Starting phenix.real_space_refine on Wed Jun 25 05:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_23786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_23786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_23786.map" model { file = "/net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_23786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7me0_23786/06_2025/7me0_23786.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.62, per 1000 atoms: 1.14 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: 4.86 Conformation dependent library (CDL) restraints added in 5.7 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: 5.27 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: 8.99 Time building geometry restraints manager: 5.61 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: 48.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 5.490 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 58.970 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.180 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:169.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 285.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP F 58 HIS 0.006 0.002 HIS F 95 PHE 0.013 0.002 PHE D 268 TYR 0.013 0.002 TYR D 225 ARG 0.004 0.001 ARG F 257 Details of bonding type rmsd hydrogen bonds : bond 0.17586 ( 596) hydrogen bonds : angle 7.51930 ( 1668) covalent geometry : bond 0.00641 (16734) covalent geometry : angle 0.55095 (22730) *********************** 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 : 1.825 Fit side-chains REVERT: A 199 ASN cc_start: 0.8371 (t0) cc_final: 0.8113 (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: B 199 ASN cc_start: 0.8695 (t0) cc_final: 0.8121 (t0) REVERT: B 201 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8160 (mm110) REVERT: C 232 PHE cc_start: 0.9097 (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: 1.2830 time to fit residues: 378.6196 Evaluate side-chains 226 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 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 172 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.105266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080717 restraints weight = 41291.784| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.25 r_work: 0.2879 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16734 Z= 0.130 Angle : 0.519 9.877 22730 Z= 0.281 Chirality : 0.046 0.141 2622 Planarity : 0.003 0.025 2924 Dihedral : 8.908 80.920 2307 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.76 % Allowed : 9.71 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2076 helix: 0.36 (0.22), residues: 528 sheet: 1.43 (0.30), residues: 324 loop : -0.45 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 332 HIS 0.005 0.001 HIS C 337 PHE 0.010 0.001 PHE A 221 TYR 0.010 0.001 TYR B 225 ARG 0.006 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 596) hydrogen bonds : angle 5.54142 ( 1668) covalent geometry : bond 0.00291 (16734) covalent geometry : angle 0.51909 (22730) *********************** 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 249 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 180 time to evaluate : 1.795 Fit side-chains REVERT: A 199 ASN cc_start: 0.8616 (t0) cc_final: 0.8214 (t0) REVERT: A 332 TRP cc_start: 0.8009 (m100) cc_final: 0.7537 (m-10) REVERT: B 199 ASN cc_start: 0.8881 (t0) cc_final: 0.8446 (t0) REVERT: B 201 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8594 (mp10) REVERT: B 259 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8404 (ptmt) REVERT: C 313 VAL cc_start: 0.8499 (t) cc_final: 0.7927 (m) REVERT: C 332 TRP cc_start: 0.8147 (m100) cc_final: 0.7838 (m100) REVERT: D 332 TRP cc_start: 0.8258 (m100) cc_final: 0.7941 (m100) REVERT: E 313 VAL cc_start: 0.8539 (t) cc_final: 0.7920 (m) REVERT: F 199 ASN cc_start: 0.8750 (t0) cc_final: 0.8427 (t0) REVERT: F 201 GLN cc_start: 0.8601 (mp10) cc_final: 0.8368 (mp10) REVERT: F 332 TRP cc_start: 0.8284 (m100) cc_final: 0.7958 (m100) outliers start: 69 outliers final: 45 residues processed: 235 average time/residue: 1.1913 time to fit residues: 313.1209 Evaluate side-chains 207 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 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 165 VAL Chi-restraints excluded: chain B residue 189 LEU 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 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 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 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 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 147 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 187 optimal weight: 0.0980 chunk 25 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 169 optimal weight: 7.9990 chunk 11 optimal weight: 0.0020 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.106487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081511 restraints weight = 45170.312| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.36 r_work: 0.2877 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 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 = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16734 Z= 0.115 Angle : 0.493 9.608 22730 Z= 0.266 Chirality : 0.045 0.146 2622 Planarity : 0.003 0.026 2924 Dihedral : 8.082 80.119 2277 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.95 % Allowed : 11.78 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2076 helix: 0.52 (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 TRP 0.022 0.001 TRP B 332 HIS 0.005 0.001 HIS D 337 PHE 0.009 0.001 PHE A 221 TYR 0.009 0.001 TYR D 225 ARG 0.005 0.000 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 596) hydrogen bonds : angle 5.24501 ( 1668) covalent geometry : bond 0.00263 (16734) covalent geometry : angle 0.49272 (22730) *********************** 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 235 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 1.858 Fit side-chains REVERT: A 199 ASN cc_start: 0.8564 (t0) cc_final: 0.8143 (t0) REVERT: A 332 TRP cc_start: 0.7999 (m100) cc_final: 0.7535 (m-10) REVERT: B 199 ASN cc_start: 0.8817 (t0) cc_final: 0.8242 (t0) REVERT: B 201 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8450 (mp10) REVERT: C 199 ASN cc_start: 0.8570 (t0) cc_final: 0.8195 (t0) REVERT: C 313 VAL cc_start: 0.8427 (t) cc_final: 0.7845 (m) REVERT: C 332 TRP cc_start: 0.8129 (m100) cc_final: 0.7805 (m100) REVERT: D 44 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8558 (tp30) REVERT: D 332 TRP cc_start: 0.8242 (m100) cc_final: 0.7926 (m-10) REVERT: E 313 VAL cc_start: 0.8498 (t) cc_final: 0.7945 (m) REVERT: F 199 ASN cc_start: 0.8761 (t0) cc_final: 0.8447 (t0) REVERT: F 201 GLN cc_start: 0.8579 (mp10) cc_final: 0.8328 (mp10) REVERT: F 332 TRP cc_start: 0.8266 (m100) cc_final: 0.7906 (m100) outliers start: 54 outliers final: 38 residues processed: 219 average time/residue: 1.2875 time to fit residues: 313.2404 Evaluate side-chains 208 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.765 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 180 optimal weight: 0.0670 chunk 179 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 112 optimal weight: 0.0980 chunk 184 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** C 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 = 0.3419 r_free = 0.3419 target = 0.106956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.081544 restraints weight = 44122.708| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.36 r_work: 0.2879 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16734 Z= 0.120 Angle : 0.496 10.220 22730 Z= 0.266 Chirality : 0.045 0.159 2622 Planarity : 0.003 0.028 2924 Dihedral : 7.916 79.813 2262 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.78 % Allowed : 12.88 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2076 helix: 0.58 (0.23), residues: 528 sheet: 1.78 (0.31), residues: 306 loop : -0.44 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 332 HIS 0.005 0.001 HIS D 337 PHE 0.008 0.001 PHE B 268 TYR 0.008 0.001 TYR D 225 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 596) hydrogen bonds : angle 5.13297 ( 1668) covalent geometry : bond 0.00276 (16734) covalent geometry : angle 0.49595 (22730) *********************** 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 227 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 1.779 Fit side-chains REVERT: A 199 ASN cc_start: 0.8535 (t0) cc_final: 0.8124 (t0) REVERT: A 332 TRP cc_start: 0.8011 (m100) cc_final: 0.7530 (m-10) REVERT: B 199 ASN cc_start: 0.8848 (t0) cc_final: 0.8446 (t0) REVERT: B 201 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8594 (mp10) REVERT: B 232 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8084 (t80) REVERT: C 199 ASN cc_start: 0.8532 (t0) cc_final: 0.8256 (t0) REVERT: C 313 VAL cc_start: 0.8381 (t) cc_final: 0.7807 (m) REVERT: C 332 TRP cc_start: 0.8120 (m100) cc_final: 0.7794 (m100) REVERT: D 44 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8541 (tp30) REVERT: D 204 LYS cc_start: 0.9068 (mptm) cc_final: 0.8773 (mptt) REVERT: D 332 TRP cc_start: 0.8195 (m100) cc_final: 0.7896 (m-10) REVERT: E 313 VAL cc_start: 0.8593 (t) cc_final: 0.8089 (m) REVERT: F 199 ASN cc_start: 0.8787 (t0) cc_final: 0.8186 (t0) REVERT: F 201 GLN cc_start: 0.8676 (mp10) cc_final: 0.8068 (mp10) REVERT: F 202 GLU cc_start: 0.8448 (pm20) cc_final: 0.8201 (pm20) REVERT: F 332 TRP cc_start: 0.8199 (m100) cc_final: 0.7847 (m100) outliers start: 51 outliers final: 37 residues processed: 216 average time/residue: 1.2799 time to fit residues: 308.0972 Evaluate side-chains 208 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 260 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 148 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 0.0470 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 180 optimal weight: 0.0970 overall best weight: 1.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** C 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 = 0.106331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.080954 restraints weight = 47695.543| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.44 r_work: 0.2863 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 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 = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16734 Z= 0.144 Angle : 0.505 10.883 22730 Z= 0.272 Chirality : 0.046 0.153 2622 Planarity : 0.003 0.029 2924 Dihedral : 7.954 79.489 2259 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.66 % Allowed : 12.27 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2076 helix: 0.55 (0.22), residues: 528 sheet: 1.78 (0.31), residues: 306 loop : -0.43 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.011 0.001 PHE F 268 TYR 0.011 0.001 TYR D 225 ARG 0.004 0.000 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 596) hydrogen bonds : angle 5.16092 ( 1668) covalent geometry : bond 0.00333 (16734) covalent geometry : angle 0.50467 (22730) *********************** 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 238 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 171 time to evaluate : 1.764 Fit side-chains REVERT: A 199 ASN cc_start: 0.8550 (t0) cc_final: 0.8126 (t0) REVERT: A 332 TRP cc_start: 0.7990 (m100) cc_final: 0.7517 (m-10) REVERT: B 199 ASN cc_start: 0.8863 (t0) cc_final: 0.8253 (t0) REVERT: B 201 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8506 (mp10) REVERT: B 202 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: B 232 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8136 (t80) REVERT: C 199 ASN cc_start: 0.8618 (t0) cc_final: 0.8417 (t0) REVERT: C 313 VAL cc_start: 0.8366 (t) cc_final: 0.7792 (m) REVERT: C 332 TRP cc_start: 0.8078 (m100) cc_final: 0.7750 (m100) REVERT: D 44 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: D 204 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8757 (mptt) REVERT: D 332 TRP cc_start: 0.8183 (m100) cc_final: 0.7801 (m100) REVERT: E 313 VAL cc_start: 0.8602 (t) cc_final: 0.8106 (m) REVERT: F 199 ASN cc_start: 0.8798 (t0) cc_final: 0.8244 (t0) REVERT: F 201 GLN cc_start: 0.8653 (mp10) cc_final: 0.8018 (mp10) REVERT: F 202 GLU cc_start: 0.8467 (pm20) cc_final: 0.8233 (pm20) REVERT: F 332 TRP cc_start: 0.8209 (m100) cc_final: 0.7861 (m100) outliers start: 67 outliers final: 43 residues processed: 223 average time/residue: 1.2083 time to fit residues: 301.3104 Evaluate side-chains 215 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 168 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 202 GLU 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 189 LEU 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 260 GLU Chi-restraints excluded: chain D residue 281 THR 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 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 218 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.106625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081058 restraints weight = 47703.220| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.45 r_work: 0.2870 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16734 Z= 0.125 Angle : 0.499 11.360 22730 Z= 0.268 Chirality : 0.045 0.150 2622 Planarity : 0.003 0.029 2924 Dihedral : 7.889 79.379 2259 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.33 % Allowed : 12.71 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2076 helix: 0.60 (0.23), residues: 528 sheet: 1.76 (0.31), residues: 306 loop : -0.42 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.009 0.001 PHE E 268 TYR 0.010 0.001 TYR D 225 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 596) hydrogen bonds : angle 5.09064 ( 1668) covalent geometry : bond 0.00289 (16734) covalent geometry : angle 0.49860 (22730) *********************** 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 234 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 2.208 Fit side-chains REVERT: A 199 ASN cc_start: 0.8513 (t0) cc_final: 0.8134 (t0) REVERT: A 332 TRP cc_start: 0.7996 (m100) cc_final: 0.7534 (m-10) REVERT: B 199 ASN cc_start: 0.8846 (t0) cc_final: 0.8183 (t0) REVERT: B 201 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8498 (mp10) REVERT: B 202 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: B 232 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8076 (t80) REVERT: C 199 ASN cc_start: 0.8618 (t0) cc_final: 0.8148 (t0) REVERT: C 232 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8804 (m-80) REVERT: C 313 VAL cc_start: 0.8352 (t) cc_final: 0.7774 (m) REVERT: C 332 TRP cc_start: 0.8106 (m100) cc_final: 0.7789 (m100) REVERT: D 44 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8535 (tp30) REVERT: D 204 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8764 (mptt) REVERT: D 332 TRP cc_start: 0.8153 (m100) cc_final: 0.7872 (m-10) REVERT: E 313 VAL cc_start: 0.8599 (t) cc_final: 0.8124 (m) REVERT: F 199 ASN cc_start: 0.8797 (t0) cc_final: 0.8209 (t0) REVERT: F 201 GLN cc_start: 0.8686 (mp10) cc_final: 0.8054 (mp10) REVERT: F 202 GLU cc_start: 0.8445 (pm20) cc_final: 0.8205 (pm20) REVERT: F 332 TRP cc_start: 0.8198 (m100) cc_final: 0.7871 (m100) outliers start: 61 outliers final: 44 residues processed: 218 average time/residue: 1.8318 time to fit residues: 444.8495 Evaluate side-chains 217 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 3.738 ------------------------------------------------------------------------------- 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 75 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 202 GLU 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 281 THR 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 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 189 LEU 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 260 GLU Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 306 ILE 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 218 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 311 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.107695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.082868 restraints weight = 36932.031| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.17 r_work: 0.2922 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16734 Z= 0.099 Angle : 0.486 11.841 22730 Z= 0.260 Chirality : 0.045 0.143 2622 Planarity : 0.003 0.028 2924 Dihedral : 7.428 77.785 2256 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.16 % Allowed : 12.88 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2076 helix: 0.69 (0.23), residues: 528 sheet: 1.78 (0.30), residues: 306 loop : -0.41 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.008 0.001 PHE A 7 TYR 0.010 0.001 TYR D 225 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 596) hydrogen bonds : angle 4.96548 ( 1668) covalent geometry : bond 0.00226 (16734) covalent geometry : angle 0.48614 (22730) *********************** 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 236 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 1.753 Fit side-chains REVERT: A 199 ASN cc_start: 0.8500 (t0) cc_final: 0.8094 (t0) REVERT: A 260 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8129 (pt0) REVERT: A 332 TRP cc_start: 0.7970 (m100) cc_final: 0.7513 (m-10) REVERT: B 199 ASN cc_start: 0.8800 (t0) cc_final: 0.8308 (t0) REVERT: B 201 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8502 (mp10) REVERT: B 232 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8196 (t80) REVERT: C 199 ASN cc_start: 0.8590 (t0) cc_final: 0.8191 (t0) REVERT: C 232 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: C 313 VAL cc_start: 0.8342 (t) cc_final: 0.7767 (m) REVERT: C 332 TRP cc_start: 0.8120 (m100) cc_final: 0.7796 (m100) REVERT: D 44 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: D 204 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8758 (mptt) REVERT: D 332 TRP cc_start: 0.8160 (m100) cc_final: 0.7907 (m-10) REVERT: E 313 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8177 (m) REVERT: F 199 ASN cc_start: 0.8740 (t0) cc_final: 0.8179 (t0) REVERT: F 201 GLN cc_start: 0.8677 (mp10) cc_final: 0.8033 (mp10) REVERT: F 332 TRP cc_start: 0.8196 (m100) cc_final: 0.7867 (m100) outliers start: 58 outliers final: 37 residues processed: 221 average time/residue: 1.3761 time to fit residues: 339.1451 Evaluate side-chains 211 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 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 259 LYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 281 THR 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 232 PHE 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 204 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 5 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 134 optimal weight: 0.0770 overall best weight: 2.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** C 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 = 0.3396 r_free = 0.3396 target = 0.105289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080165 restraints weight = 40497.684| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.24 r_work: 0.2862 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16734 Z= 0.199 Angle : 0.555 11.471 22730 Z= 0.295 Chirality : 0.048 0.196 2622 Planarity : 0.003 0.032 2924 Dihedral : 7.656 80.723 2252 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.95 % Allowed : 13.42 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2076 helix: 0.45 (0.22), residues: 534 sheet: 1.66 (0.30), residues: 306 loop : -0.40 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.011 0.002 PHE F 268 TYR 0.012 0.001 TYR D 225 ARG 0.005 0.001 ARG F 135 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 596) hydrogen bonds : angle 5.23275 ( 1668) covalent geometry : bond 0.00466 (16734) covalent geometry : angle 0.55546 (22730) *********************** 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 216 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: A 199 ASN cc_start: 0.8578 (t0) cc_final: 0.8159 (t0) REVERT: A 332 TRP cc_start: 0.7989 (m100) cc_final: 0.7153 (m-10) REVERT: B 199 ASN cc_start: 0.8874 (t0) cc_final: 0.8235 (t0) REVERT: B 201 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8518 (mp10) REVERT: B 202 GLU cc_start: 0.8692 (pm20) cc_final: 0.8296 (pm20) REVERT: B 232 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8116 (t80) REVERT: C 232 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: C 313 VAL cc_start: 0.8347 (t) cc_final: 0.7771 (m) REVERT: C 332 TRP cc_start: 0.8082 (m100) cc_final: 0.7768 (m100) REVERT: D 204 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8749 (mptt) REVERT: D 332 TRP cc_start: 0.8138 (m100) cc_final: 0.7779 (m100) REVERT: E 313 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8147 (m) REVERT: F 199 ASN cc_start: 0.8833 (t0) cc_final: 0.8267 (t0) REVERT: F 201 GLN cc_start: 0.8650 (mp10) cc_final: 0.8014 (mp10) REVERT: F 202 GLU cc_start: 0.8445 (pm20) cc_final: 0.8203 (pm20) REVERT: F 332 TRP cc_start: 0.8178 (m100) cc_final: 0.7853 (m100) outliers start: 54 outliers final: 39 residues processed: 204 average time/residue: 1.5930 time to fit residues: 362.5634 Evaluate side-chains 203 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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 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 204 LYS Chi-restraints excluded: chain D residue 218 MET 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 179 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080802 restraints weight = 45274.443| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.38 r_work: 0.2873 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.30 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) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1571 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= 0.137 Angle : 0.523 12.027 22730 Z= 0.279 Chirality : 0.046 0.164 2622 Planarity : 0.003 0.034 2924 Dihedral : 7.517 80.755 2252 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.62 % Allowed : 13.97 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2076 helix: 0.58 (0.23), residues: 528 sheet: 1.64 (0.30), residues: 306 loop : -0.43 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.009 0.001 PHE E 268 TYR 0.011 0.001 TYR D 225 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 596) hydrogen bonds : angle 5.11422 ( 1668) covalent geometry : bond 0.00319 (16734) covalent geometry : angle 0.52309 (22730) *********************** 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 219 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 1.748 Fit side-chains REVERT: A 199 ASN cc_start: 0.8574 (t0) cc_final: 0.8164 (t0) REVERT: A 332 TRP cc_start: 0.7969 (m100) cc_final: 0.7145 (m-10) REVERT: B 199 ASN cc_start: 0.8847 (t0) cc_final: 0.8429 (t0) REVERT: B 201 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8574 (mp10) REVERT: B 232 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8136 (t80) REVERT: C 232 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8773 (m-80) REVERT: C 313 VAL cc_start: 0.8339 (t) cc_final: 0.7768 (m) REVERT: C 332 TRP cc_start: 0.8090 (m100) cc_final: 0.7783 (m100) REVERT: D 44 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (tp30) REVERT: D 204 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8761 (mptt) REVERT: D 332 TRP cc_start: 0.8134 (m100) cc_final: 0.7862 (m-10) REVERT: E 313 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8171 (m) REVERT: E 332 TRP cc_start: 0.7973 (m100) cc_final: 0.7644 (m100) REVERT: F 199 ASN cc_start: 0.8812 (t0) cc_final: 0.8196 (t0) REVERT: F 201 GLN cc_start: 0.8653 (mp10) cc_final: 0.8025 (mp10) REVERT: F 202 GLU cc_start: 0.8426 (pm20) cc_final: 0.8179 (pm20) REVERT: F 332 TRP cc_start: 0.8177 (m100) cc_final: 0.7854 (m100) outliers start: 48 outliers final: 41 residues processed: 208 average time/residue: 1.2708 time to fit residues: 293.8595 Evaluate side-chains 211 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU 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 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 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 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 204 LYS 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 259 LYS 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 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 126 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.0270 chunk 176 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** C 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 = 0.3416 r_free = 0.3416 target = 0.106632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081111 restraints weight = 46672.969| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.42 r_work: 0.2873 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16734 Z= 0.129 Angle : 0.522 11.822 22730 Z= 0.278 Chirality : 0.046 0.159 2622 Planarity : 0.003 0.030 2924 Dihedral : 7.400 80.099 2251 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.73 % Allowed : 13.97 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2076 helix: 0.60 (0.23), residues: 528 sheet: 1.62 (0.30), residues: 306 loop : -0.42 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 332 HIS 0.005 0.001 HIS F 337 PHE 0.009 0.001 PHE E 268 TYR 0.011 0.001 TYR D 225 ARG 0.005 0.000 ARG D 135 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 596) hydrogen bonds : angle 5.08003 ( 1668) covalent geometry : bond 0.00300 (16734) covalent geometry : angle 0.52162 (22730) ********************** 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 221 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 171 time to evaluate : 2.019 Fit side-chains REVERT: A 199 ASN cc_start: 0.8594 (t0) cc_final: 0.8165 (t0) REVERT: A 332 TRP cc_start: 0.7948 (m100) cc_final: 0.7115 (m-10) REVERT: B 199 ASN cc_start: 0.8830 (t0) cc_final: 0.8148 (t0) REVERT: B 201 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8495 (mp10) REVERT: B 202 GLU cc_start: 0.8674 (pm20) cc_final: 0.8245 (pm20) REVERT: B 232 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8125 (t80) REVERT: C 232 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8775 (m-80) REVERT: C 313 VAL cc_start: 0.8336 (t) cc_final: 0.7758 (m) REVERT: C 332 TRP cc_start: 0.8107 (m100) cc_final: 0.7799 (m100) REVERT: D 44 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: D 204 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8757 (mptt) REVERT: D 332 TRP cc_start: 0.8166 (m100) cc_final: 0.7900 (m-10) REVERT: E 313 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8180 (m) REVERT: E 332 TRP cc_start: 0.7925 (m100) cc_final: 0.7600 (m100) REVERT: F 199 ASN cc_start: 0.8797 (t0) cc_final: 0.8169 (t0) REVERT: F 201 GLN cc_start: 0.8674 (mp10) cc_final: 0.8021 (mp10) REVERT: F 202 GLU cc_start: 0.8440 (pm20) cc_final: 0.8197 (pm20) REVERT: F 332 TRP cc_start: 0.8169 (m100) cc_final: 0.7818 (m100) outliers start: 50 outliers final: 42 residues processed: 208 average time/residue: 1.3042 time to fit residues: 304.7940 Evaluate side-chains 216 residues out of total 1842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 259 LYS Chi-restraints excluded: chain B residue 281 THR 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 44 GLU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 189 LEU 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 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 259 LYS 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 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 79 optimal weight: 1.9990 chunk 167 optimal weight: 0.0010 chunk 114 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 81 optimal weight: 0.0980 chunk 160 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.108071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083253 restraints weight = 37548.878| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.18 r_work: 0.2921 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16734 Z= 0.103 Angle : 0.503 10.477 22730 Z= 0.268 Chirality : 0.045 0.151 2622 Planarity : 0.003 0.029 2924 Dihedral : 7.200 78.423 2251 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.51 % Allowed : 14.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.17), residues: 2076 helix: 0.68 (0.23), residues: 528 sheet: 1.65 (0.30), residues: 306 loop : -0.37 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 332 HIS 0.005 0.001 HIS F 337 PHE 0.008 0.001 PHE E 268 TYR 0.010 0.001 TYR D 225 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 596) hydrogen bonds : angle 4.96691 ( 1668) covalent geometry : bond 0.00237 (16734) covalent geometry : angle 0.50296 (22730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14534.21 seconds wall clock time: 253 minutes 21.34 seconds (15201.34 seconds total)