20495 1.30 - 2.61: 1560 2.61 - 3.91: 202 3.91 - 5.21: 66 5.21 - 6.51: 15 Bond angle restraints: 22338 Sorted by residual: 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 angle pdb=" CA TYR E 231 " pdb=" CB TYR E 231 " pdb=" CG TYR E 231 " ideal model delta sigma weight residual 113.90 109.36 4.54 1.80e+00 3.09e-01 6.36e+00 angle pdb=" CA TYR D 231 " pdb=" CB TYR D 231 " pdb=" CG TYR D 231 " ideal model delta sigma weight residual 113.90 109.36 4.54 1.80e+00 3.09e-01 6.35e+00 angle pdb=" CA TYR F 231 " pdb=" CB TYR F 231 " pdb=" CG TYR F 231 " ideal model delta sigma weight residual 113.90 109.38 4.52 1.80e+00 3.09e-01 6.32e+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 - 0.032: 1261 0.032 - 0.063: 726 0.063 - 0.095: 398 0.095 - 0.127: 168 0.127 - 0.158: 69 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 80 " pdb=" N ILE A 80 " pdb=" C ILE A 80 " pdb=" CB ILE A 80 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CB ILE B 28 " pdb=" CA ILE B 28 " pdb=" CG1 ILE B 28 " pdb=" CG2 ILE B 28 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.94e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (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: 1.070 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.430 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- 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 0.065 16374 Z= 0.426 Angle : 0.779 6.513 22338 Z= 0.433 Chirality : 0.054 0.158 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 0.00968 / 0.43 (16374) covalent geometry : angle 0.77945 / 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 : 0.648 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: 0.1271 time to fit residues: 26.8662 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 : 0.740 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.066300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.058037 restraints weight = 60246.601| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.55 r_work: 0.3315 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16374 Z= 0.125 Angle : 0.491 4.536 22338 Z= 0.271 Chirality : 0.045 0.172 2622 Planarity : 0.003 0.035 2856 Dihedral : 5.242 40.849 2198 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.11 % Allowed : 7.31 % Favored : 91.58 % 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: 0.11 (0.17), residues: 2058 helix: 0.24 (0.22), residues: 534 sheet: 0.88 (0.26), residues: 318 loop : -0.16 (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 B 179 PHE 0.012 0.001 PHE A 330 TRP 0.012 0.001 TRP B 59 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16374) covalent geometry : angle 0.49053 / 0.27 (22338) hydrogen bonds : bond 0.03859 / 2.58 ( 606) hydrogen bonds : angle 5.64663 / 4.11 ( 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 93 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.620 Fit side-chains REVERT: B 105 MET cc_start: 0.8182 (mmm) cc_final: 0.7917 (tpt) REVERT: B 331 MET cc_start: 0.6894 (mmm) cc_final: 0.6653 (tpp) REVERT: C 105 MET cc_start: 0.8468 (tpt) cc_final: 0.8012 (tpt) REVERT: C 219 MET cc_start: 0.7875 (ttp) cc_final: 0.7620 (ttm) REVERT: E 331 MET cc_start: 0.6228 (mtp) cc_final: 0.6025 (ttm) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.1282 time to fit residues: 18.3178 Evaluate side-chains 69 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 2 SER 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: 5.9990 chunk 4 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 164 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN B 29 ASN D 29 ASN E 29 ASN F 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.064135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.055753 restraints weight = 61610.494| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.52 r_work: 0.3248 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.005 0.049 16374 Z= 0.223 Angle : 0.588 7.910 22338 Z= 0.318 Chirality : 0.048 0.176 2622 Planarity : 0.004 0.027 2856 Dihedral : 5.003 21.567 2192 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.64 % Allowed : 7.66 % Favored : 90.70 % 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: -0.01 (0.17), residues: 2058 helix: 0.30 (0.22), residues: 534 sheet: 0.21 (0.26), residues: 354 loop : -0.12 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 136 TYR 0.025 0.002 TYR E 238 PHE 0.013 0.002 PHE E 269 TRP 0.012 0.002 TRP F 59 HIS 0.006 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (16374) covalent geometry : angle 0.58801 / 0.32 (22338) hydrogen bonds : bond 0.04661 / 3.18 ( 606) hydrogen bonds : angle 5.59484 / 4.07 ( 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: 28 poor density : 57 time to evaluate : 0.600 Fit side-chains REVERT: B 331 MET cc_start: 0.7606 (mmm) cc_final: 0.7163 (tpp) REVERT: C 219 MET cc_start: 0.8140 (ttp) cc_final: 0.7885 (ttm) outliers start: 28 outliers final: 14 residues processed: 81 average time/residue: 0.1079 time to fit residues: 14.9957 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain C residue 52 VAL 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 E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 314 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.062989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054377 restraints weight = 61562.006| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.65 r_work: 0.3221 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5665 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= 0.139 Angle : 0.454 6.600 22338 Z= 0.249 Chirality : 0.045 0.158 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.580 17.783 2190 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.35 % Allowed : 8.30 % Favored : 90.35 % 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: 0.24 (0.18), residues: 2058 helix: 0.55 (0.23), residues: 534 sheet: 0.92 (0.28), residues: 318 loop : -0.16 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.021 0.001 TYR B 238 PHE 0.007 0.001 PHE A 269 TRP 0.009 0.001 TRP C 333 HIS 0.004 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (16374) covalent geometry : angle 0.45397 / 0.25 (22338) hydrogen bonds : bond 0.03383 / 2.29 ( 606) hydrogen bonds : angle 5.08344 / 3.70 ( 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 72 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.672 Fit side-chains REVERT: B 219 MET cc_start: 0.8192 (mmt) cc_final: 0.7817 (mmt) REVERT: B 331 MET cc_start: 0.7745 (mmm) cc_final: 0.7246 (tpt) REVERT: D 219 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8315 (mmt) REVERT: E 331 MET cc_start: 0.6730 (tpt) cc_final: 0.6389 (tpp) outliers start: 23 outliers final: 13 residues processed: 70 average time/residue: 0.1157 time to fit residues: 13.6994 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 : 0.706 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 301 ASP 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 52 VAL Chi-restraints excluded: chain D residue 219 MET 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: 8.9990 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 129 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.061609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.052966 restraints weight = 62035.774| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.66 r_work: 0.3175 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16374 Z= 0.191 Angle : 0.496 5.050 22338 Z= 0.268 Chirality : 0.046 0.155 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.628 16.207 2190 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.64 % Allowed : 8.54 % 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: 0.14 (0.18), residues: 2058 helix: 0.56 (0.23), residues: 534 sheet: 0.25 (0.27), residues: 372 loop : -0.08 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 139 TYR 0.018 0.002 TYR B 238 PHE 0.012 0.001 PHE C 233 TRP 0.009 0.001 TRP C 333 HIS 0.005 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (16374) covalent geometry : angle 0.49632 / 0.27 (22338) hydrogen bonds : bond 0.03657 / 2.47 ( 606) hydrogen bonds : angle 5.21416 / 3.79 ( 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 72 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 0.731 Fit side-chains REVERT: B 331 MET cc_start: 0.7984 (mmm) cc_final: 0.7351 (tpt) REVERT: D 201 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8279 (tp) REVERT: E 331 MET cc_start: 0.7484 (tpt) cc_final: 0.6905 (tpp) REVERT: F 331 MET cc_start: 0.8010 (mmm) cc_final: 0.7070 (tpt) outliers start: 28 outliers final: 21 residues processed: 70 average time/residue: 0.1077 time to fit residues: 12.9349 Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL 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 2 SER 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 F residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 135 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.062628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054019 restraints weight = 61570.322| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.64 r_work: 0.3184 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 16374 Z= 0.116 Angle : 0.432 6.022 22338 Z= 0.236 Chirality : 0.044 0.150 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.407 16.235 2190 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.17 % Allowed : 9.18 % Favored : 89.65 % 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: 0.31 (0.18), residues: 2058 helix: 0.65 (0.23), residues: 534 sheet: 0.98 (0.29), residues: 318 loop : -0.16 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.008 0.001 TYR D 226 PHE 0.007 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16374) covalent geometry : angle 0.43174 / 0.24 (22338) hydrogen bonds : bond 0.03162 / 2.15 ( 606) hydrogen bonds : angle 4.92622 / 3.58 ( 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 63 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.695 Fit side-chains REVERT: B 219 MET cc_start: 0.7934 (mmt) cc_final: 0.7036 (mmp) REVERT: B 331 MET cc_start: 0.7955 (mmm) cc_final: 0.7360 (tpt) REVERT: E 331 MET cc_start: 0.7623 (tpt) cc_final: 0.7066 (tpp) REVERT: F 331 MET cc_start: 0.7998 (mmm) cc_final: 0.7059 (tpt) outliers start: 20 outliers final: 16 residues processed: 63 average time/residue: 0.1085 time to fit residues: 11.9656 Evaluate side-chains 58 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 C residue 52 VAL 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 97 ILE Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 0.0000 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.062887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054329 restraints weight = 61310.489| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.63 r_work: 0.3187 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16374 Z= 0.113 Angle : 0.427 7.659 22338 Z= 0.233 Chirality : 0.044 0.148 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.284 15.887 2190 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.52 % Allowed : 9.12 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 2058 helix: 0.79 (0.23), residues: 528 sheet: 1.11 (0.30), residues: 318 loop : -0.15 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.011 0.001 TYR B 238 PHE 0.007 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (16374) covalent geometry : angle 0.42705 / 0.23 (22338) hydrogen bonds : bond 0.03063 / 2.08 ( 606) hydrogen bonds : angle 4.81198 / 3.49 ( 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 71 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.677 Fit side-chains REVERT: B 219 MET cc_start: 0.8379 (mmt) cc_final: 0.7569 (mmp) REVERT: B 331 MET cc_start: 0.7983 (mmm) cc_final: 0.7375 (tpt) REVERT: E 331 MET cc_start: 0.7758 (tpt) cc_final: 0.7162 (tpp) REVERT: F 331 MET cc_start: 0.8001 (mmm) cc_final: 0.7137 (tpt) outliers start: 26 outliers final: 22 residues processed: 71 average time/residue: 0.1125 time to fit residues: 13.5476 Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 97 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL 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 233 PHE Chi-restraints excluded: chain E residue 2 SER 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 255 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 97 ILE 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: 0.9990 chunk 77 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 76 optimal weight: 0.0030 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.063556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055013 restraints weight = 61364.151| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.65 r_work: 0.3210 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16374 Z= 0.089 Angle : 0.410 7.114 22338 Z= 0.225 Chirality : 0.044 0.143 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.154 15.759 2190 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.29 % Allowed : 9.42 % 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: 0.50 (0.19), residues: 2058 helix: 0.86 (0.23), residues: 528 sheet: 1.22 (0.30), residues: 318 loop : -0.09 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 139 TYR 0.012 0.001 TYR D 238 PHE 0.007 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.002 0.000 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (16374) covalent geometry : angle 0.41033 / 0.22 (22338) hydrogen bonds : bond 0.02870 / 1.95 ( 606) hydrogen bonds : angle 4.64688 / 3.37 ( 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 67 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 45 time to evaluate : 0.586 Fit side-chains REVERT: B 219 MET cc_start: 0.8533 (mmt) cc_final: 0.7745 (mmp) REVERT: B 331 MET cc_start: 0.7935 (mmm) cc_final: 0.7422 (tpt) REVERT: E 331 MET cc_start: 0.7800 (tpt) cc_final: 0.7233 (tpp) REVERT: F 331 MET cc_start: 0.7962 (mmm) cc_final: 0.7143 (tpt) outliers start: 22 outliers final: 19 residues processed: 67 average time/residue: 0.0954 time to fit residues: 11.1143 Evaluate side-chains 64 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 C residue 52 VAL 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 233 PHE Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 52 VAL 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: 6.9990 chunk 171 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 203 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 69 optimal weight: 0.0870 chunk 133 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.062926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054323 restraints weight = 61523.940| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.66 r_work: 0.3187 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16374 Z= 0.124 Angle : 0.425 4.976 22338 Z= 0.232 Chirality : 0.044 0.147 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.199 15.518 2190 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.05 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: 0.49 (0.19), residues: 2058 helix: 0.84 (0.23), residues: 528 sheet: 1.22 (0.31), residues: 318 loop : -0.10 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.019 0.001 TYR D 238 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.002 0.001 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16374) covalent geometry : angle 0.42522 / 0.23 (22338) hydrogen bonds : bond 0.03030 / 2.05 ( 606) hydrogen bonds : angle 4.78084 / 3.47 ( 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 : 0.602 Fit side-chains REVERT: B 331 MET cc_start: 0.7974 (mmm) cc_final: 0.7396 (tpt) REVERT: D 219 MET cc_start: 0.7717 (mmp) cc_final: 0.7355 (mmt) REVERT: E 331 MET cc_start: 0.7947 (tpt) cc_final: 0.7505 (tpp) REVERT: F 331 MET cc_start: 0.7968 (mmm) cc_final: 0.7160 (tpt) outliers start: 24 outliers final: 20 residues processed: 68 average time/residue: 0.0954 time to fit residues: 11.7490 Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 C residue 2 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL 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 233 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 97 ILE 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: 0.0070 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.063236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054664 restraints weight = 61232.925| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.64 r_work: 0.3222 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.7055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.109 Angle : 0.418 7.526 22338 Z= 0.228 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.159 15.631 2190 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.40 % Allowed : 9.53 % 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: 0.54 (0.19), residues: 2058 helix: 0.85 (0.23), residues: 528 sheet: 1.30 (0.31), residues: 318 loop : -0.06 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 139 TYR 0.014 0.001 TYR D 238 PHE 0.007 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.002 0.000 HIS E 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16374) covalent geometry : angle 0.41804 / 0.23 (22338) hydrogen bonds : bond 0.02971 / 2.02 ( 606) hydrogen bonds : angle 4.73140 / 3.43 ( 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 70 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 46 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 331 MET cc_start: 0.7970 (mmm) cc_final: 0.7467 (tpt) REVERT: C 219 MET cc_start: 0.8620 (mmm) cc_final: 0.8286 (tpp) REVERT: D 201 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8339 (tp) REVERT: D 219 MET cc_start: 0.7808 (mmp) cc_final: 0.7425 (mmt) REVERT: E 331 MET cc_start: 0.7930 (tpt) cc_final: 0.7448 (tpp) REVERT: F 331 MET cc_start: 0.7956 (mmm) cc_final: 0.7145 (tpt) outliers start: 24 outliers final: 20 residues processed: 70 average time/residue: 0.0955 time to fit residues: 12.0671 Evaluate side-chains 65 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 255 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 52 VAL 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 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 97 ILE 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: 0.3980 chunk 200 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 202 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.064272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055808 restraints weight = 60662.344| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.62 r_work: 0.3232 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16374 Z= 0.074 Angle : 0.395 6.678 22338 Z= 0.217 Chirality : 0.043 0.144 2622 Planarity : 0.003 0.027 2856 Dihedral : 3.995 15.535 2190 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.11 % Allowed : 10.06 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.19), residues: 2058 helix: 0.94 (0.23), residues: 528 sheet: 1.44 (0.31), residues: 318 loop : 0.03 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 139 TYR 0.012 0.001 TYR D 238 PHE 0.007 0.001 PHE B 233 TRP 0.006 0.001 TRP B 87 HIS 0.006 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00157 / 0.07 (16374) covalent geometry : angle 0.39451 / 0.22 (22338) hydrogen bonds : bond 0.02612 / 1.78 ( 606) hydrogen bonds : angle 4.52704 / 3.28 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.04 seconds wall clock time: 47 minutes 54.51 seconds (2874.51 seconds total)