Starting phenix.real_space_refine on Sat Mar 7 09:48:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4h_24826/03_2026/7s4h_24826.map" } resolution = 2.14 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 19395 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22889 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 273 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 4.81, per 1000 atoms: 0.21 Number of scatterers: 22889 At special positions: 0 Unit cell: (106.722, 106.722, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 O 4304 8.00 N 3417 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 780.9 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 18 sheets defined 53.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.546A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.940A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.719A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 114 Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 208 through 220 Proline residue: C 217 - end of helix removed outlier: 3.548A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.703A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'B' and resid 10 through 45 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.673A pdb=" N TRP B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 69 through 84 removed outlier: 3.992A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 107 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 140 through 155 removed outlier: 4.107A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.750A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 45 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.777A pdb=" N TRP F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 69 through 84 removed outlier: 3.990A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 107 Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 140 through 155 removed outlier: 4.115A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.750A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.695A pdb=" N TRP J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 69 Proline residue: J 65 - end of helix Processing helix chain 'J' and resid 69 through 84 removed outlier: 3.994A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 124 through 137 Processing helix chain 'J' and resid 140 through 155 removed outlier: 4.113A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 240 removed outlier: 3.798A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 382 removed outlier: 3.545A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 375 through 382 removed outlier: 3.547A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.940A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.719A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 114 Processing helix chain 'G' and resid 123 through 150 Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 170 through 177 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 208 through 220 Proline residue: G 217 - end of helix removed outlier: 3.547A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 233 Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 254 removed outlier: 3.703A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.940A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.720A pdb=" N GLU K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K 87 " --> pdb=" O PRO K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 114 Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 163 Processing helix chain 'K' and resid 170 through 177 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 208 through 220 Proline residue: K 217 - end of helix removed outlier: 3.547A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 233 Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 254 removed outlier: 3.703A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.306A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.702A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 140 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.573A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER A 283 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N ASP A 406 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS A 285 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLU A 287 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'F' and resid 243 through 244 Processing sheet with id=AA9, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AB1, first strand: chain 'J' and resid 243 through 244 Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.305A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.702A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB5, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.573A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER E 283 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N ASP E 406 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS E 285 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLU E 287 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.306A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.702A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.573A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N SER I 283 " --> pdb=" O GLN I 404 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N ASP I 406 " --> pdb=" O SER I 283 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N LYS I 285 " --> pdb=" O ASP I 406 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N GLU I 287 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3315 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: 3.71 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3390 1.32 - 1.44: 6724 1.44 - 1.57: 12700 1.57 - 1.69: 133 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC C 310 " pdb=" O3 PLC C 310 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC J 302 " pdb=" O3 PLC J 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 30972 4.32 - 8.65: 258 8.65 - 12.97: 60 12.97 - 17.30: 0 17.30 - 21.62: 3 Bond angle restraints: 31293 Sorted by residual: angle pdb=" C HIS K 173 " pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " ideal model delta sigma weight residual 110.85 98.59 12.26 1.70e+00 3.46e-01 5.20e+01 angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C9' PLC B 301 " pdb=" CA' PLC B 301 " pdb=" CB' PLC B 301 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C HIS C 173 " pdb=" CA HIS C 173 " pdb=" CB HIS C 173 " ideal model delta sigma weight residual 110.85 98.60 12.25 1.70e+00 3.46e-01 5.19e+01 angle pdb=" C9' PLC J 302 " pdb=" CA' PLC J 302 " pdb=" CB' PLC J 302 " ideal model delta sigma weight residual 112.96 134.57 -21.61 3.00e+00 1.11e-01 5.19e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12629 34.45 - 68.91: 761 68.91 - 103.36: 101 103.36 - 137.81: 30 137.81 - 172.27: 24 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" C HIS K 173 " pdb=" N HIS K 173 " pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " ideal model delta harmonic sigma weight residual -122.60 -109.35 -13.25 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" C HIS C 173 " pdb=" N HIS C 173 " pdb=" CA HIS C 173 " pdb=" CB HIS C 173 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C HIS G 173 " pdb=" N HIS G 173 " pdb=" CA HIS G 173 " pdb=" CB HIS G 173 " ideal model delta harmonic sigma weight residual -122.60 -109.43 -13.17 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2491 0.056 - 0.111: 597 0.111 - 0.167: 91 0.167 - 0.222: 19 0.222 - 0.278: 9 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA HIS K 173 " pdb=" N HIS K 173 " pdb=" C HIS K 173 " pdb=" CB HIS K 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA HIS C 173 " pdb=" N HIS C 173 " pdb=" C HIS C 173 " pdb=" CB HIS C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA HIS G 173 " pdb=" N HIS G 173 " pdb=" C HIS G 173 " pdb=" CB HIS G 173 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 234 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C TRP C 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP C 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE C 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 234 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TRP G 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP G 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE G 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP K 234 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TRP K 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP K 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE K 235 " -0.025 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 21 2.18 - 2.86: 8444 2.86 - 3.54: 34411 3.54 - 4.22: 64534 4.22 - 4.90: 106933 Nonbonded interactions: 214343 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.502 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.503 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.503 2.320 nonbonded pdb=" NE2 HIS C 231 " pdb="CU CU C 301 " model vdw 1.997 2.320 nonbonded pdb=" NE2 HIS K 231 " pdb="CU CU K 302 " model vdw 1.997 2.320 ... (remaining 214338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 414 or resid 502)) selection = (chain 'E' and (resid 33 through 414 or resid 502)) selection = (chain 'I' and (resid 33 through 414 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 303 through 304 or resid 308)) selection = (chain 'G' and (resid 45 through 280 or resid 303 through 304 or resid 308)) selection = (chain 'K' and (resid 45 through 280 or resid 303 through 304 or resid 308)) } 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.580 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.009 0.127 23127 Z= 0.439 Angle : 1.029 21.624 31293 Z= 0.502 Chirality : 0.051 0.278 3207 Planarity : 0.005 0.045 3732 Dihedral : 22.825 172.265 8787 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.83 % Allowed : 17.60 % Favored : 79.56 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2559 helix: 0.86 (0.15), residues: 1230 sheet: 1.31 (0.28), residues: 357 loop : -0.22 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 117 TYR 0.022 0.002 TYR K 184 PHE 0.017 0.002 PHE B 31 TRP 0.016 0.002 TRP B 152 HIS 0.009 0.001 HIS K 173 Details of bonding type rmsd covalent geometry : bond 0.00855 (23127) covalent geometry : angle 1.02922 (31293) hydrogen bonds : bond 0.11526 ( 1135) hydrogen bonds : angle 6.27325 ( 3315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 235 time to evaluate : 0.914 Fit side-chains REVERT: A 399 ASN cc_start: 0.7641 (p0) cc_final: 0.7244 (p0) REVERT: F 18 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (t) REVERT: E 399 ASN cc_start: 0.7661 (p0) cc_final: 0.7269 (p0) REVERT: I 108 GLN cc_start: 0.8029 (pt0) cc_final: 0.7678 (pp30) REVERT: I 399 ASN cc_start: 0.7612 (p0) cc_final: 0.7198 (p0) REVERT: G 86 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7281 (tp30) REVERT: G 117 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7696 (mpt180) REVERT: K 117 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7753 (mpt180) outliers start: 62 outliers final: 30 residues processed: 288 average time/residue: 0.7033 time to fit residues: 228.7774 Evaluate side-chains 249 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0070 chunk 103 optimal weight: 0.8980 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 161 GLN F 174 ASN J 174 ASN G 160 HIS G 161 GLN K 160 HIS K 161 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099749 restraints weight = 24073.697| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.22 r_work: 0.3083 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23127 Z= 0.149 Angle : 0.613 6.158 31293 Z= 0.318 Chirality : 0.046 0.292 3207 Planarity : 0.004 0.037 3732 Dihedral : 22.783 179.210 4191 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.97 % Allowed : 17.60 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.17), residues: 2559 helix: 1.05 (0.15), residues: 1227 sheet: 0.76 (0.26), residues: 390 loop : -0.02 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 375 TYR 0.021 0.001 TYR G 184 PHE 0.016 0.001 PHE B 31 TRP 0.017 0.002 TRP A 206 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00303 (23127) covalent geometry : angle 0.61334 (31293) hydrogen bonds : bond 0.05144 ( 1135) hydrogen bonds : angle 5.45055 ( 3315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 222 time to evaluate : 0.714 Fit side-chains REVERT: A 108 GLN cc_start: 0.8257 (pt0) cc_final: 0.7905 (pp30) REVERT: A 145 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: A 299 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7341 (ptm-80) REVERT: A 399 ASN cc_start: 0.7610 (p0) cc_final: 0.7190 (p0) REVERT: F 18 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8736 (t) REVERT: E 108 GLN cc_start: 0.8172 (pt0) cc_final: 0.7901 (pp30) REVERT: E 299 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7417 (ptm-80) REVERT: E 399 ASN cc_start: 0.7662 (p0) cc_final: 0.7246 (p0) REVERT: I 108 GLN cc_start: 0.8193 (pt0) cc_final: 0.7830 (pp30) REVERT: I 299 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7565 (ptm-80) REVERT: I 399 ASN cc_start: 0.7588 (p0) cc_final: 0.7154 (p0) REVERT: G 86 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7622 (tp30) outliers start: 65 outliers final: 28 residues processed: 273 average time/residue: 0.7355 time to fit residues: 225.6047 Evaluate side-chains 247 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 228 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097429 restraints weight = 24001.148| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.20 r_work: 0.3040 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23127 Z= 0.173 Angle : 0.616 6.310 31293 Z= 0.325 Chirality : 0.047 0.242 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.509 178.045 4167 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.24 % Favored : 94.53 % Rotamer: Outliers : 3.61 % Allowed : 16.83 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2559 helix: 1.04 (0.15), residues: 1230 sheet: 0.90 (0.28), residues: 342 loop : -0.12 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 84 TYR 0.023 0.002 TYR K 184 PHE 0.019 0.002 PHE B 31 TRP 0.016 0.002 TRP J 231 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00377 (23127) covalent geometry : angle 0.61593 (31293) hydrogen bonds : bond 0.05395 ( 1135) hydrogen bonds : angle 5.37430 ( 3315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 231 time to evaluate : 0.870 Fit side-chains REVERT: A 112 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8678 (mtm180) REVERT: A 208 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7748 (mtp180) REVERT: A 299 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7505 (ptm-80) REVERT: A 399 ASN cc_start: 0.7638 (p0) cc_final: 0.7239 (p0) REVERT: F 124 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9068 (mt) REVERT: J 13 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: E 108 GLN cc_start: 0.8274 (pt0) cc_final: 0.8013 (pp30) REVERT: E 299 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7430 (ptm-80) REVERT: E 399 ASN cc_start: 0.7661 (p0) cc_final: 0.7255 (p0) REVERT: I 112 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8625 (mtt180) REVERT: I 208 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7766 (mtp180) REVERT: I 299 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7332 (ptm-80) REVERT: I 399 ASN cc_start: 0.7604 (p0) cc_final: 0.7189 (p0) outliers start: 79 outliers final: 30 residues processed: 292 average time/residue: 0.7249 time to fit residues: 238.4457 Evaluate side-chains 257 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 273 LYS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 213 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.092732 restraints weight = 24151.937| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.22 r_work: 0.2959 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 23127 Z= 0.348 Angle : 0.775 9.906 31293 Z= 0.408 Chirality : 0.054 0.291 3207 Planarity : 0.006 0.043 3732 Dihedral : 22.264 174.278 4166 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.28 % Favored : 94.29 % Rotamer: Outliers : 3.61 % Allowed : 15.82 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.16), residues: 2559 helix: 0.92 (0.15), residues: 1206 sheet: 0.96 (0.28), residues: 339 loop : -0.20 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 125 TYR 0.024 0.003 TYR G 184 PHE 0.026 0.003 PHE B 31 TRP 0.020 0.003 TRP J 231 HIS 0.008 0.002 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00794 (23127) covalent geometry : angle 0.77493 (31293) hydrogen bonds : bond 0.06535 ( 1135) hydrogen bonds : angle 5.69100 ( 3315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 223 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8727 (mtm180) REVERT: A 208 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7770 (mtp180) REVERT: A 399 ASN cc_start: 0.7651 (p0) cc_final: 0.7225 (p0) REVERT: C 84 GLU cc_start: 0.8176 (pm20) cc_final: 0.7957 (pm20) REVERT: B 13 GLU cc_start: 0.8589 (tt0) cc_final: 0.8386 (tt0) REVERT: E 108 GLN cc_start: 0.8362 (pt0) cc_final: 0.8110 (pp30) REVERT: E 112 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8706 (mtt180) REVERT: E 208 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: E 399 ASN cc_start: 0.7700 (p0) cc_final: 0.7289 (p0) REVERT: I 108 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8104 (pp30) REVERT: I 112 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8671 (mtt180) REVERT: I 208 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7690 (mtp180) REVERT: I 363 ASP cc_start: 0.8375 (m-30) cc_final: 0.8131 (m-30) REVERT: I 399 ASN cc_start: 0.7635 (p0) cc_final: 0.7213 (p0) outliers start: 79 outliers final: 33 residues processed: 280 average time/residue: 0.7406 time to fit residues: 233.2498 Evaluate side-chains 254 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.0870 chunk 229 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 236 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096830 restraints weight = 23843.782| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.21 r_work: 0.3031 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23127 Z= 0.160 Angle : 0.620 8.377 31293 Z= 0.324 Chirality : 0.047 0.259 3207 Planarity : 0.004 0.039 3732 Dihedral : 21.473 178.659 4162 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 2.97 % Allowed : 17.24 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2559 helix: 0.96 (0.15), residues: 1230 sheet: 1.01 (0.28), residues: 339 loop : -0.14 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.021 0.002 TYR G 184 PHE 0.018 0.002 PHE F 31 TRP 0.018 0.002 TRP I 206 HIS 0.003 0.001 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00355 (23127) covalent geometry : angle 0.61995 (31293) hydrogen bonds : bond 0.05271 ( 1135) hydrogen bonds : angle 5.42395 ( 3315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7773 (mtp180) REVERT: A 399 ASN cc_start: 0.7635 (p0) cc_final: 0.7194 (p0) REVERT: A 401 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8455 (mt0) REVERT: C 84 GLU cc_start: 0.8101 (pm20) cc_final: 0.7791 (pm20) REVERT: B 13 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: B 198 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7038 (ttp-170) REVERT: J 198 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.7687 (ttp-170) REVERT: E 108 GLN cc_start: 0.8246 (pt0) cc_final: 0.8037 (pp30) REVERT: E 299 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7409 (ptm-80) REVERT: E 399 ASN cc_start: 0.7692 (p0) cc_final: 0.7278 (p0) REVERT: I 108 GLN cc_start: 0.8244 (pt0) cc_final: 0.7940 (pp30) REVERT: I 208 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: I 363 ASP cc_start: 0.8321 (m-30) cc_final: 0.8067 (m-30) outliers start: 65 outliers final: 32 residues processed: 285 average time/residue: 0.7323 time to fit residues: 234.7659 Evaluate side-chains 254 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 67 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 175 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 204 optimal weight: 20.0000 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN J 187 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096961 restraints weight = 24025.231| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.22 r_work: 0.3032 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23127 Z= 0.166 Angle : 0.611 8.047 31293 Z= 0.320 Chirality : 0.047 0.255 3207 Planarity : 0.004 0.039 3732 Dihedral : 20.968 179.556 4162 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.28 % Favored : 94.49 % Rotamer: Outliers : 2.70 % Allowed : 17.60 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1236 sheet: 0.93 (0.28), residues: 339 loop : -0.14 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 84 TYR 0.022 0.002 TYR G 184 PHE 0.019 0.002 PHE B 31 TRP 0.015 0.002 TRP I 206 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00365 (23127) covalent geometry : angle 0.61075 (31293) hydrogen bonds : bond 0.05244 ( 1135) hydrogen bonds : angle 5.33256 ( 3315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7762 (mtp180) REVERT: A 399 ASN cc_start: 0.7637 (p0) cc_final: 0.7200 (p0) REVERT: C 84 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: B 13 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: E 108 GLN cc_start: 0.8293 (pt0) cc_final: 0.8077 (pp30) REVERT: E 208 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7692 (mtt180) REVERT: E 399 ASN cc_start: 0.7660 (p0) cc_final: 0.7237 (p0) REVERT: I 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8277 (mm-30) REVERT: I 108 GLN cc_start: 0.8269 (pt0) cc_final: 0.7966 (pp30) REVERT: I 208 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7744 (mtp180) REVERT: I 299 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7540 (ptm-80) REVERT: I 363 ASP cc_start: 0.8323 (m-30) cc_final: 0.8048 (m-30) outliers start: 59 outliers final: 36 residues processed: 274 average time/residue: 0.7366 time to fit residues: 227.2255 Evaluate side-chains 265 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 138 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN J 187 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098721 restraints weight = 23788.505| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.20 r_work: 0.3059 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23127 Z= 0.145 Angle : 0.588 7.539 31293 Z= 0.307 Chirality : 0.046 0.248 3207 Planarity : 0.004 0.039 3732 Dihedral : 20.287 179.820 4162 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 2.56 % Allowed : 17.92 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1227 sheet: 0.90 (0.28), residues: 339 loop : -0.18 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 129 TYR 0.022 0.001 TYR K 184 PHE 0.017 0.001 PHE B 31 TRP 0.016 0.002 TRP E 206 HIS 0.003 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00315 (23127) covalent geometry : angle 0.58759 (31293) hydrogen bonds : bond 0.04971 ( 1135) hydrogen bonds : angle 5.26316 ( 3315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8321 (pt0) cc_final: 0.7931 (pp30) REVERT: A 208 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7738 (mtp180) REVERT: A 399 ASN cc_start: 0.7620 (p0) cc_final: 0.7193 (p0) REVERT: C 84 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: C 274 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5436 (tt) REVERT: B 13 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: B 198 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: E 108 GLN cc_start: 0.8258 (pt0) cc_final: 0.8046 (pp30) REVERT: E 299 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7421 (ptm-80) REVERT: I 108 GLN cc_start: 0.8240 (pt0) cc_final: 0.7998 (pp30) REVERT: I 299 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7535 (ptm-80) REVERT: I 363 ASP cc_start: 0.8312 (m-30) cc_final: 0.8035 (m-30) REVERT: I 401 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8365 (mt0) outliers start: 56 outliers final: 32 residues processed: 274 average time/residue: 0.7486 time to fit residues: 230.2679 Evaluate side-chains 255 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 239 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094723 restraints weight = 23766.053| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.19 r_work: 0.2992 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23127 Z= 0.252 Angle : 0.684 8.682 31293 Z= 0.361 Chirality : 0.050 0.262 3207 Planarity : 0.005 0.042 3732 Dihedral : 20.702 178.753 4160 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.86 % Favored : 93.86 % Rotamer: Outliers : 2.65 % Allowed : 17.92 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1224 sheet: 0.92 (0.28), residues: 339 loop : -0.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 129 TYR 0.023 0.002 TYR G 184 PHE 0.023 0.002 PHE B 31 TRP 0.020 0.002 TRP K 74 HIS 0.006 0.001 HIS K 160 Details of bonding type rmsd covalent geometry : bond 0.00568 (23127) covalent geometry : angle 0.68419 (31293) hydrogen bonds : bond 0.05892 ( 1135) hydrogen bonds : angle 5.47458 ( 3315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7778 (mtp180) REVERT: A 316 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: C 84 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: B 13 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8300 (tt0) REVERT: E 108 GLN cc_start: 0.8357 (pt0) cc_final: 0.8122 (pp30) REVERT: E 288 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7974 (p0) REVERT: I 108 GLN cc_start: 0.8364 (pt0) cc_final: 0.8073 (pp30) REVERT: I 363 ASP cc_start: 0.8329 (m-30) cc_final: 0.8081 (m-30) outliers start: 58 outliers final: 34 residues processed: 267 average time/residue: 0.7365 time to fit residues: 220.8374 Evaluate side-chains 259 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 195 optimal weight: 0.1980 chunk 193 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099537 restraints weight = 23944.626| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.23 r_work: 0.3085 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23127 Z= 0.127 Angle : 0.581 7.259 31293 Z= 0.302 Chirality : 0.046 0.246 3207 Planarity : 0.004 0.039 3732 Dihedral : 19.536 179.413 4160 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 1.87 % Allowed : 18.93 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1233 sheet: 0.88 (0.29), residues: 339 loop : -0.19 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 115 TYR 0.020 0.001 TYR K 184 PHE 0.016 0.001 PHE B 31 TRP 0.020 0.002 TRP K 74 HIS 0.002 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00271 (23127) covalent geometry : angle 0.58125 (31293) hydrogen bonds : bond 0.04708 ( 1135) hydrogen bonds : angle 5.22534 ( 3315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8263 (pt0) cc_final: 0.7881 (pp30) REVERT: A 112 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8659 (mtm180) REVERT: A 316 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: C 84 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: B 13 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: B 198 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.6985 (ttp-170) REVERT: E 299 ARG cc_start: 0.7741 (ttp80) cc_final: 0.7410 (ptm-80) REVERT: I 108 GLN cc_start: 0.8173 (pt0) cc_final: 0.7935 (pp30) REVERT: I 112 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8592 (mtt180) REVERT: I 299 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7572 (ptm-80) REVERT: I 363 ASP cc_start: 0.8318 (m-30) cc_final: 0.8051 (m-30) outliers start: 41 outliers final: 23 residues processed: 264 average time/residue: 0.7828 time to fit residues: 230.3456 Evaluate side-chains 247 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 21 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.093811 restraints weight = 24210.008| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.21 r_work: 0.2984 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23127 Z= 0.254 Angle : 0.697 8.684 31293 Z= 0.368 Chirality : 0.050 0.255 3207 Planarity : 0.005 0.042 3732 Dihedral : 19.951 179.491 4159 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.90 % Favored : 93.86 % Rotamer: Outliers : 1.78 % Allowed : 18.88 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1224 sheet: 0.92 (0.28), residues: 339 loop : -0.17 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 375 TYR 0.023 0.002 TYR G 184 PHE 0.023 0.002 PHE K 248 TRP 0.025 0.002 TRP C 74 HIS 0.006 0.002 HIS K 160 Details of bonding type rmsd covalent geometry : bond 0.00571 (23127) covalent geometry : angle 0.69661 (31293) hydrogen bonds : bond 0.05915 ( 1135) hydrogen bonds : angle 5.47103 ( 3315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: C 84 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7820 (pm20) REVERT: B 13 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: E 316 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: I 112 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8610 (mtt180) REVERT: I 363 ASP cc_start: 0.8345 (m-30) cc_final: 0.8109 (m-30) outliers start: 39 outliers final: 24 residues processed: 254 average time/residue: 0.7826 time to fit residues: 222.3933 Evaluate side-chains 248 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 108 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN E 168 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099732 restraints weight = 24043.154| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.24 r_work: 0.3081 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23127 Z= 0.129 Angle : 0.590 7.893 31293 Z= 0.307 Chirality : 0.046 0.248 3207 Planarity : 0.004 0.039 3732 Dihedral : 18.987 179.404 4159 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 1.42 % Allowed : 19.52 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1233 sheet: 0.87 (0.29), residues: 339 loop : -0.20 (0.21), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 115 TYR 0.021 0.001 TYR C 184 PHE 0.015 0.001 PHE B 31 TRP 0.023 0.002 TRP C 74 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00276 (23127) covalent geometry : angle 0.58964 (31293) hydrogen bonds : bond 0.04710 ( 1135) hydrogen bonds : angle 5.23700 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8715.85 seconds wall clock time: 149 minutes 8.15 seconds (8948.15 seconds total)