Starting phenix.real_space_refine on Fri Mar 6 07:22:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7me0_23786/03_2026/7me0_23786.map" } resolution = 2.48 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 128 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: 6.34, per 1000 atoms: 0.39 Number of scatterers: 16386 At special positions: 0 Unit cell: (113.016, 108.861, 123.819, 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: 1.03 Conformation dependent library (CDL) restraints added in 1.5 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: 60 helices and 48 sheets defined 27.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.664A 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 1 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.692A 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 1 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'D' and resid 1 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.590A 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 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 137 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 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 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 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.827A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.602A 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: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.951A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266 removed outlier: 4.792A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 322 removed outlier: 7.163A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 26 removed outlier: 6.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.179A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.179A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.970A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.820A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.212A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.601A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.186A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.186A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.936A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.804A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.114A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 24 through 26 removed outlier: 6.591A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.162A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.162A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AD2, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.940A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.791A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 322 removed outlier: 7.244A pdb=" N SER D 328 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET D 330 " --> pdb=" O PHE D 341 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE D 341 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 26 removed outlier: 6.622A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.183A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.183A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.051A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 266 removed outlier: 3.638A pdb=" N GLU E 264 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.162A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.595A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.181A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.181A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE9, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.933A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.835A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.188A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) 650 hydrogen bonds defined for protein. 1668 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: 2.78 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5307 1.34 - 1.46: 3096 1.46 - 1.57: 8229 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 16734 Sorted by residual: bond pdb=" C PHE A 341 " pdb=" N TYR A 342 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.35e-02 5.49e+03 3.39e+00 bond pdb=" C PHE D 341 " pdb=" N TYR D 342 " ideal model delta sigma weight residual 1.329 1.305 0.024 1.35e-02 5.49e+03 3.16e+00 bond pdb=" C PHE C 341 " pdb=" N TYR C 342 " ideal model delta sigma weight residual 1.329 1.314 0.015 1.35e-02 5.49e+03 1.26e+00 bond pdb=" C THR C 120 " pdb=" N VAL C 121 " ideal model delta sigma weight residual 1.330 1.310 0.021 1.97e-02 2.58e+03 1.09e+00 bond pdb=" C THR A 120 " pdb=" N VAL A 121 " ideal model delta sigma weight residual 1.330 1.310 0.020 1.97e-02 2.58e+03 1.07e+00 ... (remaining 16729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 21127 0.98 - 1.97: 1391 1.97 - 2.95: 131 2.95 - 3.94: 74 3.94 - 4.92: 7 Bond angle restraints: 22730 Sorted by residual: angle pdb=" C VAL A 22 " pdb=" CA VAL A 22 " pdb=" CB VAL A 22 " ideal model delta sigma weight residual 109.33 113.54 -4.21 9.80e-01 1.04e+00 1.84e+01 angle pdb=" CA VAL A 22 " pdb=" C VAL A 22 " pdb=" N PRO A 23 " ideal model delta sigma weight residual 116.57 119.42 -2.85 9.80e-01 1.04e+00 8.44e+00 angle pdb=" N VAL B 314 " pdb=" CA VAL B 314 " pdb=" C VAL B 314 " ideal model delta sigma weight residual 111.45 108.77 2.68 9.30e-01 1.16e+00 8.29e+00 angle pdb=" C ASN F 28 " pdb=" CA ASN F 28 " pdb=" CB ASN F 28 " ideal model delta sigma weight residual 112.11 108.69 3.42 1.46e+00 4.69e-01 5.48e+00 angle pdb=" N VAL A 22 " pdb=" CA VAL A 22 " pdb=" C VAL A 22 " ideal model delta sigma weight residual 109.19 107.36 1.83 8.20e-01 1.49e+00 5.00e+00 ... (remaining 22725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9220 17.90 - 35.79: 535 35.79 - 53.69: 168 53.69 - 71.58: 62 71.58 - 89.48: 15 Dihedral angle restraints: 10000 sinusoidal: 3934 harmonic: 6066 Sorted by residual: dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR E 192 " pdb=" C THR E 192 " pdb=" N TYR E 193 " pdb=" CA TYR E 193 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 9997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1268 0.029 - 0.059: 826 0.059 - 0.088: 311 0.088 - 0.118: 181 0.118 - 0.147: 36 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CB VAL E 22 " pdb=" CA VAL E 22 " pdb=" CG1 VAL E 22 " pdb=" CG2 VAL E 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE D 79 " pdb=" N ILE D 79 " pdb=" C ILE D 79 " pdb=" CB ILE D 79 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CB VAL A 22 " pdb=" CA VAL A 22 " pdb=" CG1 VAL A 22 " pdb=" CG2 VAL A 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 2619 not shown) Planarity restraints: 2924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 262 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 224 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C ARG A 224 " -0.020 2.00e-02 2.50e+03 pdb=" O ARG A 224 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR A 225 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 156 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO C 157 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 157 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 157 " 0.016 5.00e-02 4.00e+02 ... (remaining 2921 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 341 2.69 - 3.24: 15815 3.24 - 3.79: 27298 3.79 - 4.35: 37097 4.35 - 4.90: 59896 Nonbonded interactions: 140447 Sorted by model distance: nonbonded pdb=" OD2 ASP A 212 " pdb=" OH TYR A 225 " model vdw 2.135 3.040 nonbonded pdb=" OD2 ASP C 212 " pdb=" OH TYR C 225 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP D 212 " pdb=" OH TYR D 225 " model vdw 2.159 3.040 nonbonded pdb=" OD2 ASP E 212 " pdb=" OH TYR E 225 " model vdw 2.160 3.040 nonbonded pdb=" OD2 ASP F 212 " pdb=" OH TYR F 225 " model vdw 2.163 3.040 ... (remaining 140442 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.340 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16734 Z= 0.280 Angle : 0.551 4.922 22730 Z= 0.318 Chirality : 0.048 0.147 2622 Planarity : 0.003 0.031 2924 Dihedral : 14.315 89.476 6088 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.96 % Allowed : 6.82 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2076 helix: 0.20 (0.22), residues: 516 sheet: 0.97 (0.30), residues: 312 loop : -0.56 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 257 TYR 0.013 0.002 TYR D 225 PHE 0.013 0.002 PHE D 268 TRP 0.007 0.001 TRP F 58 HIS 0.006 0.002 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00641 (16734) covalent geometry : angle 0.55095 (22730) hydrogen bonds : bond 0.17586 ( 596) hydrogen bonds : angle 7.51930 ( 1668) *********************** 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 281 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 190 time to evaluate : 0.638 Fit side-chains REVERT: A 199 ASN cc_start: 0.8371 (t0) cc_final: 0.8112 (t0) REVERT: A 332 TRP cc_start: 0.7875 (m100) cc_final: 0.7184 (m-10) REVERT: B 113 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: C 201 GLN cc_start: 0.8524 (mp10) cc_final: 0.7672 (mp10) REVERT: C 202 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: C 232 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: C 332 TRP cc_start: 0.8040 (m100) cc_final: 0.7759 (m100) REVERT: D 332 TRP cc_start: 0.8044 (m100) cc_final: 0.7803 (m100) REVERT: E 313 VAL cc_start: 0.8448 (t) cc_final: 0.7856 (m) REVERT: F 199 ASN cc_start: 0.8486 (t0) cc_final: 0.8092 (t0) REVERT: F 201 GLN cc_start: 0.8193 (mp10) cc_final: 0.7753 (mp10) REVERT: F 332 TRP cc_start: 0.8164 (m100) cc_final: 0.7919 (m100) outliers start: 91 outliers final: 58 residues processed: 263 average time/residue: 0.5662 time to fit residues: 166.1114 Evaluate side-chains 228 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 219 ASP Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 219 ASP Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.1980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.104469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079580 restraints weight = 45998.325| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.36 r_work: 0.2847 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16734 Z= 0.164 Angle : 0.534 9.960 22730 Z= 0.290 Chirality : 0.047 0.143 2622 Planarity : 0.003 0.028 2924 Dihedral : 9.147 81.472 2310 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.98 % Allowed : 9.82 % 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: 0.01 (0.17), residues: 2076 helix: 0.28 (0.22), residues: 528 sheet: 1.38 (0.30), residues: 324 loop : -0.47 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 138 TYR 0.011 0.001 TYR D 225 PHE 0.010 0.001 PHE A 221 TRP 0.018 0.001 TRP B 332 HIS 0.005 0.001 HIS C 337 Details of bonding type rmsd covalent geometry : bond 0.00373 (16734) covalent geometry : angle 0.53353 (22730) hydrogen bonds : bond 0.04455 ( 596) hydrogen bonds : angle 5.62611 ( 1668) *********************** 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 250 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 0.544 Fit side-chains REVERT: A 199 ASN cc_start: 0.8640 (t0) cc_final: 0.8259 (t0) REVERT: A 332 TRP cc_start: 0.8055 (m100) cc_final: 0.7530 (m-10) REVERT: B 113 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: B 259 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8462 (ptmt) REVERT: C 201 GLN cc_start: 0.8703 (mp10) cc_final: 0.8316 (mp10) REVERT: C 232 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8900 (m-80) REVERT: C 313 VAL cc_start: 0.8490 (t) cc_final: 0.7909 (m) REVERT: C 332 TRP cc_start: 0.8122 (m100) cc_final: 0.7806 (m100) REVERT: D 332 TRP cc_start: 0.8254 (m100) cc_final: 0.7921 (m100) REVERT: E 313 VAL cc_start: 0.8513 (t) cc_final: 0.7876 (m) REVERT: F 199 ASN cc_start: 0.8772 (t0) cc_final: 0.8551 (t0) REVERT: F 332 TRP cc_start: 0.8285 (m100) cc_final: 0.7953 (m100) outliers start: 73 outliers final: 51 residues processed: 234 average time/residue: 0.5815 time to fit residues: 151.4288 Evaluate side-chains 215 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 219 ASP Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 181 optimal weight: 0.0370 chunk 191 optimal weight: 0.7980 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN F 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.079034 restraints weight = 36935.333| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.25 r_work: 0.2816 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2696 r_free = 0.2696 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16734 Z= 0.105 Angle : 0.490 9.854 22730 Z= 0.264 Chirality : 0.045 0.147 2622 Planarity : 0.003 0.023 2924 Dihedral : 8.296 79.594 2287 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.16 % Allowed : 11.51 % Favored : 85.32 % 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: 0.20 (0.17), residues: 2076 helix: 0.51 (0.23), residues: 528 sheet: 1.56 (0.30), residues: 324 loop : -0.41 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 138 TYR 0.008 0.001 TYR B 225 PHE 0.009 0.001 PHE A 221 TRP 0.023 0.001 TRP B 332 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00238 (16734) covalent geometry : angle 0.48971 (22730) hydrogen bonds : bond 0.03449 ( 596) hydrogen bonds : angle 5.21150 ( 1668) *********************** 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 241 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 183 time to evaluate : 0.460 Fit side-chains REVERT: A 199 ASN cc_start: 0.8496 (t0) cc_final: 0.8025 (t0) REVERT: A 332 TRP cc_start: 0.7957 (m100) cc_final: 0.7480 (m-10) REVERT: B 201 GLN cc_start: 0.8665 (mm110) cc_final: 0.8430 (mp10) REVERT: B 232 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8024 (t80) REVERT: C 201 GLN cc_start: 0.8726 (mp10) cc_final: 0.8263 (mp10) REVERT: C 313 VAL cc_start: 0.8386 (t) cc_final: 0.7788 (m) REVERT: C 332 TRP cc_start: 0.8105 (m100) cc_final: 0.7767 (m100) REVERT: D 44 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8559 (tp30) REVERT: D 259 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8453 (tmtm) REVERT: D 332 TRP cc_start: 0.8221 (m100) cc_final: 0.7898 (m-10) REVERT: E 313 VAL cc_start: 0.8521 (t) cc_final: 0.7970 (m) REVERT: F 199 ASN cc_start: 0.8730 (t0) cc_final: 0.8473 (t0) REVERT: F 332 TRP cc_start: 0.8238 (m100) cc_final: 0.7860 (m100) outliers start: 58 outliers final: 36 residues processed: 226 average time/residue: 0.6193 time to fit residues: 154.5958 Evaluate side-chains 210 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 151 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 201 GLN F 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080583 restraints weight = 56028.319| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.62 r_work: 0.2851 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1345 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= 0.143 Angle : 0.508 10.408 22730 Z= 0.273 Chirality : 0.046 0.164 2622 Planarity : 0.003 0.029 2924 Dihedral : 8.035 80.758 2263 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.00 % Allowed : 12.60 % Favored : 84.40 % 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: 0.23 (0.17), residues: 2076 helix: 0.53 (0.23), residues: 528 sheet: 1.54 (0.30), residues: 324 loop : -0.38 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 138 TYR 0.009 0.001 TYR C 225 PHE 0.009 0.001 PHE F 268 TRP 0.024 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00332 (16734) covalent geometry : angle 0.50804 (22730) hydrogen bonds : bond 0.03718 ( 596) hydrogen bonds : angle 5.21761 ( 1668) *********************** 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 234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8566 (t0) cc_final: 0.8179 (t0) REVERT: B 201 GLN cc_start: 0.8758 (mm110) cc_final: 0.8473 (mp10) REVERT: C 201 GLN cc_start: 0.8785 (mp10) cc_final: 0.8301 (mp10) REVERT: C 313 VAL cc_start: 0.8376 (t) cc_final: 0.7788 (m) REVERT: C 332 TRP cc_start: 0.8102 (m100) cc_final: 0.7768 (m100) REVERT: D 44 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8590 (tp30) REVERT: D 204 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8765 (mptt) REVERT: D 332 TRP cc_start: 0.8176 (m100) cc_final: 0.7817 (m100) REVERT: E 313 VAL cc_start: 0.8595 (t) cc_final: 0.8078 (m) REVERT: F 199 ASN cc_start: 0.8796 (t0) cc_final: 0.8581 (t0) REVERT: F 332 TRP cc_start: 0.8219 (m100) cc_final: 0.7867 (m100) outliers start: 55 outliers final: 39 residues processed: 221 average time/residue: 0.6172 time to fit residues: 150.8040 Evaluate side-chains 215 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 44 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 120 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 78 optimal weight: 0.1980 chunk 123 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN F 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.084885 restraints weight = 49790.757| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.51 r_work: 0.2921 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16734 Z= 0.085 Angle : 0.470 11.234 22730 Z= 0.252 Chirality : 0.044 0.152 2622 Planarity : 0.003 0.026 2924 Dihedral : 7.607 77.433 2259 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.89 % Allowed : 13.09 % Favored : 84.02 % 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: 0.35 (0.18), residues: 2076 helix: 0.73 (0.23), residues: 528 sheet: 1.80 (0.30), residues: 306 loop : -0.37 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.007 0.001 TYR D 225 PHE 0.009 0.001 PHE A 221 TRP 0.028 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00190 (16734) covalent geometry : angle 0.46969 (22730) hydrogen bonds : bond 0.02799 ( 596) hydrogen bonds : angle 4.88704 ( 1668) *********************** 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 248 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.685 Fit side-chains REVERT: A 199 ASN cc_start: 0.8464 (t0) cc_final: 0.8015 (t0) REVERT: A 260 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: A 332 TRP cc_start: 0.7986 (m100) cc_final: 0.7508 (m-10) REVERT: B 201 GLN cc_start: 0.8698 (mm110) cc_final: 0.8412 (mp10) REVERT: B 232 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8140 (t80) REVERT: C 201 GLN cc_start: 0.8827 (mp10) cc_final: 0.8323 (mp10) REVERT: C 232 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: C 313 VAL cc_start: 0.8352 (t) cc_final: 0.7771 (m) REVERT: C 332 TRP cc_start: 0.8105 (m100) cc_final: 0.7752 (m100) REVERT: D 332 TRP cc_start: 0.8182 (m100) cc_final: 0.7919 (m-10) REVERT: D 342 TYR cc_start: 0.8732 (p90) cc_final: 0.8469 (p90) REVERT: E 291 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9090 (t) REVERT: E 313 VAL cc_start: 0.8585 (t) cc_final: 0.8114 (m) REVERT: F 199 ASN cc_start: 0.8775 (t0) cc_final: 0.8541 (t0) REVERT: F 332 TRP cc_start: 0.8186 (m100) cc_final: 0.7872 (m-10) REVERT: F 342 TYR cc_start: 0.8746 (p90) cc_final: 0.8448 (p90) outliers start: 53 outliers final: 26 residues processed: 236 average time/residue: 0.6085 time to fit residues: 159.4263 Evaluate side-chains 206 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 88 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 0.0470 chunk 169 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 overall best weight: 1.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN E 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081641 restraints weight = 44183.351| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.35 r_work: 0.2886 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16734 Z= 0.142 Angle : 0.526 11.327 22730 Z= 0.278 Chirality : 0.046 0.171 2622 Planarity : 0.003 0.029 2924 Dihedral : 7.119 77.563 2246 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.51 % Allowed : 13.91 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2076 helix: 0.65 (0.23), residues: 528 sheet: 1.76 (0.30), residues: 306 loop : -0.39 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.010 0.001 TYR D 225 PHE 0.010 0.001 PHE B 268 TRP 0.032 0.001 TRP B 332 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00333 (16734) covalent geometry : angle 0.52592 (22730) hydrogen bonds : bond 0.03506 ( 596) hydrogen bonds : angle 5.07878 ( 1668) *********************** 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 220 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.678 Fit side-chains REVERT: A 199 ASN cc_start: 0.8527 (t0) cc_final: 0.8156 (t0) REVERT: A 332 TRP cc_start: 0.8009 (m100) cc_final: 0.7509 (m-10) REVERT: B 201 GLN cc_start: 0.8725 (mm110) cc_final: 0.8444 (mp10) REVERT: B 232 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8192 (t80) REVERT: C 201 GLN cc_start: 0.8795 (mp10) cc_final: 0.8298 (mp10) REVERT: C 232 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: C 313 VAL cc_start: 0.8368 (t) cc_final: 0.7802 (m) REVERT: C 332 TRP cc_start: 0.8110 (m100) cc_final: 0.7792 (m100) REVERT: D 332 TRP cc_start: 0.8147 (m100) cc_final: 0.7862 (m-10) REVERT: E 313 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8159 (m) REVERT: F 332 TRP cc_start: 0.8157 (m100) cc_final: 0.7833 (m100) outliers start: 46 outliers final: 35 residues processed: 210 average time/residue: 0.6399 time to fit residues: 148.4449 Evaluate side-chains 211 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL 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: 0.0270 chunk 169 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 overall best weight: 0.9658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.083448 restraints weight = 36682.356| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.15 r_work: 0.2924 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16734 Z= 0.100 Angle : 0.491 11.884 22730 Z= 0.262 Chirality : 0.045 0.153 2622 Planarity : 0.003 0.028 2924 Dihedral : 6.926 77.196 2245 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.40 % Allowed : 14.13 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2076 helix: 0.72 (0.23), residues: 528 sheet: 1.77 (0.30), residues: 306 loop : -0.38 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.009 0.001 TYR D 225 PHE 0.009 0.001 PHE A 7 TRP 0.035 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00232 (16734) covalent geometry : angle 0.49057 (22730) hydrogen bonds : bond 0.03027 ( 596) hydrogen bonds : angle 4.92764 ( 1668) *********************** 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 223 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.538 Fit side-chains REVERT: A 199 ASN cc_start: 0.8491 (t0) cc_final: 0.8075 (t0) REVERT: A 204 LYS cc_start: 0.9031 (mptm) cc_final: 0.8791 (mptt) REVERT: A 260 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: A 332 TRP cc_start: 0.7954 (m100) cc_final: 0.7511 (m-10) REVERT: B 201 GLN cc_start: 0.8683 (mm110) cc_final: 0.8350 (mp10) REVERT: B 232 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8127 (t80) REVERT: C 201 GLN cc_start: 0.8788 (mp10) cc_final: 0.8299 (mp10) REVERT: C 232 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: C 313 VAL cc_start: 0.8356 (t) cc_final: 0.7784 (m) REVERT: C 332 TRP cc_start: 0.8140 (m100) cc_final: 0.7821 (m100) REVERT: D 332 TRP cc_start: 0.8170 (m100) cc_final: 0.7909 (m-10) REVERT: D 342 TYR cc_start: 0.8694 (p90) cc_final: 0.8408 (p90) REVERT: E 313 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8184 (m) REVERT: F 332 TRP cc_start: 0.8167 (m100) cc_final: 0.7851 (m100) outliers start: 44 outliers final: 33 residues processed: 215 average time/residue: 0.6329 time to fit residues: 150.6088 Evaluate side-chains 204 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.081010 restraints weight = 45090.737| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.39 r_work: 0.2875 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1640 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= 0.146 Angle : 0.529 11.464 22730 Z= 0.280 Chirality : 0.046 0.163 2622 Planarity : 0.003 0.030 2924 Dihedral : 7.095 78.883 2245 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.62 % Allowed : 14.13 % Favored : 83.25 % 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: 0.28 (0.17), residues: 2076 helix: 0.63 (0.23), residues: 528 sheet: 1.72 (0.31), residues: 306 loop : -0.39 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 138 TYR 0.011 0.001 TYR D 225 PHE 0.010 0.001 PHE E 268 TRP 0.039 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00340 (16734) covalent geometry : angle 0.52884 (22730) hydrogen bonds : bond 0.03505 ( 596) hydrogen bonds : angle 5.08026 ( 1668) *********************** 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 222 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.651 Fit side-chains REVERT: A 0 MET cc_start: 0.8077 (ppp) cc_final: 0.7776 (tpp) REVERT: A 199 ASN cc_start: 0.8551 (t0) cc_final: 0.8111 (t0) REVERT: A 204 LYS cc_start: 0.9094 (mptm) cc_final: 0.8834 (mptt) REVERT: A 332 TRP cc_start: 0.7992 (m100) cc_final: 0.7156 (m-10) REVERT: B 232 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8155 (t80) REVERT: C 201 GLN cc_start: 0.8817 (mp10) cc_final: 0.8333 (mp10) REVERT: C 232 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: C 313 VAL cc_start: 0.8345 (t) cc_final: 0.7765 (m) REVERT: C 332 TRP cc_start: 0.8100 (m100) cc_final: 0.7808 (m100) REVERT: D 332 TRP cc_start: 0.8104 (m100) cc_final: 0.7755 (m100) REVERT: E 313 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8213 (m) REVERT: F 332 TRP cc_start: 0.8167 (m100) cc_final: 0.7842 (m100) outliers start: 48 outliers final: 36 residues processed: 212 average time/residue: 0.6266 time to fit residues: 146.5109 Evaluate side-chains 209 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 104 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.106306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081047 restraints weight = 45247.266| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.37 r_work: 0.2878 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.1631 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= 0.146 Angle : 0.534 12.394 22730 Z= 0.283 Chirality : 0.046 0.161 2622 Planarity : 0.003 0.031 2924 Dihedral : 7.131 80.337 2245 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.29 % Allowed : 14.68 % Favored : 83.03 % 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: 0.26 (0.17), residues: 2076 helix: 0.62 (0.23), residues: 528 sheet: 1.67 (0.30), residues: 306 loop : -0.38 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.012 0.001 TYR D 225 PHE 0.010 0.001 PHE E 268 TRP 0.042 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00341 (16734) covalent geometry : angle 0.53397 (22730) hydrogen bonds : bond 0.03504 ( 596) hydrogen bonds : angle 5.09264 ( 1668) *********************** 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 210 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 0 MET cc_start: 0.8047 (ppp) cc_final: 0.7720 (tpp) REVERT: A 199 ASN cc_start: 0.8590 (t0) cc_final: 0.8195 (t0) REVERT: B 232 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8151 (t80) REVERT: B 332 TRP cc_start: 0.8060 (m100) cc_final: 0.7758 (m100) REVERT: C 201 GLN cc_start: 0.8812 (mp10) cc_final: 0.8325 (mp10) REVERT: C 232 PHE cc_start: 0.9106 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: C 313 VAL cc_start: 0.8330 (t) cc_final: 0.7757 (m) REVERT: C 332 TRP cc_start: 0.8116 (m100) cc_final: 0.7854 (m100) REVERT: D 332 TRP cc_start: 0.8102 (m100) cc_final: 0.7855 (m-10) REVERT: E 313 VAL cc_start: 0.8660 (t) cc_final: 0.8244 (m) REVERT: E 332 TRP cc_start: 0.7955 (m100) cc_final: 0.7684 (m100) REVERT: F 332 TRP cc_start: 0.8172 (m100) cc_final: 0.7862 (m100) outliers start: 42 outliers final: 36 residues processed: 203 average time/residue: 0.6308 time to fit residues: 141.5508 Evaluate side-chains 205 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 0.7980 chunk 203 optimal weight: 0.3980 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.107228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081593 restraints weight = 49596.832| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.51 r_work: 0.2884 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16734 Z= 0.119 Angle : 0.523 12.211 22730 Z= 0.277 Chirality : 0.045 0.146 2622 Planarity : 0.003 0.030 2924 Dihedral : 7.010 79.360 2245 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.24 % Allowed : 14.78 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 2076 helix: 0.75 (0.23), residues: 522 sheet: 1.67 (0.30), residues: 306 loop : -0.39 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 138 TYR 0.011 0.001 TYR D 225 PHE 0.009 0.001 PHE E 268 TRP 0.041 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00276 (16734) covalent geometry : angle 0.52266 (22730) hydrogen bonds : bond 0.03238 ( 596) hydrogen bonds : angle 5.01867 ( 1668) ********************** 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 213 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.655 Fit side-chains REVERT: A 0 MET cc_start: 0.8092 (ppp) cc_final: 0.7676 (tpp) REVERT: A 199 ASN cc_start: 0.8590 (t0) cc_final: 0.8178 (t0) REVERT: A 204 LYS cc_start: 0.9087 (mptm) cc_final: 0.8814 (mptt) REVERT: A 260 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: A 332 TRP cc_start: 0.7954 (m100) cc_final: 0.7505 (m-10) REVERT: B 232 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8174 (t80) REVERT: B 332 TRP cc_start: 0.8048 (m100) cc_final: 0.7755 (m100) REVERT: C 201 GLN cc_start: 0.8765 (mp10) cc_final: 0.8257 (mp10) REVERT: C 232 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: C 313 VAL cc_start: 0.8322 (t) cc_final: 0.7751 (m) REVERT: C 332 TRP cc_start: 0.8121 (m100) cc_final: 0.7846 (m100) REVERT: D 44 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: D 332 TRP cc_start: 0.8149 (m100) cc_final: 0.7912 (m-10) REVERT: E 313 VAL cc_start: 0.8637 (t) cc_final: 0.8233 (m) REVERT: E 332 TRP cc_start: 0.7943 (m100) cc_final: 0.7705 (m100) REVERT: F 219 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7029 (p0) REVERT: F 332 TRP cc_start: 0.8167 (m100) cc_final: 0.7826 (m100) outliers start: 41 outliers final: 33 residues processed: 207 average time/residue: 0.6421 time to fit residues: 146.9389 Evaluate side-chains 207 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 219 ASP Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 202 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 203 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 GLN E 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085479 restraints weight = 38972.891| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.21 r_work: 0.2947 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2835 r_free = 0.2835 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16734 Z= 0.089 Angle : 0.495 11.092 22730 Z= 0.262 Chirality : 0.044 0.145 2622 Planarity : 0.003 0.028 2924 Dihedral : 6.719 75.847 2245 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.85 % Allowed : 15.22 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 2076 helix: 0.79 (0.23), residues: 528 sheet: 1.73 (0.30), residues: 306 loop : -0.32 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 138 TYR 0.009 0.001 TYR D 225 PHE 0.009 0.001 PHE A 7 TRP 0.037 0.001 TRP B 332 HIS 0.004 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00200 (16734) covalent geometry : angle 0.49515 (22730) hydrogen bonds : bond 0.02696 ( 596) hydrogen bonds : angle 4.84972 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6551.16 seconds wall clock time: 111 minutes 52.73 seconds (6712.73 seconds total)