Starting phenix.real_space_refine on Thu Feb 5 03:04:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.map" model { file = "/net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vfw_65040/02_2026/9vfw_65040.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 9121 2.51 5 N 2471 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14455 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "A" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "B" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "C" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "D" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "E" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Chain: "G" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2065 Classifications: {'peptide': 252} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 242} Chain breaks: 2 Time building chain proxies: 2.59, per 1000 atoms: 0.18 Number of scatterers: 14455 At special positions: 0 Unit cell: (110.4, 112.24, 82.8, 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 42 16.00 O 2821 8.00 N 2471 7.00 C 9121 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: 0.80 Conformation dependent library (CDL) restraints added in 540.5 milliseconds 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 43 sheets defined 2.4% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.579A pdb=" N ILE F 5 " --> pdb=" O ASP F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 223 removed outlier: 4.088A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.582A pdb=" N ILE A 5 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.638A pdb=" N ILE B 5 " --> pdb=" O ASP B 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.714A pdb=" N ILE C 5 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.680A pdb=" N ILE D 5 " --> pdb=" O ASP D 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.627A pdb=" N ILE E 5 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.598A pdb=" N ILE G 5 " --> pdb=" O ASP G 2 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 21 through 23 removed outlier: 4.103A pdb=" N TYR F 40 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA F 229 " --> pdb=" O TYR F 101 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N TYR F 101 " --> pdb=" O ALA F 229 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL F 231 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.876A pdb=" N THR F 27 " --> pdb=" O LYS F 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.558A pdb=" N ARG F 66 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR F 68 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY F 77 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU F 70 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYS F 75 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP F 274 " --> pdb=" O ARG F 253 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.621A pdb=" N VAL F 169 " --> pdb=" O PHE F 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 83 through 84 removed outlier: 3.621A pdb=" N VAL F 169 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 156 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 111 through 112 removed outlier: 3.676A pdb=" N TYR A 148 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.638A pdb=" N TYR F 148 " --> pdb=" O TYR G 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AA9, first strand: chain 'A' and resid 21 through 23 removed outlier: 4.085A pdb=" N TYR A 40 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 228 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA A 229 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TYR A 101 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 231 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 29 removed outlier: 3.889A pdb=" N THR A 27 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 29 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.556A pdb=" N VAL A 67 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 79 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER A 69 " --> pdb=" O GLY A 77 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 252 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 84 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU A 250 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 86 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 248 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 88 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP A 246 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG A 251 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TRP A 274 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ARG A 253 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP A 272 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 255 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 156 through 158 removed outlier: 3.576A pdb=" N ILE A 156 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 86 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 252 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE A 84 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU A 250 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 86 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A 248 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 88 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP A 246 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 111 through 112 removed outlier: 3.683A pdb=" N TYR B 148 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.643A pdb=" N PHE B 228 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA B 229 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N TYR B 101 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 231 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.617A pdb=" N ASP B 29 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 34 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.518A pdb=" N ILE B 156 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 86 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG B 251 " --> pdb=" O TRP B 274 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N TRP B 274 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG B 253 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP B 272 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 255 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.518A pdb=" N ILE B 156 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL B 86 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 111 through 112 removed outlier: 3.591A pdb=" N TYR C 148 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AC3, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.536A pdb=" N GLY C 23 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ALA C 229 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR C 101 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 231 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 26 through 29 removed outlier: 3.931A pdb=" N THR C 27 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.648A pdb=" N ARG C 66 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 68 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL C 86 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.648A pdb=" N ARG C 66 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR C 68 " --> pdb=" O GLY C 77 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY C 77 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU C 70 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LYS C 75 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE C 245 " --> pdb=" O GLU C 280 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N GLU C 280 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL C 247 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER C 278 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR C 249 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASP C 276 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG C 251 " --> pdb=" O TRP C 274 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N TRP C 274 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG C 253 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP C 272 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 255 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 283 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.511A pdb=" N TYR D 148 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AC9, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.549A pdb=" N GLY D 23 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 228 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA D 229 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR D 101 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL D 231 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.777A pdb=" N THR D 27 " --> pdb=" O LYS D 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.591A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR D 68 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 86 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.591A pdb=" N ARG D 66 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR D 68 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLY D 77 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU D 70 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS D 75 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL D 252 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N PHE D 84 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU D 250 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL D 86 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE D 248 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 88 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP D 246 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 245 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU D 280 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 247 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER D 278 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N TYR D 249 " --> pdb=" O ASP D 276 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASP D 276 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG D 251 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N TRP D 274 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG D 253 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP D 272 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP D 255 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 283 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 111 through 112 removed outlier: 3.508A pdb=" N TYR E 148 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AD6, first strand: chain 'E' and resid 21 through 23 removed outlier: 3.592A pdb=" N GLY E 23 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL E 231 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.790A pdb=" N THR E 27 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.585A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR E 68 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL E 86 " --> pdb=" O TRP E 167 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.585A pdb=" N ARG E 66 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR E 68 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLY E 77 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU E 70 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS E 75 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL E 252 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE E 84 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU E 250 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL E 86 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE E 248 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 88 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP E 246 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS E 283 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 111 through 112 removed outlier: 3.544A pdb=" N TYR G 148 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AE3, first strand: chain 'G' and resid 21 through 23 removed outlier: 3.535A pdb=" N GLY G 23 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR G 40 " --> pdb=" O GLY G 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE G 228 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA G 229 " --> pdb=" O TYR G 101 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR G 101 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL G 231 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.825A pdb=" N THR G 27 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 66 through 71 removed outlier: 5.658A pdb=" N VAL G 67 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ALA G 79 " --> pdb=" O VAL G 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER G 69 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 77 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL G 252 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE G 84 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU G 250 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL G 86 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE G 248 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU G 88 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP G 246 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG G 251 " --> pdb=" O TRP G 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP G 274 " --> pdb=" O ARG G 251 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG G 253 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP G 272 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP G 255 " --> pdb=" O THR G 270 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 156 through 158 removed outlier: 3.532A pdb=" N ILE G 156 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL G 86 " --> pdb=" O TRP G 167 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL G 252 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE G 84 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLU G 250 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL G 86 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE G 248 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU G 88 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP G 246 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 283 " --> pdb=" O THR G 292 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 174 through 175 387 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.07 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: 4660 1.34 - 1.46: 2760 1.46 - 1.57: 7280 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 14784 Sorted by residual: bond pdb=" C TRP A 80 " pdb=" N PRO A 81 " ideal model delta sigma weight residual 1.334 1.342 -0.008 1.11e-02 8.12e+03 5.10e-01 bond pdb=" CG LEU C 157 " pdb=" CD1 LEU C 157 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.10e-01 bond pdb=" CG LYS B 168 " pdb=" CD LYS B 168 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.70e-01 bond pdb=" CB TRP A 167 " pdb=" CG TRP A 167 " ideal model delta sigma weight residual 1.498 1.478 0.020 3.10e-02 1.04e+03 4.09e-01 bond pdb=" N GLY D 267 " pdb=" CA GLY D 267 " ideal model delta sigma weight residual 1.449 1.442 0.007 1.14e-02 7.69e+03 3.91e-01 ... (remaining 14779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 19106 0.97 - 1.95: 757 1.95 - 2.92: 72 2.92 - 3.90: 46 3.90 - 4.87: 4 Bond angle restraints: 19985 Sorted by residual: angle pdb=" N ILE C 5 " pdb=" CA ILE C 5 " pdb=" C ILE C 5 " ideal model delta sigma weight residual 111.77 108.41 3.36 1.04e+00 9.25e-01 1.04e+01 angle pdb=" N GLN F 242 " pdb=" CA GLN F 242 " pdb=" C GLN F 242 " ideal model delta sigma weight residual 108.32 111.64 -3.32 1.64e+00 3.72e-01 4.09e+00 angle pdb=" N GLN G 242 " pdb=" CA GLN G 242 " pdb=" C GLN G 242 " ideal model delta sigma weight residual 108.32 111.52 -3.20 1.64e+00 3.72e-01 3.80e+00 angle pdb=" N GLN A 242 " pdb=" CA GLN A 242 " pdb=" C GLN A 242 " ideal model delta sigma weight residual 108.32 111.51 -3.19 1.64e+00 3.72e-01 3.79e+00 angle pdb=" N GLN E 242 " pdb=" CA GLN E 242 " pdb=" C GLN E 242 " ideal model delta sigma weight residual 108.32 111.40 -3.08 1.64e+00 3.72e-01 3.53e+00 ... (remaining 19980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 7853 11.96 - 23.91: 679 23.91 - 35.87: 194 35.87 - 47.83: 93 47.83 - 59.79: 50 Dihedral angle restraints: 8869 sinusoidal: 3675 harmonic: 5194 Sorted by residual: dihedral pdb=" N ARG A 184 " pdb=" CA ARG A 184 " pdb=" CB ARG A 184 " pdb=" CG ARG A 184 " ideal model delta sinusoidal sigma weight residual 60.00 0.21 59.79 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU F 90 " pdb=" CA LEU F 90 " pdb=" CB LEU F 90 " pdb=" CG LEU F 90 " ideal model delta sinusoidal sigma weight residual -180.00 -120.24 -59.76 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N HIS F 48 " pdb=" CA HIS F 48 " pdb=" CB HIS F 48 " pdb=" CG HIS F 48 " ideal model delta sinusoidal sigma weight residual -180.00 -120.56 -59.44 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1296 0.028 - 0.056: 518 0.056 - 0.083: 116 0.083 - 0.111: 135 0.111 - 0.139: 42 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA VAL E 86 " pdb=" N VAL E 86 " pdb=" C VAL E 86 " pdb=" CB VAL E 86 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 245 " pdb=" N ILE B 245 " pdb=" C ILE B 245 " pdb=" CB ILE B 245 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE A 248 " pdb=" N ILE A 248 " pdb=" C ILE A 248 " pdb=" CB ILE A 248 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 2104 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 90 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO G 91 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 90 " 0.017 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO E 91 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 91 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 91 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 90 " 0.016 5.00e-02 4.00e+02 2.48e-02 9.81e-01 pdb=" N PRO B 91 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " 0.014 5.00e-02 4.00e+02 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1070 2.74 - 3.28: 14250 3.28 - 3.82: 23451 3.82 - 4.36: 28692 4.36 - 4.90: 49798 Nonbonded interactions: 117261 Sorted by model distance: nonbonded pdb=" OH TYR C 101 " pdb=" OG1 THR D 60 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR B 101 " pdb=" OG1 THR C 60 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OD1 ASN A 193 " model vdw 2.274 3.040 nonbonded pdb=" OG SER C 186 " pdb=" OD1 ASN C 193 " model vdw 2.276 3.040 nonbonded pdb=" O ASN D 32 " pdb=" NE2 GLN D 64 " model vdw 2.289 3.120 ... (remaining 117256 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 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 : 0.002 0.024 14784 Z= 0.108 Angle : 0.457 4.873 19985 Z= 0.253 Chirality : 0.041 0.139 2107 Planarity : 0.003 0.027 2562 Dihedral : 11.847 59.786 5509 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.80 % Allowed : 9.23 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.20), residues: 1722 helix: None (None), residues: 0 sheet: -1.97 (0.17), residues: 854 loop : -1.50 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 251 TYR 0.012 0.001 TYR C 65 PHE 0.012 0.001 PHE G 84 TRP 0.009 0.001 TRP B 167 HIS 0.002 0.000 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00217 (14784) covalent geometry : angle 0.45679 (19985) hydrogen bonds : bond 0.28737 ( 355) hydrogen bonds : angle 12.49899 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 420 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 PHE cc_start: 0.4191 (OUTLIER) cc_final: 0.3645 (m-80) REVERT: A 258 LEU cc_start: 0.6128 (tt) cc_final: 0.5840 (tt) REVERT: C 248 ILE cc_start: 0.8514 (mp) cc_final: 0.8308 (pt) REVERT: D 57 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7025 (m) REVERT: E 36 LYS cc_start: 0.5167 (ttmm) cc_final: 0.4743 (ttmm) REVERT: E 70 GLU cc_start: 0.5286 (pp20) cc_final: 0.4844 (pm20) REVERT: G 36 LYS cc_start: 0.5978 (ttmm) cc_final: 0.5672 (ttmm) REVERT: G 146 LEU cc_start: 0.8117 (tt) cc_final: 0.7581 (mt) REVERT: G 153 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.3246 (m-80) REVERT: G 196 PHE cc_start: 0.6877 (m-80) cc_final: 0.6314 (m-10) outliers start: 93 outliers final: 42 residues processed: 486 average time/residue: 0.1344 time to fit residues: 90.8076 Evaluate side-chains 285 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 153 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 HIS F 89 GLN F 97 GLN F 188 ASN ** F 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN A 48 HIS ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 89 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN C 49 ASN C 89 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN D 89 GLN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN D 242 GLN D 269 ASN E 89 GLN E 188 ASN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 ASN G 89 GLN G 105 ASN G 188 ASN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 269 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5155 r_free = 0.5155 target = 0.249617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.212292 restraints weight = 19672.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.211877 restraints weight = 17073.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.212307 restraints weight = 16526.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.212581 restraints weight = 15880.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.212783 restraints weight = 15460.861| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14784 Z= 0.226 Angle : 0.704 8.548 19985 Z= 0.375 Chirality : 0.046 0.159 2107 Planarity : 0.005 0.049 2562 Dihedral : 8.226 58.312 1985 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 5.43 % Allowed : 15.72 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.20), residues: 1722 helix: None (None), residues: 0 sheet: -2.10 (0.17), residues: 847 loop : -1.61 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 104 TYR 0.024 0.002 TYR G 65 PHE 0.018 0.003 PHE F 196 TRP 0.015 0.002 TRP B 260 HIS 0.009 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00512 (14784) covalent geometry : angle 0.70387 (19985) hydrogen bonds : bond 0.04948 ( 355) hydrogen bonds : angle 8.73746 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 270 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.4654 (mtm) cc_final: 0.4407 (ptp) REVERT: C 67 VAL cc_start: 0.7867 (t) cc_final: 0.7588 (m) REVERT: D 286 TRP cc_start: 0.4499 (m100) cc_final: 0.4283 (m100) REVERT: E 56 ARG cc_start: 0.5148 (mmt180) cc_final: 0.4853 (tpp-160) REVERT: E 70 GLU cc_start: 0.6059 (pp20) cc_final: 0.5593 (pm20) REVERT: E 153 PHE cc_start: 0.5145 (OUTLIER) cc_final: 0.4874 (m-10) REVERT: G 153 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4944 (m-80) outliers start: 87 outliers final: 54 residues processed: 335 average time/residue: 0.1215 time to fit residues: 59.2154 Evaluate side-chains 272 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 210 PHE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 153 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 224 PHE Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 153 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 ASN F 35 HIS F 48 HIS F 257 GLN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** A 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 49 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 GLN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN G 242 GLN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.273896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.254116 restraints weight = 21564.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5057 r_free = 0.5057 target = 0.253221 restraints weight = 27933.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.254250 restraints weight = 27120.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.254155 restraints weight = 22436.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.254511 restraints weight = 21208.459| |-----------------------------------------------------------------------------| r_work (final): 0.4858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14784 Z= 0.179 Angle : 0.621 7.041 19985 Z= 0.334 Chirality : 0.045 0.146 2107 Planarity : 0.004 0.048 2562 Dihedral : 7.018 53.359 1957 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.55 % Allowed : 18.09 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.20), residues: 1722 helix: None (None), residues: 0 sheet: -2.13 (0.17), residues: 861 loop : -1.61 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 253 TYR 0.020 0.001 TYR B 65 PHE 0.015 0.002 PHE E 224 TRP 0.023 0.001 TRP C 260 HIS 0.006 0.001 HIS F 48 Details of bonding type rmsd covalent geometry : bond 0.00397 (14784) covalent geometry : angle 0.62133 (19985) hydrogen bonds : bond 0.04423 ( 355) hydrogen bonds : angle 8.08491 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 254 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 PHE cc_start: 0.5119 (OUTLIER) cc_final: 0.4665 (m-10) REVERT: A 204 MET cc_start: 0.5010 (mtm) cc_final: 0.4802 (ptp) REVERT: B 194 GLN cc_start: 0.7163 (mt0) cc_final: 0.6887 (mt0) REVERT: D 56 ARG cc_start: 0.5435 (mmt90) cc_final: 0.5154 (mmt90) REVERT: D 150 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: E 35 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7426 (t-170) REVERT: E 56 ARG cc_start: 0.5152 (mmt180) cc_final: 0.4692 (tpp-160) REVERT: E 70 GLU cc_start: 0.5526 (pp20) cc_final: 0.5076 (pm20) REVERT: E 153 PHE cc_start: 0.5295 (OUTLIER) cc_final: 0.5049 (m-10) REVERT: E 255 ASP cc_start: 0.5078 (t0) cc_final: 0.4859 (t0) REVERT: E 257 GLN cc_start: 0.6508 (mp10) cc_final: 0.6032 (tm-30) REVERT: G 153 PHE cc_start: 0.5495 (OUTLIER) cc_final: 0.4063 (m-80) REVERT: G 171 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5548 (t80) REVERT: G 196 PHE cc_start: 0.7269 (m-80) cc_final: 0.6902 (m-10) outliers start: 89 outliers final: 58 residues processed: 322 average time/residue: 0.1215 time to fit residues: 56.8814 Evaluate side-chains 286 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 TRP Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 153 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 153 PHE Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 183 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 150 optimal weight: 0.0470 chunk 102 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 259 HIS ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** E 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.277140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.252479 restraints weight = 21419.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.252240 restraints weight = 27258.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.5064 r_free = 0.5064 target = 0.253480 restraints weight = 26345.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.253665 restraints weight = 21149.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5067 r_free = 0.5067 target = 0.253907 restraints weight = 23686.723| |-----------------------------------------------------------------------------| r_work (final): 0.4931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14784 Z= 0.132 Angle : 0.575 7.628 19985 Z= 0.309 Chirality : 0.044 0.146 2107 Planarity : 0.003 0.050 2562 Dihedral : 6.432 48.725 1949 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.87 % Allowed : 18.71 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.20), residues: 1722 helix: None (None), residues: 0 sheet: -2.12 (0.17), residues: 882 loop : -1.48 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 184 TYR 0.015 0.001 TYR D 65 PHE 0.013 0.002 PHE G 224 TRP 0.030 0.001 TRP B 260 HIS 0.005 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00287 (14784) covalent geometry : angle 0.57463 (19985) hydrogen bonds : bond 0.03949 ( 355) hydrogen bonds : angle 7.43430 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 250 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 150 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7868 (pm20) REVERT: C 257 GLN cc_start: 0.6893 (mp10) cc_final: 0.6396 (tm-30) REVERT: D 150 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: E 56 ARG cc_start: 0.5125 (mmt180) cc_final: 0.4611 (tpp-160) REVERT: G 171 PHE cc_start: 0.5931 (OUTLIER) cc_final: 0.5285 (t80) outliers start: 78 outliers final: 56 residues processed: 305 average time/residue: 0.1199 time to fit residues: 52.8734 Evaluate side-chains 278 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 219 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 70 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 35 HIS ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 HIS ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.265981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.246552 restraints weight = 21451.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.246077 restraints weight = 30873.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.247062 restraints weight = 30530.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.247075 restraints weight = 24661.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.247218 restraints weight = 22234.043| |-----------------------------------------------------------------------------| r_work (final): 0.4865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14784 Z= 0.260 Angle : 0.740 8.292 19985 Z= 0.391 Chirality : 0.046 0.153 2107 Planarity : 0.004 0.055 2562 Dihedral : 7.599 53.885 1947 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 6.92 % Allowed : 17.65 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.19), residues: 1722 helix: None (None), residues: 0 sheet: -2.36 (0.17), residues: 861 loop : -1.75 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 200 TYR 0.029 0.002 TYR D 65 PHE 0.018 0.003 PHE F 171 TRP 0.033 0.002 TRP B 260 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00593 (14784) covalent geometry : angle 0.74042 (19985) hydrogen bonds : bond 0.04441 ( 355) hydrogen bonds : angle 8.25513 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 224 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 153 PHE cc_start: 0.5651 (OUTLIER) cc_final: 0.5321 (m-10) REVERT: A 174 MET cc_start: 0.5960 (mmm) cc_final: 0.5523 (mmm) REVERT: A 210 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.6989 (m-10) REVERT: C 48 HIS cc_start: 0.5374 (OUTLIER) cc_final: 0.4848 (m-70) REVERT: D 48 HIS cc_start: 0.4797 (OUTLIER) cc_final: 0.3699 (m-70) REVERT: D 150 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: E 56 ARG cc_start: 0.5302 (mmt180) cc_final: 0.4615 (tpp-160) REVERT: E 150 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: E 255 ASP cc_start: 0.5338 (t0) cc_final: 0.5074 (t70) REVERT: E 257 GLN cc_start: 0.6386 (mp10) cc_final: 0.6163 (tm-30) REVERT: G 153 PHE cc_start: 0.6055 (OUTLIER) cc_final: 0.5000 (m-80) outliers start: 111 outliers final: 75 residues processed: 308 average time/residue: 0.1229 time to fit residues: 54.3885 Evaluate side-chains 281 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 199 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 153 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 153 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 251 ARG Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 167 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 126 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 264 ASN C 173 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 244 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.253637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.217695 restraints weight = 19266.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.219894 restraints weight = 16352.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.221536 restraints weight = 14645.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.222666 restraints weight = 13528.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.223121 restraints weight = 12810.070| |-----------------------------------------------------------------------------| r_work (final): 0.4973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14784 Z= 0.117 Angle : 0.583 7.617 19985 Z= 0.310 Chirality : 0.044 0.152 2107 Planarity : 0.003 0.045 2562 Dihedral : 6.389 53.079 1945 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.36 % Allowed : 19.40 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.20), residues: 1722 helix: None (None), residues: 0 sheet: -2.18 (0.17), residues: 882 loop : -1.43 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 184 TYR 0.013 0.001 TYR B 65 PHE 0.018 0.002 PHE G 196 TRP 0.030 0.001 TRP C 260 HIS 0.004 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00246 (14784) covalent geometry : angle 0.58257 (19985) hydrogen bonds : bond 0.03650 ( 355) hydrogen bonds : angle 7.08315 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 249 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 HIS cc_start: 0.5128 (OUTLIER) cc_final: 0.4523 (m-70) REVERT: D 48 HIS cc_start: 0.4235 (OUTLIER) cc_final: 0.3230 (m-70) REVERT: D 174 MET cc_start: 0.6120 (mmm) cc_final: 0.5776 (mmm) REVERT: D 204 MET cc_start: 0.8342 (pmm) cc_final: 0.7958 (pmm) REVERT: E 150 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: G 171 PHE cc_start: 0.6244 (OUTLIER) cc_final: 0.5817 (t80) REVERT: G 205 LYS cc_start: 0.5704 (ttpp) cc_final: 0.4948 (tttp) outliers start: 86 outliers final: 57 residues processed: 310 average time/residue: 0.1148 time to fit residues: 51.4784 Evaluate side-chains 279 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 218 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 173 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 HIS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 50 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 171 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 173 ASN ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN B 49 ASN ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN C 264 ASN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.257816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225079 restraints weight = 21376.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225079 restraints weight = 21807.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225079 restraints weight = 21807.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225079 restraints weight = 21807.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.225079 restraints weight = 21807.821| |-----------------------------------------------------------------------------| r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.095 14784 Z= 0.368 Angle : 0.875 8.968 19985 Z= 0.463 Chirality : 0.051 0.183 2107 Planarity : 0.005 0.063 2562 Dihedral : 8.183 55.077 1944 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 6.67 % Allowed : 19.28 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.18), residues: 1722 helix: -4.83 (0.39), residues: 42 sheet: -2.95 (0.17), residues: 798 loop : -1.98 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 253 TYR 0.037 0.003 TYR B 65 PHE 0.021 0.004 PHE C 153 TRP 0.029 0.003 TRP C 260 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00856 (14784) covalent geometry : angle 0.87479 (19985) hydrogen bonds : bond 0.05013 ( 355) hydrogen bonds : angle 8.79528 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 214 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.6381 (mmm) cc_final: 0.5937 (mmm) REVERT: A 241 GLN cc_start: 0.5757 (mm-40) cc_final: 0.5549 (mm-40) REVERT: B 50 LYS cc_start: 0.7283 (mmtt) cc_final: 0.6840 (ptmm) REVERT: C 48 HIS cc_start: 0.5271 (OUTLIER) cc_final: 0.4839 (m-70) REVERT: C 204 MET cc_start: 0.7862 (pmm) cc_final: 0.7615 (pmm) REVERT: C 260 TRP cc_start: 0.7176 (t-100) cc_final: 0.6602 (t-100) REVERT: D 91 PRO cc_start: 0.5712 (Cg_endo) cc_final: 0.5454 (Cg_exo) REVERT: D 174 MET cc_start: 0.6295 (mmm) cc_final: 0.5958 (mmm) REVERT: D 204 MET cc_start: 0.8585 (pmm) cc_final: 0.8248 (pmm) REVERT: E 56 ARG cc_start: 0.5398 (mmt180) cc_final: 0.4677 (mmt90) REVERT: G 253 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7652 (ttt180) outliers start: 107 outliers final: 85 residues processed: 298 average time/residue: 0.1284 time to fit residues: 54.4332 Evaluate side-chains 289 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 203 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 173 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 243 THR Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 251 ARG Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 143 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN B 177 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5131 r_free = 0.5131 target = 0.267441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.246355 restraints weight = 21218.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.245656 restraints weight = 27643.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.246175 restraints weight = 26537.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.246488 restraints weight = 22455.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.246616 restraints weight = 22534.567| |-----------------------------------------------------------------------------| r_work (final): 0.4956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.7412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14784 Z= 0.154 Angle : 0.659 9.366 19985 Z= 0.344 Chirality : 0.046 0.195 2107 Planarity : 0.004 0.056 2562 Dihedral : 7.061 55.126 1944 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.87 % Allowed : 21.77 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.19), residues: 1722 helix: -4.74 (0.45), residues: 42 sheet: -2.61 (0.17), residues: 840 loop : -1.74 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 253 TYR 0.019 0.001 TYR B 65 PHE 0.013 0.002 PHE G 196 TRP 0.031 0.002 TRP B 260 HIS 0.004 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00336 (14784) covalent geometry : angle 0.65883 (19985) hydrogen bonds : bond 0.03669 ( 355) hydrogen bonds : angle 7.60578 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 204 MET cc_start: 0.5962 (ppp) cc_final: 0.5426 (ppp) REVERT: B 211 LEU cc_start: 0.5964 (tp) cc_final: 0.5709 (tp) REVERT: C 48 HIS cc_start: 0.5146 (OUTLIER) cc_final: 0.4643 (m-70) REVERT: C 174 MET cc_start: 0.5994 (mmm) cc_final: 0.5673 (mmm) REVERT: D 150 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: E 56 ARG cc_start: 0.5162 (mmt180) cc_final: 0.4591 (mmt90) REVERT: E 150 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: G 204 MET cc_start: 0.7134 (pmm) cc_final: 0.6925 (pmm) outliers start: 78 outliers final: 67 residues processed: 301 average time/residue: 0.1224 time to fit residues: 52.3570 Evaluate side-chains 287 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 217 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 6.9990 chunk 134 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 overall best weight: 2.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 HIS ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 ASN G 209 ASN ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.262226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.242565 restraints weight = 21481.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.241964 restraints weight = 27913.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.242937 restraints weight = 30143.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.242830 restraints weight = 24460.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.243122 restraints weight = 22706.157| |-----------------------------------------------------------------------------| r_work (final): 0.4915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14784 Z= 0.215 Angle : 0.720 9.247 19985 Z= 0.375 Chirality : 0.046 0.199 2107 Planarity : 0.004 0.061 2562 Dihedral : 7.325 50.331 1944 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 5.55 % Allowed : 21.40 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.19), residues: 1722 helix: -4.73 (0.46), residues: 42 sheet: -2.82 (0.17), residues: 812 loop : -1.80 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 253 TYR 0.024 0.002 TYR B 65 PHE 0.012 0.002 PHE D 84 TRP 0.036 0.002 TRP C 260 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00491 (14784) covalent geometry : angle 0.71982 (19985) hydrogen bonds : bond 0.03959 ( 355) hydrogen bonds : angle 7.92135 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 217 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 194 GLN cc_start: 0.7635 (mm110) cc_final: 0.7275 (mt0) REVERT: B 194 GLN cc_start: 0.7930 (mp10) cc_final: 0.7431 (mp10) REVERT: C 48 HIS cc_start: 0.5319 (OUTLIER) cc_final: 0.4795 (m-70) REVERT: C 174 MET cc_start: 0.6029 (mmm) cc_final: 0.5719 (mmm) REVERT: D 150 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: E 56 ARG cc_start: 0.5152 (mmt180) cc_final: 0.4487 (mmt90) REVERT: E 150 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: G 49 ASN cc_start: 0.7861 (p0) cc_final: 0.7591 (p0) outliers start: 89 outliers final: 79 residues processed: 285 average time/residue: 0.1187 time to fit residues: 48.0818 Evaluate side-chains 290 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 208 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 173 ASN Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 7 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.268298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.246322 restraints weight = 21326.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.245663 restraints weight = 26990.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.246202 restraints weight = 26270.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.246237 restraints weight = 22569.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.246343 restraints weight = 22332.160| |-----------------------------------------------------------------------------| r_work (final): 0.4955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14784 Z= 0.141 Angle : 0.663 12.027 19985 Z= 0.344 Chirality : 0.045 0.202 2107 Planarity : 0.004 0.062 2562 Dihedral : 6.765 45.347 1944 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.68 % Allowed : 21.90 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.19), residues: 1722 helix: -4.69 (0.48), residues: 42 sheet: -2.60 (0.17), residues: 833 loop : -1.68 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 253 TYR 0.016 0.001 TYR B 65 PHE 0.016 0.002 PHE A 210 TRP 0.040 0.002 TRP C 260 HIS 0.004 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00312 (14784) covalent geometry : angle 0.66277 (19985) hydrogen bonds : bond 0.03499 ( 355) hydrogen bonds : angle 7.29570 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 194 GLN cc_start: 0.7700 (mm110) cc_final: 0.7308 (mt0) REVERT: B 204 MET cc_start: 0.5980 (ppp) cc_final: 0.5487 (ppp) REVERT: C 48 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4720 (m-70) REVERT: D 150 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: E 56 ARG cc_start: 0.5091 (mmt180) cc_final: 0.4513 (mmt90) REVERT: E 150 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: G 49 ASN cc_start: 0.7735 (p0) cc_final: 0.7499 (p0) REVERT: G 195 LEU cc_start: 0.7730 (tp) cc_final: 0.7475 (tp) outliers start: 75 outliers final: 70 residues processed: 278 average time/residue: 0.1218 time to fit residues: 48.1908 Evaluate side-chains 280 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 171 PHE Chi-restraints excluded: chain F residue 176 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 251 ARG Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 171 PHE Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 PHE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 171 PHE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 150 GLN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain G residue 35 HIS Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 92 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 171 PHE Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 251 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 122 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 135 optimal weight: 0.0050 chunk 98 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 214 ASN G 173 ASN G 264 ASN ** G 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5139 r_free = 0.5139 target = 0.268650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.248406 restraints weight = 21349.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.247582 restraints weight = 26258.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.248799 restraints weight = 27690.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.248506 restraints weight = 21559.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.248823 restraints weight = 20985.333| |-----------------------------------------------------------------------------| r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14784 Z= 0.142 Angle : 0.659 11.447 19985 Z= 0.341 Chirality : 0.045 0.201 2107 Planarity : 0.004 0.061 2562 Dihedral : 6.577 41.889 1944 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 4.93 % Allowed : 22.21 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.19), residues: 1722 helix: -4.65 (0.49), residues: 42 sheet: -2.55 (0.17), residues: 826 loop : -1.66 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.016 0.001 TYR B 65 PHE 0.017 0.002 PHE E 210 TRP 0.035 0.002 TRP B 260 HIS 0.003 0.001 HIS F 259 Details of bonding type rmsd covalent geometry : bond 0.00317 (14784) covalent geometry : angle 0.65870 (19985) hydrogen bonds : bond 0.03471 ( 355) hydrogen bonds : angle 7.19787 ( 978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.98 seconds wall clock time: 36 minutes 8.40 seconds (2168.40 seconds total)