Starting phenix.real_space_refine on Fri Mar 6 07:20:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.map" model { file = "/net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rb2_24392/03_2026/7rb2_24392.cif" } resolution = 3.27 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16352 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10537 2.51 5 N 2659 2.21 5 O 3124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 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: 16386 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2783 Chain: "B" Number of atoms: 2737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2732 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2783 Chain: "C" Number of atoms: 2721 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2716 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 347, 2716 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 2767 Chain: "D" Number of atoms: 2725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2720 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2771 Chain: "E" Number of atoms: 2733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 2779 Chain: "F" Number of atoms: 2733 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 347, 2728 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2779 Time building chain proxies: 6.63, per 1000 atoms: 0.40 Number of scatterers: 16386 At special positions: 0 Unit cell: (111.354, 110.523, 124.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3124 8.00 N 2659 7.00 C 10537 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: 1.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3912 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 39 sheets defined 27.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 removed outlier: 3.554A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.920A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.726A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 removed outlier: 3.507A pdb=" N LEU B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 removed outlier: 3.848A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.691A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.761A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.567A pdb=" N LEU C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 removed outlier: 3.702A pdb=" N LEU C 133 " --> pdb=" O GLY C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 227 through 230 removed outlier: 3.961A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.668A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.572A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 137 removed outlier: 3.670A pdb=" N LEU D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 226 Processing helix chain 'D' and resid 227 through 230 removed outlier: 3.736A pdb=" N TYR D 230 " --> pdb=" O LEU D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.727A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 1 through 13 removed outlier: 3.922A pdb=" N VAL E 5 " --> pdb=" O SER E 1 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 removed outlier: 3.592A pdb=" N LEU E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 137 removed outlier: 3.908A pdb=" N LEU E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.509A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 removed outlier: 3.593A pdb=" N LEU F 72 " --> pdb=" O GLU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 removed outlier: 3.849A pdb=" N LEU F 133 " --> pdb=" O GLY F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 removed outlier: 3.688A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.698A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.578A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.124A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 142 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.002A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.766A pdb=" N GLU A 264 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 281 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 266 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 322 removed outlier: 6.733A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.555A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.042A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.508A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB2, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.749A pdb=" N GLU B 264 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 281 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.358A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.539A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.217A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.419A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AB8, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.916A pdb=" N GLU C 264 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 281 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.359A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.531A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.198A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC4, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.488A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AC6, first strand: chain 'D' and resid 264 through 266 removed outlier: 3.838A pdb=" N GLU D 264 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 281 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 315 through 322 removed outlier: 6.582A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 24 through 26 removed outlier: 6.570A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.151A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.525A pdb=" N ALA E 92 " --> pdb=" O ASP E 87 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.346A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AD4, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AD5, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.184A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR E 281 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.427A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 25 through 26 removed outlier: 6.560A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.121A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.555A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AE2, first strand: chain 'F' and resid 264 through 266 removed outlier: 3.927A pdb=" N GLU F 264 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 281 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.356A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1419 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: 2.50 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3423 1.33 - 1.45: 3727 1.45 - 1.57: 9482 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16734 Sorted by residual: bond pdb=" N THR D 340 " pdb=" CA THR D 340 " ideal model delta sigma weight residual 1.455 1.494 -0.040 1.25e-02 6.40e+03 1.01e+01 bond pdb=" N THR F 340 " pdb=" CA THR F 340 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.27e-02 6.20e+03 8.78e+00 bond pdb=" C PRO D 343 " pdb=" O PRO D 343 " ideal model delta sigma weight residual 1.233 1.205 0.029 1.06e-02 8.90e+03 7.30e+00 bond pdb=" N THR C 340 " pdb=" CA THR C 340 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.25e-02 6.40e+03 6.88e+00 bond pdb=" C PRO B 343 " pdb=" O PRO B 343 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.08e-02 8.57e+03 6.31e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 21609 1.53 - 3.06: 940 3.06 - 4.58: 130 4.58 - 6.11: 38 6.11 - 7.64: 13 Bond angle restraints: 22730 Sorted by residual: angle pdb=" N GLU E 223 " pdb=" CA GLU E 223 " pdb=" CB GLU E 223 " ideal model delta sigma weight residual 110.30 117.22 -6.92 1.54e+00 4.22e-01 2.02e+01 angle pdb=" C TYR C 342 " pdb=" CA TYR C 342 " pdb=" CB TYR C 342 " ideal model delta sigma weight residual 109.42 116.23 -6.81 1.57e+00 4.06e-01 1.88e+01 angle pdb=" N GLU F 223 " pdb=" CA GLU F 223 " pdb=" CB GLU F 223 " ideal model delta sigma weight residual 110.20 116.58 -6.38 1.49e+00 4.50e-01 1.83e+01 angle pdb=" C PRO F 343 " pdb=" CA PRO F 343 " pdb=" CB PRO F 343 " ideal model delta sigma weight residual 111.46 106.28 5.18 1.21e+00 6.83e-01 1.83e+01 angle pdb=" C PRO D 343 " pdb=" CA PRO D 343 " pdb=" CB PRO D 343 " ideal model delta sigma weight residual 111.11 106.18 4.93 1.17e+00 7.31e-01 1.78e+01 ... (remaining 22725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9088 17.97 - 35.94: 734 35.94 - 53.91: 120 53.91 - 71.88: 41 71.88 - 89.85: 17 Dihedral angle restraints: 10000 sinusoidal: 3934 harmonic: 6066 Sorted by residual: dihedral pdb=" CA LEU F 297 " pdb=" C LEU F 297 " pdb=" N LEU F 298 " pdb=" CA LEU F 298 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A 340 " pdb=" C THR A 340 " pdb=" N PHE A 341 " pdb=" CA PHE A 341 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TYR E 230 " pdb=" C TYR E 230 " pdb=" N ALA E 231 " pdb=" CA ALA E 231 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1735 0.047 - 0.095: 703 0.095 - 0.142: 169 0.142 - 0.190: 10 0.190 - 0.237: 5 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CG LEU D 227 " pdb=" CB LEU D 227 " pdb=" CD1 LEU D 227 " pdb=" CD2 LEU D 227 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PHE F 341 " pdb=" N PHE F 341 " pdb=" C PHE F 341 " pdb=" CB PHE F 341 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR C 342 " pdb=" N TYR C 342 " pdb=" C TYR C 342 " pdb=" CB TYR C 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2619 not shown) Planarity restraints: 2924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C THR A 340 " -0.073 2.00e-02 2.50e+03 pdb=" O THR A 340 " 0.027 2.00e-02 2.50e+03 pdb=" N PHE A 341 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 194 " -0.019 2.00e-02 2.50e+03 2.03e-02 7.25e+00 pdb=" CG PHE F 194 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE F 194 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE F 194 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 194 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 194 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE F 194 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 328 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C SER C 328 " 0.037 2.00e-02 2.50e+03 pdb=" O SER C 328 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 329 " -0.012 2.00e-02 2.50e+03 ... (remaining 2921 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 15210 3.20 - 3.77: 24677 3.77 - 4.33: 35792 4.33 - 4.90: 60090 Nonbonded interactions: 136001 Sorted by model distance: nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.075 3.040 nonbonded pdb=" OH TYR F 193 " pdb=" OE2 GLU F 304 " model vdw 2.081 3.040 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.082 3.040 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.105 3.040 nonbonded pdb=" OD2 ASP A 212 " pdb=" OH TYR A 225 " model vdw 2.109 3.040 ... (remaining 135996 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB )) or resid 265 through 333 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 345)) selection = (chain 'B' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB )) or resid 265 through 333 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 345)) selection = (chain 'C' and (resid -1 through 35 or resid 37 through 201 or (resid 202 and (n \ ame N or name CA or name C or name O or name CB )) or resid 203 or (resid 204 an \ d (name N or name CA or name C or name O or name CB )) or resid 205 through 225 \ or (resid 226 and (name N or name CA or name C or name O or name CB )) or resid \ 227 through 263 or (resid 264 and (name N or name CA or name C or name O or name \ CB )) or resid 265 through 345)) selection = (chain 'D' and (resid -1 through 35 or resid 37 through 190 or (resid 191 and (n \ ame N or name CA or name C or name O or name CB )) or resid 192 through 203 or ( \ resid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 \ through 222 or (resid 223 and (name N or name CA or name C or name O or name CB \ )) or resid 224 through 263 or (resid 264 and (name N or name CA or name C or na \ me O or name CB )) or resid 265 through 333 or (resid 334 and (name N or name CA \ or name C or name O or name CB )) or resid 335 through 345)) selection = (chain 'E' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 222 or (resid 223 and (name N or name CA or name C or na \ me O or name CB )) or resid 224 through 225 or (resid 226 and (name N or name CA \ or name C or name O or name CB )) or resid 227 through 263 or (resid 264 and (n \ ame N or name CA or name C or name O or name CB )) or resid 265 through 333 or ( \ resid 334 and (name N or name CA or name C or name O or name CB )) or resid 335 \ through 345)) selection = (chain 'F' and (resid -1 through 35 or resid 37 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 190 or ( \ resid 191 and (name N or name CA or name C or name O or name CB )) or resid 192 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 or (resid 204 and (name N or name CA or name C or name O or name \ CB )) or resid 205 through 222 or (resid 223 and (name N or name CA or name C o \ r name O or name CB )) or resid 224 through 225 or (resid 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 333 or (resid 334 an \ d (name N or name CA or name C or name O or name CB )) or resid 335 through 345) \ ) } 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=0.22 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: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.350 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.008 0.067 16734 Z= 0.345 Angle : 0.743 7.639 22730 Z= 0.434 Chirality : 0.051 0.237 2622 Planarity : 0.004 0.042 2924 Dihedral : 14.446 89.852 6088 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.33 % Allowed : 0.65 % Favored : 99.02 % 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: -1.06 (0.19), residues: 2076 helix: -0.83 (0.22), residues: 516 sheet: -1.02 (0.30), residues: 366 loop : -0.42 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 138 TYR 0.021 0.002 TYR E 179 PHE 0.046 0.003 PHE F 194 TRP 0.007 0.002 TRP C 58 HIS 0.005 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00767 (16734) covalent geometry : angle 0.74252 (22730) hydrogen bonds : bond 0.20432 ( 535) hydrogen bonds : angle 8.65865 ( 1419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 0.498 Fit side-chains REVERT: A 199 ASN cc_start: 0.7720 (t0) cc_final: 0.7514 (t0) REVERT: A 301 ASP cc_start: 0.7884 (m-30) cc_final: 0.7592 (m-30) REVERT: B 342 TYR cc_start: 0.6896 (p90) cc_final: 0.6193 (m-10) REVERT: C 199 ASN cc_start: 0.7765 (t0) cc_final: 0.7345 (t0) REVERT: C 301 ASP cc_start: 0.7923 (m-30) cc_final: 0.7616 (m-30) REVERT: D 172 VAL cc_start: 0.8885 (p) cc_final: 0.8485 (m) REVERT: D 330 MET cc_start: 0.6994 (tpt) cc_final: 0.6341 (tpt) REVERT: D 342 TYR cc_start: 0.6736 (p90) cc_final: 0.6014 (m-10) REVERT: E 199 ASN cc_start: 0.8293 (t0) cc_final: 0.8004 (t0) REVERT: E 264 GLU cc_start: 0.6732 (pt0) cc_final: 0.6510 (pt0) REVERT: E 266 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7832 (mm-30) REVERT: F 21 GLU cc_start: 0.8070 (mp0) cc_final: 0.7722 (mp0) REVERT: F 183 ASP cc_start: 0.8337 (m-30) cc_final: 0.8114 (m-30) REVERT: F 235 ILE cc_start: 0.8819 (pt) cc_final: 0.8593 (pt) REVERT: F 301 ASP cc_start: 0.7738 (m-30) cc_final: 0.7454 (m-30) REVERT: F 340 THR cc_start: 0.4671 (OUTLIER) cc_final: 0.4290 (p) outliers start: 6 outliers final: 3 residues processed: 252 average time/residue: 0.1251 time to fit residues: 48.0688 Evaluate side-chains 214 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 210 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.3980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN A 28 ASN B 28 ASN B 249 HIS C 4 ASN D 163 ASN D 309 GLN E 28 ASN F 11 ASN F 244 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115024 restraints weight = 37167.207| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.30 r_work: 0.3026 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16734 Z= 0.115 Angle : 0.545 6.260 22730 Z= 0.299 Chirality : 0.045 0.246 2622 Planarity : 0.004 0.027 2924 Dihedral : 5.083 50.312 2214 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.60 % Allowed : 6.06 % Favored : 93.34 % 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: 2076 helix: -0.00 (0.23), residues: 522 sheet: -0.46 (0.31), residues: 360 loop : -0.22 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.014 0.001 TYR A 342 PHE 0.026 0.001 PHE F 194 TRP 0.007 0.001 TRP D 332 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00254 (16734) covalent geometry : angle 0.54482 (22730) hydrogen bonds : bond 0.03669 ( 535) hydrogen bonds : angle 6.10910 ( 1419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 277 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.8472 (m-80) cc_final: 0.7773 (m-80) REVERT: A 301 ASP cc_start: 0.8135 (m-30) cc_final: 0.7900 (t0) REVERT: B 342 TYR cc_start: 0.7046 (p90) cc_final: 0.6037 (m-10) REVERT: C 199 ASN cc_start: 0.8142 (t0) cc_final: 0.7872 (t0) REVERT: C 236 VAL cc_start: 0.8946 (t) cc_final: 0.8677 (t) REVERT: C 301 ASP cc_start: 0.8211 (m-30) cc_final: 0.7905 (m-30) REVERT: D 193 TYR cc_start: 0.8407 (m-80) cc_final: 0.7070 (m-80) REVERT: D 330 MET cc_start: 0.7286 (tpt) cc_final: 0.6859 (tpt) REVERT: D 342 TYR cc_start: 0.6793 (p90) cc_final: 0.5903 (m-10) REVERT: E 199 ASN cc_start: 0.8486 (t0) cc_final: 0.8211 (t0) REVERT: E 235 ILE cc_start: 0.8814 (pt) cc_final: 0.8473 (mt) REVERT: E 342 TYR cc_start: 0.7010 (p90) cc_final: 0.5612 (m-10) REVERT: F 235 ILE cc_start: 0.8873 (pt) cc_final: 0.8649 (pt) outliers start: 11 outliers final: 7 residues processed: 287 average time/residue: 0.1294 time to fit residues: 55.2499 Evaluate side-chains 229 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain F residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 0.0170 chunk 167 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 181 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS C 28 ASN F 28 ASN F 199 ASN F 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112104 restraints weight = 36128.225| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.15 r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16734 Z= 0.216 Angle : 0.573 6.209 22730 Z= 0.312 Chirality : 0.047 0.189 2622 Planarity : 0.004 0.030 2924 Dihedral : 5.047 48.700 2210 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.93 % Allowed : 8.51 % Favored : 90.56 % 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: -0.43 (0.19), residues: 2076 helix: -0.02 (0.23), residues: 522 sheet: -0.22 (0.30), residues: 360 loop : -0.33 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 138 TYR 0.018 0.002 TYR F 193 PHE 0.030 0.002 PHE C 194 TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00516 (16734) covalent geometry : angle 0.57274 (22730) hydrogen bonds : bond 0.04189 ( 535) hydrogen bonds : angle 6.02203 ( 1419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8619 (mp0) cc_final: 0.8356 (mp0) REVERT: A 193 TYR cc_start: 0.8471 (m-80) cc_final: 0.7706 (m-80) REVERT: A 301 ASP cc_start: 0.8149 (m-30) cc_final: 0.7906 (t0) REVERT: B 342 TYR cc_start: 0.7165 (p90) cc_final: 0.6059 (m-10) REVERT: C 193 TYR cc_start: 0.8484 (m-80) cc_final: 0.7821 (m-80) REVERT: C 199 ASN cc_start: 0.8259 (t0) cc_final: 0.7945 (t0) REVERT: C 236 VAL cc_start: 0.8942 (t) cc_final: 0.8688 (t) REVERT: C 301 ASP cc_start: 0.8209 (m-30) cc_final: 0.7935 (t0) REVERT: C 342 TYR cc_start: 0.6786 (p90) cc_final: 0.5244 (m-10) REVERT: D 330 MET cc_start: 0.7360 (tpt) cc_final: 0.6977 (tpt) REVERT: D 342 TYR cc_start: 0.7033 (p90) cc_final: 0.5839 (m-10) REVERT: E 199 ASN cc_start: 0.8529 (t0) cc_final: 0.8217 (t0) REVERT: F 28 ASN cc_start: 0.8095 (m-40) cc_final: 0.7818 (m110) REVERT: F 193 TYR cc_start: 0.8144 (m-80) cc_final: 0.7720 (m-80) REVERT: F 199 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8074 (p0) REVERT: F 235 ILE cc_start: 0.8905 (pt) cc_final: 0.8676 (pt) outliers start: 17 outliers final: 12 residues processed: 246 average time/residue: 0.1312 time to fit residues: 49.0974 Evaluate side-chains 242 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 151 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN F 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117172 restraints weight = 46729.538| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 5.41 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16734 Z= 0.112 Angle : 0.496 7.000 22730 Z= 0.271 Chirality : 0.044 0.161 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.701 50.962 2210 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.38 % Allowed : 10.42 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.17 (0.19), residues: 2076 helix: 0.27 (0.23), residues: 522 sheet: 0.11 (0.30), residues: 360 loop : -0.28 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 138 TYR 0.018 0.001 TYR F 193 PHE 0.022 0.001 PHE A 194 TRP 0.008 0.001 TRP E 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00261 (16734) covalent geometry : angle 0.49613 (22730) hydrogen bonds : bond 0.03131 ( 535) hydrogen bonds : angle 5.54350 ( 1419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7865 (m-80) cc_final: 0.7162 (m-80) REVERT: B 138 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7671 (mtp-110) REVERT: B 183 ASP cc_start: 0.8483 (m-30) cc_final: 0.8228 (m-30) REVERT: B 193 TYR cc_start: 0.7821 (m-80) cc_final: 0.7441 (m-80) REVERT: B 342 TYR cc_start: 0.7006 (p90) cc_final: 0.5997 (m-10) REVERT: C 193 TYR cc_start: 0.7757 (m-80) cc_final: 0.7164 (m-80) REVERT: D 227 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5751 (mp) REVERT: D 330 MET cc_start: 0.6839 (tpt) cc_final: 0.6528 (tpt) REVERT: D 342 TYR cc_start: 0.6795 (p90) cc_final: 0.5851 (m-10) REVERT: E 193 TYR cc_start: 0.7806 (m-80) cc_final: 0.6642 (m-80) REVERT: E 199 ASN cc_start: 0.8309 (t0) cc_final: 0.7978 (t0) REVERT: E 292 CYS cc_start: 0.7478 (t) cc_final: 0.7197 (t) REVERT: F 193 TYR cc_start: 0.7426 (m-80) cc_final: 0.6953 (m-80) REVERT: F 235 ILE cc_start: 0.8914 (pt) cc_final: 0.8664 (pt) outliers start: 7 outliers final: 5 residues processed: 273 average time/residue: 0.1221 time to fit residues: 50.5463 Evaluate side-chains 254 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 136 ASN A 234 HIS F 152 GLN F 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115516 restraints weight = 47072.770| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 5.60 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16734 Z= 0.135 Angle : 0.504 6.513 22730 Z= 0.276 Chirality : 0.045 0.197 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.645 51.413 2210 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.55 % Allowed : 12.49 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2076 helix: 0.35 (0.23), residues: 522 sheet: 0.22 (0.30), residues: 360 loop : -0.29 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 257 TYR 0.019 0.002 TYR F 193 PHE 0.026 0.002 PHE B 194 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00320 (16734) covalent geometry : angle 0.50407 (22730) hydrogen bonds : bond 0.03276 ( 535) hydrogen bonds : angle 5.52254 ( 1419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 256 time to evaluate : 0.610 Fit side-chains REVERT: B 193 TYR cc_start: 0.7844 (m-80) cc_final: 0.6601 (m-80) REVERT: B 342 TYR cc_start: 0.6910 (p90) cc_final: 0.5904 (m-10) REVERT: C 193 TYR cc_start: 0.7533 (m-80) cc_final: 0.6709 (m-80) REVERT: D 227 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5793 (mp) REVERT: D 330 MET cc_start: 0.6894 (tpt) cc_final: 0.6593 (tpt) REVERT: D 342 TYR cc_start: 0.6792 (p90) cc_final: 0.5785 (m-10) REVERT: E 193 TYR cc_start: 0.7850 (m-80) cc_final: 0.6622 (m-80) REVERT: E 199 ASN cc_start: 0.8305 (t0) cc_final: 0.7975 (t0) REVERT: E 264 GLU cc_start: 0.6685 (pt0) cc_final: 0.6381 (pt0) REVERT: E 266 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7534 (mm-30) REVERT: E 292 CYS cc_start: 0.7448 (t) cc_final: 0.7197 (t) REVERT: F 172 VAL cc_start: 0.8812 (p) cc_final: 0.8541 (m) REVERT: F 199 ASN cc_start: 0.8033 (p0) cc_final: 0.7824 (p0) REVERT: F 235 ILE cc_start: 0.8899 (pt) cc_final: 0.8640 (pt) outliers start: 10 outliers final: 6 residues processed: 260 average time/residue: 0.1271 time to fit residues: 50.1924 Evaluate side-chains 246 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 239 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 330 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.0670 chunk 31 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN F 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114727 restraints weight = 35828.932| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.28 r_work: 0.3026 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16734 Z= 0.139 Angle : 0.502 6.643 22730 Z= 0.275 Chirality : 0.045 0.186 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.632 51.756 2210 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.60 % Allowed : 13.20 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.18), residues: 2076 helix: 0.37 (0.23), residues: 522 sheet: 0.32 (0.30), residues: 360 loop : -0.29 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.020 0.002 TYR F 193 PHE 0.030 0.002 PHE C 194 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00331 (16734) covalent geometry : angle 0.50245 (22730) hydrogen bonds : bond 0.03247 ( 535) hydrogen bonds : angle 5.46905 ( 1419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 251 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: B 193 TYR cc_start: 0.8449 (m-80) cc_final: 0.7074 (m-80) REVERT: B 342 TYR cc_start: 0.7209 (p90) cc_final: 0.5923 (m-10) REVERT: C 193 TYR cc_start: 0.8255 (m-80) cc_final: 0.7309 (m-80) REVERT: D 227 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5732 (mp) REVERT: D 330 MET cc_start: 0.7281 (tpt) cc_final: 0.6957 (tpt) REVERT: D 342 TYR cc_start: 0.7053 (p90) cc_final: 0.5793 (m-10) REVERT: E 193 TYR cc_start: 0.8419 (m-80) cc_final: 0.7054 (m-80) REVERT: E 199 ASN cc_start: 0.8478 (t0) cc_final: 0.8153 (t0) REVERT: E 264 GLU cc_start: 0.7200 (pt0) cc_final: 0.6957 (pt0) REVERT: E 266 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8050 (mm-30) REVERT: E 292 CYS cc_start: 0.8239 (t) cc_final: 0.8036 (t) REVERT: F 172 VAL cc_start: 0.9008 (p) cc_final: 0.8520 (m) REVERT: F 235 ILE cc_start: 0.8913 (pt) cc_final: 0.8680 (pt) outliers start: 11 outliers final: 8 residues processed: 257 average time/residue: 0.1183 time to fit residues: 46.4669 Evaluate side-chains 253 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 28 ASN C 28 ASN E 28 ASN E 175 GLN F 4 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116892 restraints weight = 33082.541| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.82 r_work: 0.3080 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16734 Z= 0.093 Angle : 0.465 6.726 22730 Z= 0.255 Chirality : 0.044 0.174 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.386 52.343 2210 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.55 % Allowed : 13.86 % Favored : 85.60 % 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: 0.07 (0.18), residues: 2076 helix: 0.53 (0.24), residues: 522 sheet: 0.68 (0.31), residues: 348 loop : -0.30 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.014 0.001 TYR F 193 PHE 0.020 0.001 PHE C 194 TRP 0.008 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00215 (16734) covalent geometry : angle 0.46541 (22730) hydrogen bonds : bond 0.02738 ( 535) hydrogen bonds : angle 5.18771 ( 1419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 TYR cc_start: 0.8399 (m-80) cc_final: 0.7032 (m-80) REVERT: C 193 TYR cc_start: 0.8163 (m-80) cc_final: 0.7149 (m-80) REVERT: D 227 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5780 (mp) REVERT: D 330 MET cc_start: 0.7242 (tpt) cc_final: 0.6932 (tpt) REVERT: D 342 TYR cc_start: 0.7156 (p90) cc_final: 0.5774 (m-10) REVERT: E 193 TYR cc_start: 0.8340 (m-80) cc_final: 0.6930 (m-80) REVERT: E 199 ASN cc_start: 0.8464 (t0) cc_final: 0.8081 (t0) REVERT: E 264 GLU cc_start: 0.7038 (pt0) cc_final: 0.6753 (pt0) REVERT: E 266 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8021 (mm-30) REVERT: E 292 CYS cc_start: 0.8153 (t) cc_final: 0.7928 (t) REVERT: F 235 ILE cc_start: 0.8911 (pt) cc_final: 0.8657 (pt) outliers start: 10 outliers final: 6 residues processed: 277 average time/residue: 0.1274 time to fit residues: 52.7676 Evaluate side-chains 256 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 249 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain F residue 291 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.141653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113788 restraints weight = 35937.385| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.15 r_work: 0.3024 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16734 Z= 0.176 Angle : 0.539 8.140 22730 Z= 0.291 Chirality : 0.046 0.171 2622 Planarity : 0.003 0.030 2924 Dihedral : 4.670 52.008 2210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.55 % Allowed : 14.73 % Favored : 84.72 % 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: -0.06 (0.18), residues: 2076 helix: 0.31 (0.23), residues: 528 sheet: 0.44 (0.30), residues: 360 loop : -0.28 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 138 TYR 0.030 0.002 TYR B 342 PHE 0.035 0.002 PHE B 194 TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00418 (16734) covalent geometry : angle 0.53908 (22730) hydrogen bonds : bond 0.03501 ( 535) hydrogen bonds : angle 5.44599 ( 1419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.632 Fit side-chains REVERT: A 172 VAL cc_start: 0.9133 (p) cc_final: 0.8705 (m) REVERT: B 193 TYR cc_start: 0.8412 (m-80) cc_final: 0.6996 (m-80) REVERT: B 342 TYR cc_start: 0.7052 (p90) cc_final: 0.5784 (m-10) REVERT: C 193 TYR cc_start: 0.8280 (m-80) cc_final: 0.7149 (m-80) REVERT: D 21 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: D 227 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5739 (mt) REVERT: D 330 MET cc_start: 0.7314 (tpt) cc_final: 0.6994 (tpt) REVERT: D 342 TYR cc_start: 0.7163 (p90) cc_final: 0.5777 (m-10) REVERT: E 193 TYR cc_start: 0.8382 (m-80) cc_final: 0.7000 (m-80) REVERT: E 199 ASN cc_start: 0.8493 (t0) cc_final: 0.8137 (t0) REVERT: E 266 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8076 (mm-30) REVERT: E 292 CYS cc_start: 0.8222 (t) cc_final: 0.7963 (t) REVERT: F 235 ILE cc_start: 0.8918 (pt) cc_final: 0.8673 (pt) outliers start: 10 outliers final: 7 residues processed: 255 average time/residue: 0.1274 time to fit residues: 49.3970 Evaluate side-chains 248 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 239 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain F residue 291 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 0.0980 chunk 142 optimal weight: 0.4980 chunk 47 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 28 ASN B 28 ASN C 28 ASN D 28 ASN E 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117057 restraints weight = 43038.434| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.98 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16734 Z= 0.099 Angle : 0.490 8.119 22730 Z= 0.264 Chirality : 0.044 0.160 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.422 52.428 2210 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.49 % Allowed : 14.95 % Favored : 84.56 % 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: 0.07 (0.18), residues: 2076 helix: 0.51 (0.24), residues: 522 sheet: 0.53 (0.30), residues: 360 loop : -0.25 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 138 TYR 0.032 0.001 TYR B 342 PHE 0.023 0.001 PHE B 194 TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00231 (16734) covalent geometry : angle 0.48994 (22730) hydrogen bonds : bond 0.02811 ( 535) hydrogen bonds : angle 5.17263 ( 1419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 193 TYR cc_start: 0.7733 (m-80) cc_final: 0.6462 (m-80) REVERT: B 342 TYR cc_start: 0.6532 (p90) cc_final: 0.5761 (m-80) REVERT: D 21 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: D 227 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5786 (mt) REVERT: D 330 MET cc_start: 0.6795 (tpt) cc_final: 0.6486 (tpt) REVERT: D 342 TYR cc_start: 0.6866 (p90) cc_final: 0.5746 (m-10) REVERT: E 193 TYR cc_start: 0.7476 (m-80) cc_final: 0.6355 (m-80) REVERT: E 199 ASN cc_start: 0.8244 (t0) cc_final: 0.7901 (t0) REVERT: E 264 GLU cc_start: 0.6550 (pt0) cc_final: 0.6184 (pt0) REVERT: E 266 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7456 (mm-30) REVERT: E 292 CYS cc_start: 0.7238 (t) cc_final: 0.6983 (t) REVERT: F 235 ILE cc_start: 0.8926 (pt) cc_final: 0.8654 (pt) outliers start: 9 outliers final: 7 residues processed: 258 average time/residue: 0.1250 time to fit residues: 48.8015 Evaluate side-chains 256 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 247 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.143255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115993 restraints weight = 46709.971| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 5.38 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16734 Z= 0.137 Angle : 0.514 7.883 22730 Z= 0.277 Chirality : 0.045 0.163 2622 Planarity : 0.003 0.030 2924 Dihedral : 4.498 52.269 2210 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.55 % Allowed : 14.84 % Favored : 84.62 % 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: 0.05 (0.18), residues: 2076 helix: 0.39 (0.23), residues: 528 sheet: 0.57 (0.30), residues: 360 loop : -0.23 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 138 TYR 0.025 0.002 TYR B 342 PHE 0.029 0.002 PHE B 194 TRP 0.008 0.001 TRP E 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00325 (16734) covalent geometry : angle 0.51449 (22730) hydrogen bonds : bond 0.03134 ( 535) hydrogen bonds : angle 5.26951 ( 1419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 246 time to evaluate : 0.660 Fit side-chains REVERT: B 193 TYR cc_start: 0.7728 (m-80) cc_final: 0.6421 (m-80) REVERT: B 342 TYR cc_start: 0.6711 (p90) cc_final: 0.5717 (m-80) REVERT: D 21 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: D 227 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5873 (mp) REVERT: D 330 MET cc_start: 0.6824 (tpt) cc_final: 0.6551 (tpt) REVERT: D 342 TYR cc_start: 0.6891 (p90) cc_final: 0.5785 (m-10) REVERT: E 193 TYR cc_start: 0.7566 (m-80) cc_final: 0.6334 (m-80) REVERT: E 199 ASN cc_start: 0.8334 (t0) cc_final: 0.7962 (t0) REVERT: E 201 GLN cc_start: 0.8738 (mp10) cc_final: 0.8481 (mp10) REVERT: E 264 GLU cc_start: 0.6610 (pt0) cc_final: 0.6227 (pt0) REVERT: E 266 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7445 (mm-30) REVERT: E 292 CYS cc_start: 0.7349 (t) cc_final: 0.7100 (t) REVERT: F 132 ASP cc_start: 0.7338 (p0) cc_final: 0.7110 (p0) REVERT: F 235 ILE cc_start: 0.8918 (pt) cc_final: 0.8642 (pt) outliers start: 10 outliers final: 8 residues processed: 254 average time/residue: 0.1274 time to fit residues: 48.8276 Evaluate side-chains 253 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain F residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 202 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN D 28 ASN D 136 ASN E 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117336 restraints weight = 38302.333| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.43 r_work: 0.3056 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16734 Z= 0.102 Angle : 0.495 8.052 22730 Z= 0.266 Chirality : 0.044 0.167 2622 Planarity : 0.003 0.029 2924 Dihedral : 4.395 52.337 2210 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.65 % Allowed : 15.06 % Favored : 84.29 % 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: 0.13 (0.18), residues: 2076 helix: 0.52 (0.24), residues: 522 sheet: 0.85 (0.31), residues: 348 loop : -0.29 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.026 0.001 TYR B 342 PHE 0.021 0.001 PHE B 194 TRP 0.007 0.001 TRP F 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00241 (16734) covalent geometry : angle 0.49485 (22730) hydrogen bonds : bond 0.02833 ( 535) hydrogen bonds : angle 5.16629 ( 1419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3383.50 seconds wall clock time: 58 minutes 47.31 seconds (3527.31 seconds total)