Starting phenix.real_space_refine on Wed Mar 4 20:31:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0r_22610/03_2026/7k0r_22610.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0r_22610/03_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_22610/03_2026/7k0r_22610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0r_22610/03_2026/7k0r_22610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0r_22610/03_2026/7k0r_22610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0r_22610/03_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-dev-5986/lib/python3.9/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: 3.76, per 1000 atoms: 0.23 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: 1.46 Conformation dependent library (CDL) restraints added in 845.8 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: 0.47 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: 2.90 Time building geometry restraints manager: 1.89 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: 8928 17.06 - 34.12: 564 34.12 - 51.19: 126 51.19 - 68.25: 78 68.25 - 85.31: 30 Dihedral angle restraints: 9726 sinusoidal: 3720 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 9723 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: 0.05 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: 1.090 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.520 Find NCS groups from input model: 0.130 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:1.320 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 14.722 85.311 5850 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 covalent geometry : bond 0.00999 (16374) covalent geometry : angle 0.79180 (22338) hydrogen bonds : bond 0.18669 ( 606) hydrogen bonds : angle 8.09397 ( 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 : 0.598 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: 0.1324 time to fit residues: 27.6184 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 : 0.631 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3628 r_free = 0.3628 target = 0.066347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.058104 restraints weight = 60426.890| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.54 r_work: 0.3313 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16374 Z= 0.127 Angle : 0.515 4.557 22338 Z= 0.278 Chirality : 0.045 0.177 2622 Planarity : 0.003 0.034 2856 Dihedral : 7.031 46.274 2330 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.11 % Allowed : 7.37 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2058 helix: 0.26 (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 0.003 0.001 ARG A 136 TYR 0.010 0.001 TYR A 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 covalent geometry : bond 0.00279 (16374) covalent geometry : angle 0.51460 (22338) hydrogen bonds : bond 0.03859 ( 606) hydrogen bonds : angle 5.66928 ( 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 94 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8164 (mmm) cc_final: 0.7892 (tpt) REVERT: B 331 MET cc_start: 0.6873 (mmm) cc_final: 0.6635 (tpp) REVERT: C 105 MET cc_start: 0.8481 (tpt) cc_final: 0.8016 (tpt) REVERT: E 331 MET cc_start: 0.6199 (mtp) cc_final: 0.5992 (ttm) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.1176 time to fit residues: 16.4610 Evaluate side-chains 70 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 0.7980 chunk 167 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3601 r_free = 0.3601 target = 0.065219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056888 restraints weight = 61192.739| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.56 r_work: 0.3277 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16374 Z= 0.167 Angle : 0.528 7.110 22338 Z= 0.284 Chirality : 0.046 0.170 2622 Planarity : 0.003 0.039 2856 Dihedral : 4.868 34.553 2324 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.58 % Allowed : 7.72 % 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: 0.27 (0.18), residues: 2058 helix: 0.68 (0.23), residues: 534 sheet: 0.56 (0.26), residues: 354 loop : -0.09 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.015 0.002 TYR D 231 PHE 0.010 0.001 PHE E 269 TRP 0.010 0.002 TRP D 87 HIS 0.006 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00378 (16374) covalent geometry : angle 0.52800 (22338) hydrogen bonds : bond 0.03946 ( 606) hydrogen bonds : angle 5.19673 ( 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: 27 poor density : 58 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 128 VAL cc_start: 0.8188 (t) cc_final: 0.7908 (t) REVERT: B 105 MET cc_start: 0.8412 (mmm) cc_final: 0.8109 (tpt) REVERT: B 331 MET cc_start: 0.7527 (mmm) cc_final: 0.7120 (tpp) outliers start: 27 outliers final: 13 residues processed: 81 average time/residue: 0.0993 time to fit residues: 13.5604 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 128 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.064795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056255 restraints weight = 60955.234| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.64 r_work: 0.3253 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16374 Z= 0.089 Angle : 0.420 4.932 22338 Z= 0.228 Chirality : 0.044 0.149 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.436 23.042 2322 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.94 % Allowed : 8.60 % Favored : 90.47 % 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: 0.57 (0.18), residues: 2058 helix: 0.82 (0.23), residues: 534 sheet: 1.59 (0.30), residues: 288 loop : -0.05 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.010 0.001 TYR E 226 PHE 0.008 0.001 PHE C 330 TRP 0.009 0.001 TRP C 333 HIS 0.004 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00201 (16374) covalent geometry : angle 0.42005 (22338) hydrogen bonds : bond 0.02753 ( 606) hydrogen bonds : angle 4.74591 ( 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: 16 poor density : 52 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: B 105 MET cc_start: 0.8507 (mmm) cc_final: 0.8161 (tpt) REVERT: B 331 MET cc_start: 0.7668 (mmm) cc_final: 0.7192 (tpt) REVERT: F 219 MET cc_start: 0.8078 (mtt) cc_final: 0.7837 (mtt) outliers start: 16 outliers final: 9 residues processed: 68 average time/residue: 0.1156 time to fit residues: 12.7745 Evaluate side-chains 57 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain B residue 2 SER 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 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: 5.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 126 optimal weight: 0.0470 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.062488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.053901 restraints weight = 61743.363| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.64 r_work: 0.3204 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16374 Z= 0.190 Angle : 0.487 5.596 22338 Z= 0.263 Chirality : 0.046 0.154 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.597 19.644 2322 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.23 % Allowed : 8.71 % Favored : 90.06 % 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: 0.39 (0.18), residues: 2058 helix: 0.71 (0.23), residues: 534 sheet: 1.12 (0.29), residues: 318 loop : -0.12 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 139 TYR 0.018 0.002 TYR D 238 PHE 0.012 0.001 PHE A 269 TRP 0.011 0.001 TRP C 333 HIS 0.005 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00441 (16374) covalent geometry : angle 0.48707 (22338) hydrogen bonds : bond 0.03481 ( 606) hydrogen bonds : angle 5.07682 ( 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 68 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: B 331 MET cc_start: 0.7897 (mmm) cc_final: 0.7262 (tpt) REVERT: E 40 ASP cc_start: 0.8299 (m-30) cc_final: 0.8032 (p0) REVERT: F 331 MET cc_start: 0.7886 (mmm) cc_final: 0.6906 (tpt) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 0.1141 time to fit residues: 12.6612 Evaluate side-chains 59 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 53 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.063190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054615 restraints weight = 61143.247| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.63 r_work: 0.3225 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16374 Z= 0.116 Angle : 0.423 4.457 22338 Z= 0.231 Chirality : 0.044 0.148 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.362 17.721 2322 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.40 % Allowed : 8.77 % 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: 0.48 (0.18), residues: 2058 helix: 0.77 (0.23), residues: 534 sheet: 1.24 (0.29), residues: 318 loop : -0.08 (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 E 226 PHE 0.008 0.001 PHE C 233 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00269 (16374) covalent geometry : angle 0.42336 (22338) hydrogen bonds : bond 0.02987 ( 606) hydrogen bonds : angle 4.81287 ( 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 72 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.798 Fit side-chains REVERT: B 331 MET cc_start: 0.7922 (mmm) cc_final: 0.7344 (tpt) REVERT: F 331 MET cc_start: 0.7890 (mmm) cc_final: 0.6924 (tpt) outliers start: 24 outliers final: 18 residues processed: 70 average time/residue: 0.1107 time to fit residues: 13.0788 Evaluate side-chains 62 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 C residue 2 SER 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 2 SER Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 201 LEU 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: 2.9990 chunk 83 optimal weight: 0.0670 chunk 28 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.063412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.054862 restraints weight = 60807.241| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.63 r_work: 0.3209 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16374 Z= 0.103 Angle : 0.413 4.472 22338 Z= 0.225 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.028 2856 Dihedral : 4.230 16.229 2322 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.58 % Allowed : 8.83 % Favored : 89.59 % 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: 0.58 (0.19), residues: 2058 helix: 0.87 (0.23), residues: 534 sheet: 1.36 (0.30), residues: 318 loop : -0.04 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.008 0.001 TYR E 226 PHE 0.008 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 covalent geometry : bond 0.00237 (16374) covalent geometry : angle 0.41293 (22338) hydrogen bonds : bond 0.02865 ( 606) hydrogen bonds : angle 4.69232 ( 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 75 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.595 Fit side-chains REVERT: B 331 MET cc_start: 0.7959 (mmm) cc_final: 0.7369 (tpt) REVERT: F 331 MET cc_start: 0.7866 (mmm) cc_final: 0.6912 (tpt) outliers start: 27 outliers final: 21 residues processed: 73 average time/residue: 0.1075 time to fit residues: 13.2534 Evaluate side-chains 67 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 233 PHE 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 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 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 233 PHE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain F residue 201 LEU 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: 5.9990 chunk 77 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 76 optimal weight: 0.0370 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.063537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055020 restraints weight = 61160.786| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.64 r_work: 0.3212 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16374 Z= 0.102 Angle : 0.414 7.075 22338 Z= 0.225 Chirality : 0.044 0.144 2622 Planarity : 0.003 0.027 2856 Dihedral : 4.195 15.959 2322 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.58 % Allowed : 9.01 % Favored : 89.42 % 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: 0.63 (0.19), residues: 2058 helix: 0.88 (0.23), residues: 534 sheet: 1.44 (0.30), residues: 318 loop : -0.01 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.008 0.001 TYR E 226 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00236 (16374) covalent geometry : angle 0.41415 (22338) hydrogen bonds : bond 0.02848 ( 606) hydrogen bonds : angle 4.64706 ( 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 75 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.690 Fit side-chains REVERT: B 331 MET cc_start: 0.7967 (mmm) cc_final: 0.7366 (tpt) REVERT: F 331 MET cc_start: 0.7886 (mmm) cc_final: 0.7022 (tpt) outliers start: 27 outliers final: 20 residues processed: 74 average time/residue: 0.1036 time to fit residues: 13.4009 Evaluate side-chains 66 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 233 PHE 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 C residue 2 SER 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 97 ILE Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 255 LEU 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: 6.9990 chunk 171 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 203 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.059256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050170 restraints weight = 62086.111| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.91 r_work: 0.3050 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 16374 Z= 0.285 Angle : 0.568 6.670 22338 Z= 0.302 Chirality : 0.048 0.172 2622 Planarity : 0.003 0.036 2856 Dihedral : 4.894 16.042 2322 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.35 % Allowed : 9.18 % Favored : 89.47 % 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: 0.22 (0.19), residues: 2058 helix: 0.64 (0.23), residues: 528 sheet: 0.45 (0.28), residues: 372 loop : -0.10 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 139 TYR 0.018 0.002 TYR C 33 PHE 0.014 0.002 PHE D 269 TRP 0.008 0.001 TRP C 333 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00669 (16374) covalent geometry : angle 0.56841 (22338) hydrogen bonds : bond 0.03924 ( 606) hydrogen bonds : angle 5.33711 ( 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 63 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.628 Fit side-chains REVERT: B 331 MET cc_start: 0.8122 (mmm) cc_final: 0.7326 (tpt) REVERT: F 331 MET cc_start: 0.7879 (mmm) cc_final: 0.6834 (tpt) outliers start: 23 outliers final: 15 residues processed: 61 average time/residue: 0.0901 time to fit residues: 9.9905 Evaluate side-chains 56 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 255 LEU 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 233 PHE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054696 restraints weight = 60993.187| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.65 r_work: 0.3204 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.002 0.030 16374 Z= 0.095 Angle : 0.426 6.707 22338 Z= 0.233 Chirality : 0.044 0.146 2622 Planarity : 0.003 0.025 2856 Dihedral : 4.367 16.888 2322 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.94 % Allowed : 9.59 % Favored : 89.47 % 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: 0.48 (0.19), residues: 2058 helix: 0.66 (0.23), residues: 540 sheet: 1.29 (0.30), residues: 318 loop : -0.03 (0.18), residues: 1200 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 0.006 0.001 PHE A 269 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00213 (16374) covalent geometry : angle 0.42596 (22338) hydrogen bonds : bond 0.02950 ( 606) hydrogen bonds : angle 4.79487 ( 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 64 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.547 Fit side-chains REVERT: B 331 MET cc_start: 0.8000 (mmm) cc_final: 0.7455 (tpt) REVERT: F 272 MET cc_start: 0.8881 (ptm) cc_final: 0.8619 (ptt) REVERT: F 331 MET cc_start: 0.7868 (mmm) cc_final: 0.7151 (tpt) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.1140 time to fit residues: 11.9893 Evaluate side-chains 57 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 255 LEU 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 233 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 255 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: 0.9980 chunk 200 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 176 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.064079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.055666 restraints weight = 60614.721| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.61 r_work: 0.3229 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16374 Z= 0.081 Angle : 0.405 6.250 22338 Z= 0.221 Chirality : 0.043 0.143 2622 Planarity : 0.003 0.026 2856 Dihedral : 4.094 17.721 2322 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.88 % Allowed : 9.77 % 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: 0.71 (0.19), residues: 2058 helix: 0.97 (0.23), residues: 528 sheet: 1.52 (0.31), residues: 318 loop : 0.01 (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 226 PHE 0.008 0.001 PHE C 233 TRP 0.007 0.001 TRP B 87 HIS 0.002 0.000 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00179 (16374) covalent geometry : angle 0.40492 (22338) hydrogen bonds : bond 0.02697 ( 606) hydrogen bonds : angle 4.56673 ( 1710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.56 seconds wall clock time: 44 minutes 57.43 seconds (2697.43 seconds total)