Starting phenix.real_space_refine on Mon Jul 6 01:05:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj5_63133/07_2026/9lj5_63133_trim.cif" } resolution = 2.9 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= 0.002 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 S 88 5.16 5 C 10244 2.51 5 N 2668 2.21 5 O 2896 1.98 5 F 4 1.80 5 H 15540 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31464 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5617 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5617 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 5617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5617 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 5617 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 1 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'9MF': 1, 'PIO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'9MF': 1, 'PIO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'9MF': 1, 'PIO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'9MF': 1, 'PIO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.34, per 1000 atoms: 0.14 Number of scatterers: 31464 At special positions: 0 Unit cell: (131.13, 131.13, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 88 16.00 P 24 15.00 F 4 9.00 O 2896 8.00 N 2668 7.00 C 10244 6.00 H 15540 1.00 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 630.2 milliseconds 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 85.6% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 103 through 120 Processing helix chain 'A' and resid 124 through 149 removed outlier: 4.059A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.894A pdb=" N GLY A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 6.256A pdb=" N ARG A 187 " --> pdb=" O CYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 200 through 223 Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.964A pdb=" N PHE A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.804A pdb=" N ASP A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 262 through 289 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 321 through 384 removed outlier: 3.807A pdb=" N LEU A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 3.754A pdb=" N ARG A 366 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Proline residue: A 369 - end of helix removed outlier: 3.556A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 541 Processing helix chain 'A' and resid 545 through 571 Processing helix chain 'E' and resid 7 through 22 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.519A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.674A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 removed outlier: 4.041A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 4.080A pdb=" N ASN E 98 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 118 through 129 removed outlier: 4.082A pdb=" N ALA E 129 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 149 Processing helix chain 'B' and resid 104 through 120 Processing helix chain 'B' and resid 124 through 149 removed outlier: 4.059A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 183 removed outlier: 3.894A pdb=" N GLY B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 6.256A pdb=" N ARG B 187 " --> pdb=" O CYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 200 through 223 Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.964A pdb=" N PHE B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.804A pdb=" N ASP B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 262 through 289 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 321 through 384 removed outlier: 3.807A pdb=" N LEU B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Proline residue: B 342 - end of helix removed outlier: 3.754A pdb=" N ARG B 366 " --> pdb=" O HIS B 362 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Proline residue: B 369 - end of helix removed outlier: 3.556A pdb=" N ASP B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 541 Processing helix chain 'B' and resid 545 through 571 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.519A pdb=" N VAL C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 75 removed outlier: 3.674A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 removed outlier: 4.041A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 4.080A pdb=" N ASN C 98 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 118 through 129 removed outlier: 4.082A pdb=" N ALA C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 124 through 149 removed outlier: 4.059A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR D 129 " --> pdb=" O TRP D 125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 removed outlier: 3.894A pdb=" N GLY D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 6.256A pdb=" N ARG D 187 " --> pdb=" O CYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 199 Processing helix chain 'D' and resid 200 through 223 Processing helix chain 'D' and resid 224 through 236 removed outlier: 3.964A pdb=" N PHE D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 removed outlier: 3.804A pdb=" N ASP D 246 " --> pdb=" O MET D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 262 through 289 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 321 through 384 removed outlier: 3.807A pdb=" N LEU D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Proline residue: D 342 - end of helix removed outlier: 3.754A pdb=" N ARG D 366 " --> pdb=" O HIS D 362 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 367 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) Proline residue: D 369 - end of helix removed outlier: 3.556A pdb=" N ASP D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 541 Processing helix chain 'D' and resid 545 through 571 Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 40 removed outlier: 3.519A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.674A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 4.041A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 98 removed outlier: 4.080A pdb=" N ASN F 98 " --> pdb=" O LYS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 113 Processing helix chain 'F' and resid 118 through 129 removed outlier: 4.082A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'G' and resid 104 through 120 Processing helix chain 'G' and resid 124 through 149 removed outlier: 4.059A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR G 129 " --> pdb=" O TRP G 125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU G 143 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 183 removed outlier: 3.894A pdb=" N GLY G 183 " --> pdb=" O ILE G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 6.256A pdb=" N ARG G 187 " --> pdb=" O CYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 199 Processing helix chain 'G' and resid 200 through 223 Processing helix chain 'G' and resid 224 through 236 removed outlier: 3.964A pdb=" N PHE G 236 " --> pdb=" O ARG G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 246 removed outlier: 3.804A pdb=" N ASP G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 262 Processing helix chain 'G' and resid 262 through 289 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 321 through 384 removed outlier: 3.807A pdb=" N LEU G 334 " --> pdb=" O GLY G 330 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) Proline residue: G 342 - end of helix removed outlier: 3.754A pdb=" N ARG G 366 " --> pdb=" O HIS G 362 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG G 367 " --> pdb=" O PHE G 363 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN G 368 " --> pdb=" O GLU G 364 " (cutoff:3.500A) Proline residue: G 369 - end of helix removed outlier: 3.556A pdb=" N ASP G 384 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 541 Processing helix chain 'G' and resid 545 through 571 Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.519A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.674A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 4.041A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 98 removed outlier: 4.080A pdb=" N ASN H 98 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 113 Processing helix chain 'H' and resid 118 through 129 removed outlier: 4.082A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 149 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 removed outlier: 3.613A pdb=" N ILE E 28 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 64 " --> pdb=" O ILE E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.613A pdb=" N ILE C 28 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 64 " --> pdb=" O ILE C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 removed outlier: 3.613A pdb=" N ILE F 28 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE F 64 " --> pdb=" O ILE F 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.613A pdb=" N ILE H 28 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE H 64 " --> pdb=" O ILE H 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1197 hydrogen bonds defined for protein. 3555 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: 6.30 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15508 1.03 - 1.23: 136 1.23 - 1.43: 6736 1.43 - 1.62: 9232 1.62 - 1.82: 176 Bond restraints: 31788 Sorted by residual: bond pdb=" C09 9MF A 802 " pdb=" N08 9MF A 802 " ideal model delta sigma weight residual 1.352 1.444 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C09 9MF B 803 " pdb=" N08 9MF B 803 " ideal model delta sigma weight residual 1.352 1.444 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C09 9MF D 803 " pdb=" N08 9MF D 803 " ideal model delta sigma weight residual 1.352 1.444 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C09 9MF G1001 " pdb=" N08 9MF G1001 " ideal model delta sigma weight residual 1.352 1.444 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1A PIO G1003 " pdb=" O2C PIO G1003 " ideal model delta sigma weight residual 1.332 1.404 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 31783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 56788 4.05 - 8.09: 207 8.09 - 12.14: 97 12.14 - 16.19: 20 16.19 - 20.23: 8 Bond angle restraints: 57120 Sorted by residual: angle pdb=" O11 PIO G1003 " pdb=" P1 PIO G1003 " pdb=" O12 PIO G1003 " ideal model delta sigma weight residual 121.09 100.86 20.23 3.00e+00 1.11e-01 4.55e+01 angle pdb=" O11 PIO D 802 " pdb=" P1 PIO D 802 " pdb=" O12 PIO D 802 " ideal model delta sigma weight residual 121.09 100.87 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" O11 PIO B 802 " pdb=" P1 PIO B 802 " pdb=" O12 PIO B 802 " ideal model delta sigma weight residual 121.09 100.87 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" O11 PIO A 801 " pdb=" P1 PIO A 801 " pdb=" O12 PIO A 801 " ideal model delta sigma weight residual 121.09 100.90 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O11 PIO B 801 " pdb=" P1 PIO B 801 " pdb=" O12 PIO B 801 " ideal model delta sigma weight residual 121.09 101.09 20.00 3.00e+00 1.11e-01 4.45e+01 ... (remaining 57115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 12660 17.42 - 34.84: 1476 34.84 - 52.26: 466 52.26 - 69.68: 142 69.68 - 87.10: 12 Dihedral angle restraints: 14756 sinusoidal: 7996 harmonic: 6760 Sorted by residual: dihedral pdb=" CA MET E 72 " pdb=" C MET E 72 " pdb=" N MET E 73 " pdb=" CA MET E 73 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET H 72 " pdb=" C MET H 72 " pdb=" N MET H 73 " pdb=" CA MET H 73 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET C 72 " pdb=" C MET C 72 " pdb=" N MET C 73 " pdb=" CA MET C 73 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 14753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1584 0.030 - 0.060: 616 0.060 - 0.091: 180 0.091 - 0.121: 56 0.121 - 0.151: 12 Chirality restraints: 2448 Sorted by residual: chirality pdb=" C4 PIO B 802 " pdb=" C3 PIO B 802 " pdb=" C5 PIO B 802 " pdb=" O4 PIO B 802 " both_signs ideal model delta sigma weight residual False 2.50 2.65 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" C4 PIO G1003 " pdb=" C3 PIO G1003 " pdb=" C5 PIO G1003 " pdb=" O4 PIO G1003 " both_signs ideal model delta sigma weight residual False 2.50 2.65 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" C4 PIO A 801 " pdb=" C3 PIO A 801 " pdb=" C5 PIO A 801 " pdb=" O4 PIO A 801 " both_signs ideal model delta sigma weight residual False 2.50 2.65 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 2445 not shown) Planarity restraints: 4584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 378 " 0.017 2.00e-02 2.50e+03 8.30e-03 2.75e+00 pdb=" CG TRP B 378 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP B 378 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 378 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 378 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 378 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP B 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 378 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 378 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 378 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 378 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP B 378 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 378 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 378 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 378 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP B 378 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 378 " 0.017 2.00e-02 2.50e+03 8.30e-03 2.75e+00 pdb=" CG TRP A 378 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 378 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 378 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 378 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 378 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 378 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 378 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 378 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 378 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 378 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 378 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 378 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 378 " 0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 378 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 378 " -0.017 2.00e-02 2.50e+03 8.30e-03 2.75e+00 pdb=" CG TRP D 378 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP D 378 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP D 378 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 378 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 378 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP D 378 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 378 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 378 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 378 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP D 378 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP D 378 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP D 378 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 378 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 378 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP D 378 " -0.000 2.00e-02 2.50e+03 ... (remaining 4581 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 1740 2.16 - 2.77: 61881 2.77 - 3.38: 93433 3.38 - 3.99: 112121 3.99 - 4.60: 175807 Nonbonded interactions: 444982 Sorted by model distance: nonbonded pdb=" OG SER B 257 " pdb=" HE3 LYS B 353 " model vdw 1.556 2.620 nonbonded pdb=" OG SER G 257 " pdb=" HE3 LYS G 353 " model vdw 1.556 2.620 nonbonded pdb=" O PRO F 67 " pdb=" HG1 THR F 71 " model vdw 1.567 2.450 nonbonded pdb=" O PRO C 67 " pdb=" HG1 THR C 71 " model vdw 1.567 2.450 nonbonded pdb=" O PRO E 67 " pdb=" HG1 THR E 71 " model vdw 1.567 2.450 ... (remaining 444977 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' and resid 103 through 571) selection = (chain 'B' and resid 103 through 571) selection = (chain 'D' and resid 103 through 571) selection = (chain 'G' and resid 103 through 571) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.012 0.548 16256 Z= 1.001 Angle : 1.161 20.235 21948 Z= 0.454 Chirality : 0.037 0.151 2448 Planarity : 0.004 0.031 2708 Dihedral : 17.094 87.095 5920 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.40 % Allowed : 28.08 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1908 helix: 1.51 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.29 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 563 TYR 0.010 0.001 TYR B 553 PHE 0.010 0.001 PHE A 236 TRP 0.023 0.002 TRP D 378 HIS 0.003 0.001 HIS D 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.37 (16248) covalent geometry : angle 1.16055 / 0.45 (21948) hydrogen bonds : bond 0.10578 / 6.90 ( 1197) hydrogen bonds : angle 5.50536 / 4.07 ( 3555) Misc. bond : bond 0.41893 / 22.13 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.702 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 31 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8557 (mppt) outliers start: 39 outliers final: 32 residues processed: 276 average time/residue: 0.9672 time to fit residues: 303.1780 Evaluate side-chains 228 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 77 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 77 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 77 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.184718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111151 restraints weight = 74344.208| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.43 r_work: 0.3306 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16256 Z= 0.252 Angle : 0.586 6.567 21948 Z= 0.310 Chirality : 0.037 0.138 2448 Planarity : 0.004 0.034 2708 Dihedral : 8.590 89.982 2344 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.19 % Allowed : 27.77 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 1908 helix: 1.74 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 0.07 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 107 TYR 0.010 0.001 TYR A 553 PHE 0.010 0.001 PHE B 138 TRP 0.017 0.002 TRP D 378 HIS 0.003 0.001 HIS H 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (16248) covalent geometry : angle 0.58626 / 0.31 (21948) hydrogen bonds : bond 0.04491 / 2.94 ( 1197) hydrogen bonds : angle 4.59000 / 3.39 ( 3555) Misc. bond : bond 0.00064 / 0.03 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.616 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: 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 197 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: E 100 TYR cc_start: 0.9045 (m-80) cc_final: 0.7897 (m-80) REVERT: E 138 ASN cc_start: 0.8941 (p0) cc_final: 0.8185 (m110) REVERT: B 197 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: C 100 TYR cc_start: 0.9040 (m-80) cc_final: 0.7883 (m-80) REVERT: C 138 ASN cc_start: 0.8943 (p0) cc_final: 0.8185 (m110) REVERT: D 197 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6597 (m-80) REVERT: F 100 TYR cc_start: 0.9046 (m-80) cc_final: 0.7896 (m-80) REVERT: F 138 ASN cc_start: 0.8944 (p0) cc_final: 0.8188 (m110) REVERT: G 197 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6586 (m-80) REVERT: H 100 TYR cc_start: 0.9041 (m-80) cc_final: 0.7888 (m-80) REVERT: H 138 ASN cc_start: 0.8938 (p0) cc_final: 0.8182 (m110) outliers start: 68 outliers final: 28 residues processed: 248 average time/residue: 0.8461 time to fit residues: 243.6360 Evaluate side-chains 216 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain B residue 184 CYS Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 184 CYS Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 184 CYS Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.183791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109760 restraints weight = 74554.363| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.42 r_work: 0.3288 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16256 Z= 0.292 Angle : 0.568 5.850 21948 Z= 0.308 Chirality : 0.038 0.140 2448 Planarity : 0.004 0.028 2708 Dihedral : 8.224 85.824 2316 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.19 % Allowed : 28.51 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.18), residues: 1908 helix: 1.58 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : 0.23 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 325 TYR 0.011 0.002 TYR G 553 PHE 0.009 0.001 PHE A 236 TRP 0.016 0.002 TRP D 378 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.29 (16248) covalent geometry : angle 0.56829 / 0.31 (21948) hydrogen bonds : bond 0.04545 / 2.96 ( 1197) hydrogen bonds : angle 4.55305 / 3.36 ( 3555) Misc. bond : bond 0.00183 / 0.10 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 0.750 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: 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 167 MET cc_start: 0.5148 (tpt) cc_final: 0.4296 (tpt) REVERT: A 197 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: E 100 TYR cc_start: 0.8999 (m-80) cc_final: 0.7767 (m-80) REVERT: E 138 ASN cc_start: 0.8949 (p0) cc_final: 0.8167 (m-40) REVERT: B 167 MET cc_start: 0.5165 (tpt) cc_final: 0.4313 (tpt) REVERT: B 197 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: C 100 TYR cc_start: 0.9006 (m-80) cc_final: 0.7781 (m-80) REVERT: C 138 ASN cc_start: 0.8954 (p0) cc_final: 0.8171 (m-40) REVERT: D 167 MET cc_start: 0.5210 (tpt) cc_final: 0.4348 (tpt) REVERT: D 197 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: F 100 TYR cc_start: 0.9011 (m-80) cc_final: 0.7788 (m-80) REVERT: F 138 ASN cc_start: 0.8957 (p0) cc_final: 0.8172 (m-40) REVERT: G 167 MET cc_start: 0.5155 (tpt) cc_final: 0.4304 (tpt) REVERT: G 197 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: H 100 TYR cc_start: 0.9001 (m-80) cc_final: 0.7776 (m-80) REVERT: H 138 ASN cc_start: 0.8951 (p0) cc_final: 0.8167 (m-40) outliers start: 68 outliers final: 40 residues processed: 258 average time/residue: 0.7900 time to fit residues: 236.8192 Evaluate side-chains 232 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 93 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.184054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110426 restraints weight = 73812.834| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.42 r_work: 0.3299 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16256 Z= 0.243 Angle : 0.544 5.063 21948 Z= 0.292 Chirality : 0.036 0.130 2448 Planarity : 0.004 0.029 2708 Dihedral : 7.628 82.309 2312 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.62 % Allowed : 27.65 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 1908 helix: 1.66 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : 0.22 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 325 TYR 0.010 0.002 TYR B 553 PHE 0.010 0.001 PHE A 134 TRP 0.016 0.002 TRP A 378 HIS 0.004 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.24 (16248) covalent geometry : angle 0.54371 / 0.29 (21948) hydrogen bonds : bond 0.04320 / 2.82 ( 1197) hydrogen bonds : angle 4.41932 / 3.25 ( 3555) Misc. bond : bond 0.00022 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 200 time to evaluate : 0.868 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: 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 167 MET cc_start: 0.5228 (tpt) cc_final: 0.5028 (tpt) REVERT: A 197 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: E 77 MET cc_start: 0.7905 (pp-130) cc_final: 0.7621 (tmm) REVERT: E 100 TYR cc_start: 0.8967 (m-80) cc_final: 0.7182 (m-80) REVERT: E 136 GLN cc_start: 0.6285 (mt0) cc_final: 0.5874 (pp30) REVERT: B 167 MET cc_start: 0.5226 (tpt) cc_final: 0.5026 (tpt) REVERT: B 197 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6181 (m-80) REVERT: C 77 MET cc_start: 0.7916 (pp-130) cc_final: 0.7631 (tmm) REVERT: C 100 TYR cc_start: 0.8965 (m-80) cc_final: 0.7159 (m-80) REVERT: C 136 GLN cc_start: 0.6281 (mt0) cc_final: 0.5875 (pp30) REVERT: D 167 MET cc_start: 0.5223 (tpt) cc_final: 0.5023 (tpt) REVERT: D 197 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: F 77 MET cc_start: 0.7910 (pp-130) cc_final: 0.7628 (tmm) REVERT: F 100 TYR cc_start: 0.8973 (m-80) cc_final: 0.7173 (m-80) REVERT: F 136 GLN cc_start: 0.6288 (mt0) cc_final: 0.5880 (pp30) REVERT: G 167 MET cc_start: 0.5217 (tpt) cc_final: 0.5014 (tpt) REVERT: G 197 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: H 77 MET cc_start: 0.7910 (pp-130) cc_final: 0.7628 (tmm) REVERT: H 100 TYR cc_start: 0.8965 (m-80) cc_final: 0.7174 (m-80) REVERT: H 136 GLN cc_start: 0.6286 (mt0) cc_final: 0.5876 (pp30) outliers start: 75 outliers final: 44 residues processed: 268 average time/residue: 0.9114 time to fit residues: 277.9581 Evaluate side-chains 244 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 146 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 GLN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.182436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108488 restraints weight = 73428.377| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.34 r_work: 0.3276 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 16256 Z= 0.385 Angle : 0.626 8.002 21948 Z= 0.343 Chirality : 0.041 0.150 2448 Planarity : 0.005 0.048 2708 Dihedral : 8.329 83.297 2312 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 6.16 % Allowed : 27.59 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.18), residues: 1908 helix: 1.22 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : 0.04 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 325 TYR 0.014 0.002 TYR A 553 PHE 0.015 0.002 PHE D 134 TRP 0.017 0.002 TRP A 378 HIS 0.004 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00848 / 0.38 (16248) covalent geometry : angle 0.62647 / 0.34 (21948) hydrogen bonds : bond 0.04655 / 3.02 ( 1197) hydrogen bonds : angle 4.66633 / 3.44 ( 3555) Misc. bond : bond 0.00026 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 188 time to evaluate : 0.759 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.5089 (tpt) REVERT: A 197 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6246 (m-80) REVERT: E 77 MET cc_start: 0.8028 (pp-130) cc_final: 0.7753 (tmm) REVERT: E 100 TYR cc_start: 0.8936 (m-80) cc_final: 0.7676 (m-80) REVERT: E 136 GLN cc_start: 0.6362 (mt0) cc_final: 0.6110 (pt0) REVERT: B 167 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.5099 (tpt) REVERT: B 197 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6248 (m-80) REVERT: C 77 MET cc_start: 0.8035 (pp-130) cc_final: 0.7762 (tmm) REVERT: C 100 TYR cc_start: 0.8943 (m-80) cc_final: 0.7668 (m-80) REVERT: C 136 GLN cc_start: 0.6368 (mt0) cc_final: 0.6104 (pt0) REVERT: D 167 MET cc_start: 0.5415 (OUTLIER) cc_final: 0.5075 (tpt) REVERT: D 197 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: F 77 MET cc_start: 0.8032 (pp-130) cc_final: 0.7763 (tmm) REVERT: F 100 TYR cc_start: 0.8952 (m-80) cc_final: 0.7703 (m-80) REVERT: F 136 GLN cc_start: 0.6370 (mt0) cc_final: 0.6119 (pt0) REVERT: G 167 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.5070 (tpt) REVERT: G 197 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: H 77 MET cc_start: 0.8036 (pp-130) cc_final: 0.7764 (tmm) REVERT: H 100 TYR cc_start: 0.8941 (m-80) cc_final: 0.7676 (m-80) REVERT: H 136 GLN cc_start: 0.6364 (mt0) cc_final: 0.6113 (pt0) outliers start: 100 outliers final: 69 residues processed: 275 average time/residue: 0.9330 time to fit residues: 294.9102 Evaluate side-chains 253 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 176 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 188 TYR Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 188 TYR Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 160 optimal weight: 0.6980 chunk 132 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 96 optimal weight: 0.3980 chunk 127 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN C 136 GLN F 136 GLN ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.183257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.110306 restraints weight = 72727.436| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.33 r_work: 0.3308 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16256 Z= 0.257 Angle : 0.567 6.086 21948 Z= 0.306 Chirality : 0.037 0.130 2448 Planarity : 0.004 0.030 2708 Dihedral : 8.004 81.322 2312 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.17 % Allowed : 28.88 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.18), residues: 1908 helix: 1.38 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : 0.02 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 535 TYR 0.011 0.002 TYR A 553 PHE 0.010 0.001 PHE B 134 TRP 0.017 0.002 TRP A 378 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (16248) covalent geometry : angle 0.56705 / 0.31 (21948) hydrogen bonds : bond 0.04408 / 2.87 ( 1197) hydrogen bonds : angle 4.49400 / 3.31 ( 3555) Misc. bond : bond 0.00006 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 186 time to evaluate : 0.919 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: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.5401 (tpt) cc_final: 0.5171 (tpt) REVERT: A 197 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: E 77 MET cc_start: 0.8029 (pp-130) cc_final: 0.7741 (tmm) REVERT: E 100 TYR cc_start: 0.8964 (m-80) cc_final: 0.7671 (m-80) REVERT: E 136 GLN cc_start: 0.6374 (mt0) cc_final: 0.6087 (pt0) REVERT: E 146 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: B 167 MET cc_start: 0.5401 (tpt) cc_final: 0.5173 (tpt) REVERT: B 197 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6269 (m-80) REVERT: C 77 MET cc_start: 0.8039 (pp-130) cc_final: 0.7752 (tmm) REVERT: C 100 TYR cc_start: 0.8959 (m-80) cc_final: 0.7664 (m-80) REVERT: C 136 GLN cc_start: 0.6431 (mt0) cc_final: 0.6140 (pt0) REVERT: C 146 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7420 (mmm) REVERT: D 167 MET cc_start: 0.5401 (tpt) cc_final: 0.5176 (tpt) REVERT: D 197 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: F 77 MET cc_start: 0.8033 (pp-130) cc_final: 0.7749 (tmm) REVERT: F 100 TYR cc_start: 0.8957 (m-80) cc_final: 0.7690 (m-80) REVERT: F 136 GLN cc_start: 0.6380 (mt0) cc_final: 0.6097 (pt0) REVERT: F 146 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7449 (mmm) REVERT: G 167 MET cc_start: 0.5402 (tpt) cc_final: 0.5173 (tpt) REVERT: G 197 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: H 77 MET cc_start: 0.8032 (pp-130) cc_final: 0.7747 (tmm) REVERT: H 100 TYR cc_start: 0.8957 (m-80) cc_final: 0.7664 (m-80) REVERT: H 136 GLN cc_start: 0.6379 (mt0) cc_final: 0.6095 (pt0) REVERT: H 146 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7457 (mmm) outliers start: 84 outliers final: 56 residues processed: 262 average time/residue: 0.9270 time to fit residues: 280.8577 Evaluate side-chains 247 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 144 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.183304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.110591 restraints weight = 73004.923| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.34 r_work: 0.3311 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16256 Z= 0.269 Angle : 0.577 6.470 21948 Z= 0.308 Chirality : 0.037 0.132 2448 Planarity : 0.004 0.030 2708 Dihedral : 7.658 78.020 2312 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.93 % Allowed : 29.13 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.18), residues: 1908 helix: 1.40 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -0.05 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 535 TYR 0.011 0.002 TYR D 553 PHE 0.013 0.001 PHE H 13 TRP 0.017 0.002 TRP B 378 HIS 0.003 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 (16248) covalent geometry : angle 0.57681 / 0.31 (21948) hydrogen bonds : bond 0.04380 / 2.85 ( 1197) hydrogen bonds : angle 4.47690 / 3.30 ( 3555) Misc. bond : bond 0.00004 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 203 time to evaluate : 0.807 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.5013 (tpt) REVERT: A 197 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: E 77 MET cc_start: 0.7909 (pp-130) cc_final: 0.7601 (tmm) REVERT: E 100 TYR cc_start: 0.8954 (m-80) cc_final: 0.7631 (m-80) REVERT: E 107 ARG cc_start: 0.9056 (mtp-110) cc_final: 0.8779 (mtp-110) REVERT: E 136 GLN cc_start: 0.6432 (mt0) cc_final: 0.6126 (pt0) REVERT: E 146 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7432 (mmm) REVERT: B 167 MET cc_start: 0.5362 (OUTLIER) cc_final: 0.5122 (tpt) REVERT: B 197 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: C 77 MET cc_start: 0.7917 (pp-130) cc_final: 0.7611 (tmm) REVERT: C 100 TYR cc_start: 0.8953 (m-80) cc_final: 0.7641 (m-80) REVERT: C 107 ARG cc_start: 0.9052 (mtp-110) cc_final: 0.8774 (mtp-110) REVERT: C 136 GLN cc_start: 0.6436 (mt0) cc_final: 0.6156 (pt0) REVERT: C 146 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7415 (mmm) REVERT: D 167 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.5052 (tpt) REVERT: D 197 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: F 77 MET cc_start: 0.7913 (pp-130) cc_final: 0.7610 (tmm) REVERT: F 100 TYR cc_start: 0.8958 (m-80) cc_final: 0.7556 (m-80) REVERT: F 107 ARG cc_start: 0.9050 (mtp-110) cc_final: 0.8773 (mtp-110) REVERT: F 136 GLN cc_start: 0.6435 (mt0) cc_final: 0.6109 (pt0) REVERT: F 146 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7429 (mmm) REVERT: G 167 MET cc_start: 0.5367 (OUTLIER) cc_final: 0.5010 (tpt) REVERT: G 197 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6347 (m-80) REVERT: H 77 MET cc_start: 0.7908 (pp-130) cc_final: 0.7603 (tmm) REVERT: H 100 TYR cc_start: 0.8948 (m-80) cc_final: 0.7623 (m-80) REVERT: H 107 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8781 (mtp-110) REVERT: H 136 GLN cc_start: 0.6429 (mt0) cc_final: 0.6127 (pt0) REVERT: H 146 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7445 (mmm) outliers start: 80 outliers final: 52 residues processed: 260 average time/residue: 0.9601 time to fit residues: 285.3189 Evaluate side-chains 259 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 162 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 GLN ** D 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.183240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.110493 restraints weight = 72998.123| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.34 r_work: 0.3318 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16256 Z= 0.256 Angle : 0.580 7.120 21948 Z= 0.309 Chirality : 0.037 0.146 2448 Planarity : 0.004 0.030 2708 Dihedral : 7.518 76.711 2308 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.17 % Allowed : 28.63 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 1908 helix: 1.41 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -0.06 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 178 TYR 0.011 0.002 TYR G 553 PHE 0.012 0.001 PHE E 13 TRP 0.018 0.002 TRP B 378 HIS 0.003 0.001 HIS D 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.26 (16248) covalent geometry : angle 0.58020 / 0.31 (21948) hydrogen bonds : bond 0.04369 / 2.84 ( 1197) hydrogen bonds : angle 4.44458 / 3.27 ( 3555) Misc. bond : bond 0.00038 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 192 time to evaluate : 0.940 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: 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 167 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.4888 (tpt) REVERT: A 197 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: E 77 MET cc_start: 0.7934 (pp-130) cc_final: 0.7618 (tmm) REVERT: E 100 TYR cc_start: 0.8930 (m-80) cc_final: 0.7574 (m-80) REVERT: E 136 GLN cc_start: 0.6462 (mt0) cc_final: 0.6160 (pt0) REVERT: E 146 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7402 (mmm) REVERT: B 167 MET cc_start: 0.5438 (OUTLIER) cc_final: 0.4895 (tpt) REVERT: B 197 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6355 (m-80) REVERT: C 77 MET cc_start: 0.7942 (pp-130) cc_final: 0.7629 (tmm) REVERT: C 100 TYR cc_start: 0.8942 (m-80) cc_final: 0.7609 (m-80) REVERT: C 136 GLN cc_start: 0.6460 (mt0) cc_final: 0.6165 (pt0) REVERT: C 146 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7395 (mmm) REVERT: D 167 MET cc_start: 0.5432 (OUTLIER) cc_final: 0.4896 (tpt) REVERT: D 197 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: F 77 MET cc_start: 0.7937 (pp-130) cc_final: 0.7626 (tmm) REVERT: F 100 TYR cc_start: 0.8931 (m-80) cc_final: 0.7610 (m-80) REVERT: F 136 GLN cc_start: 0.6470 (mt0) cc_final: 0.6170 (pt0) REVERT: F 146 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: G 167 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.4789 (tpt) REVERT: G 197 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: H 77 MET cc_start: 0.7931 (pp-130) cc_final: 0.7617 (tmm) REVERT: H 100 TYR cc_start: 0.8930 (m-80) cc_final: 0.7578 (m-80) REVERT: H 136 GLN cc_start: 0.6465 (mt0) cc_final: 0.6163 (pt0) REVERT: H 146 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7403 (mmm) outliers start: 84 outliers final: 64 residues processed: 260 average time/residue: 0.8655 time to fit residues: 260.2460 Evaluate side-chains 268 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 192 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 146 MET Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 146 MET Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 56 optimal weight: 0.0050 chunk 133 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.182539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109290 restraints weight = 73499.782| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.36 r_work: 0.3304 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 16256 Z= 0.312 Angle : 0.614 7.280 21948 Z= 0.329 Chirality : 0.039 0.144 2448 Planarity : 0.004 0.035 2708 Dihedral : 7.515 75.941 2308 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.23 % Allowed : 29.31 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.18), residues: 1908 helix: 1.31 (0.12), residues: 1528 sheet: None (None), residues: 0 loop : -0.19 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 178 TYR 0.012 0.002 TYR A 553 PHE 0.017 0.002 PHE H 13 TRP 0.018 0.002 TRP G 378 HIS 0.003 0.001 HIS B 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.31 (16248) covalent geometry : angle 0.61377 / 0.33 (21948) hydrogen bonds : bond 0.04460 / 2.90 ( 1197) hydrogen bonds : angle 4.51963 / 3.33 ( 3555) Misc. bond : bond 0.00066 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 190 time to evaluate : 0.854 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: 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 197 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: E 77 MET cc_start: 0.7981 (pp-130) cc_final: 0.7656 (tmm) REVERT: E 100 TYR cc_start: 0.8856 (m-80) cc_final: 0.7453 (m-80) REVERT: E 136 GLN cc_start: 0.6593 (mt0) cc_final: 0.6245 (pt0) REVERT: B 197 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: C 77 MET cc_start: 0.7958 (pp-130) cc_final: 0.7644 (tmm) REVERT: C 100 TYR cc_start: 0.8884 (m-80) cc_final: 0.7453 (m-80) REVERT: C 125 MET cc_start: 0.7484 (mmm) cc_final: 0.7278 (mmm) REVERT: C 136 GLN cc_start: 0.6593 (mt0) cc_final: 0.6254 (pt0) REVERT: D 197 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: F 77 MET cc_start: 0.7979 (pp-130) cc_final: 0.7661 (tmm) REVERT: F 100 TYR cc_start: 0.8905 (m-80) cc_final: 0.7535 (m-80) REVERT: F 136 GLN cc_start: 0.6595 (mt0) cc_final: 0.6255 (pt0) REVERT: G 197 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: H 77 MET cc_start: 0.7978 (pp-130) cc_final: 0.7656 (tmm) REVERT: H 100 TYR cc_start: 0.8850 (m-80) cc_final: 0.7445 (m-80) REVERT: H 136 GLN cc_start: 0.6599 (mt0) cc_final: 0.6250 (pt0) outliers start: 85 outliers final: 64 residues processed: 262 average time/residue: 0.7805 time to fit residues: 237.8548 Evaluate side-chains 252 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 147 SER Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain G residue 297 THR Chi-restraints excluded: chain G residue 377 VAL Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 180 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.185223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114078 restraints weight = 73040.190| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.33 r_work: 0.3376 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16256 Z= 0.144 Angle : 0.584 8.631 21948 Z= 0.303 Chirality : 0.035 0.130 2448 Planarity : 0.004 0.031 2708 Dihedral : 7.293 74.298 2308 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.26 % Allowed : 31.53 % Favored : 65.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.19), residues: 1908 helix: 1.55 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.08 (0.34), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 535 TYR 0.008 0.001 TYR A 553 PHE 0.011 0.001 PHE A 134 TRP 0.018 0.001 TRP B 378 HIS 0.003 0.001 HIS A 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16248) covalent geometry : angle 0.58403 / 0.30 (21948) hydrogen bonds : bond 0.04200 / 2.75 ( 1197) hydrogen bonds : angle 4.37135 / 3.24 ( 3555) Misc. bond : bond 0.00006 / 0.00 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.753 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: 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 197 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: E 77 MET cc_start: 0.7934 (pp-130) cc_final: 0.7617 (tmm) REVERT: E 100 TYR cc_start: 0.8898 (m-80) cc_final: 0.7540 (m-80) REVERT: E 107 ARG cc_start: 0.9069 (mtp-110) cc_final: 0.8822 (mtp-110) REVERT: E 136 GLN cc_start: 0.6448 (mt0) cc_final: 0.6138 (pt0) REVERT: B 197 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6258 (m-80) REVERT: C 77 MET cc_start: 0.7941 (pp-130) cc_final: 0.7625 (tmm) REVERT: C 100 TYR cc_start: 0.8909 (m-80) cc_final: 0.7638 (m-80) REVERT: C 107 ARG cc_start: 0.9057 (mtp-110) cc_final: 0.8835 (mtp-110) REVERT: C 136 GLN cc_start: 0.6395 (mt0) cc_final: 0.6139 (pt0) REVERT: D 197 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6260 (m-80) REVERT: F 77 MET cc_start: 0.7932 (pp-130) cc_final: 0.7619 (tmm) REVERT: F 100 TYR cc_start: 0.8918 (m-80) cc_final: 0.7653 (m-80) REVERT: F 107 ARG cc_start: 0.9052 (mtp-110) cc_final: 0.8823 (mtp-110) REVERT: F 136 GLN cc_start: 0.6404 (mt0) cc_final: 0.6145 (pt0) REVERT: G 197 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: H 77 MET cc_start: 0.7929 (pp-130) cc_final: 0.7614 (tmm) REVERT: H 100 TYR cc_start: 0.8898 (m-80) cc_final: 0.7538 (m-80) REVERT: H 107 ARG cc_start: 0.9067 (mtp-110) cc_final: 0.8823 (mtp-110) REVERT: H 136 GLN cc_start: 0.6454 (mt0) cc_final: 0.6143 (pt0) outliers start: 53 outliers final: 49 residues processed: 255 average time/residue: 0.9343 time to fit residues: 272.3276 Evaluate side-chains 257 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 204 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 531 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 531 HIS Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 197 PHE Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 248 ARG Chi-restraints excluded: chain G residue 531 HIS Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 54 ASN Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 147 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 157 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 144 GLN C 144 GLN F 144 GLN H 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.184314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.112308 restraints weight = 73519.330| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.34 r_work: 0.3346 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16256 Z= 0.215 Angle : 0.608 7.644 21948 Z= 0.318 Chirality : 0.036 0.140 2448 Planarity : 0.004 0.041 2708 Dihedral : 7.318 74.661 2308 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.14 % Allowed : 31.96 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.19), residues: 1908 helix: 1.52 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.01 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 91 TYR 0.010 0.001 TYR D 553 PHE 0.022 0.001 PHE H 13 TRP 0.020 0.002 TRP D 378 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (16248) covalent geometry : angle 0.60812 / 0.32 (21948) hydrogen bonds : bond 0.04251 / 2.78 ( 1197) hydrogen bonds : angle 4.39731 / 3.26 ( 3555) Misc. bond : bond 0.00009 / 0.00 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14465.36 seconds wall clock time: 244 minutes 43.39 seconds (14683.39 seconds total)