Starting phenix.real_space_refine on Tue Jul 7 00:40:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4h_24826/07_2026/7s4h_24826_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4h_24826/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s4h_24826/07_2026/7s4h_24826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4h_24826/07_2026/7s4h_24826.map" model { file = "/net/cci-nas-00/data/ceres_data/7s4h_24826/07_2026/7s4h_24826_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4h_24826/07_2026/7s4h_24826_trim.cif" } 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-6108/lib/python3.11/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, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 314 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 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, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 272 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "K" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 230 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 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: 4.69, per 1000 atoms: 0.20 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: 1.90 Conformation dependent library (CDL) restraints added in 698.7 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: 0.66 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: 3.42 Time building geometry restraints manager: 2.35 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 3.060 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.503 3.060 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.503 3.060 nonbonded pdb=" NE2 HIS C 231 " pdb="CU CU C 301 " model vdw 1.997 3.060 nonbonded pdb=" NE2 HIS K 231 " pdb="CU CU K 302 " model vdw 1.997 3.060 ... (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: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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/Z covalent geometry : bond 0.00855 / 0.44 (23127) covalent geometry : angle 1.02922 / 0.50 (31293) hydrogen bonds : bond 0.11526 / 7.47 ( 1135) hydrogen bonds : angle 6.27325 / 4.44 ( 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 : 0.749 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: 0.6664 time to fit residues: 218.0360 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 : 0.814 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 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: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 HIS C 161 GLN F 174 ASN G 160 HIS G 161 GLN K 160 HIS K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.098518 restraints weight = 23423.376| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.21 r_work: 0.3071 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23127 Z= 0.156 Angle : 0.624 5.923 31293 Z= 0.325 Chirality : 0.047 0.330 3207 Planarity : 0.005 0.038 3732 Dihedral : 22.935 179.844 4191 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.97 % Allowed : 17.33 % 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: 0.82 (0.17), residues: 2559 helix: 1.04 (0.15), residues: 1227 sheet: 0.75 (0.26), residues: 390 loop : -0.06 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.022 0.001 TYR G 184 PHE 0.017 0.001 PHE B 31 TRP 0.018 0.002 TRP I 206 HIS 0.005 0.001 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (23127) covalent geometry : angle 0.62365 / 0.33 (31293) hydrogen bonds : bond 0.05324 / 3.60 ( 1135) hydrogen bonds : angle 5.47924 / 3.91 ( 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 286 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 0.743 Fit side-chains REVERT: A 108 GLN cc_start: 0.8289 (pt0) cc_final: 0.7940 (pp30) REVERT: A 145 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: A 299 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7329 (ptm-80) REVERT: A 399 ASN cc_start: 0.7613 (p0) cc_final: 0.7191 (p0) REVERT: F 18 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8749 (t) REVERT: E 108 GLN cc_start: 0.8216 (pt0) cc_final: 0.7945 (pp30) REVERT: E 299 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7379 (ptm-80) REVERT: E 399 ASN cc_start: 0.7658 (p0) cc_final: 0.7242 (p0) REVERT: I 108 GLN cc_start: 0.8234 (pt0) cc_final: 0.7885 (pp30) REVERT: I 299 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7523 (ptm-80) REVERT: I 399 ASN cc_start: 0.7588 (p0) cc_final: 0.7153 (p0) outliers start: 65 outliers final: 30 residues processed: 273 average time/residue: 0.7202 time to fit residues: 221.5564 Evaluate side-chains 250 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 218 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 33 ILE 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 228 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS C 161 GLN F 187 ASN J 187 ASN E 137 HIS E 168 ASN I 137 HIS I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094429 restraints weight = 23179.377| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.19 r_work: 0.2990 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23127 Z= 0.269 Angle : 0.708 7.487 31293 Z= 0.374 Chirality : 0.051 0.305 3207 Planarity : 0.005 0.042 3732 Dihedral : 22.401 179.773 4169 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.16 % Favored : 94.41 % Rotamer: Outliers : 3.61 % Allowed : 16.14 % Favored : 80.25 % 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: 0.73 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1206 sheet: 0.94 (0.28), residues: 339 loop : -0.19 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 117 TYR 0.024 0.002 TYR G 184 PHE 0.024 0.002 PHE B 31 TRP 0.018 0.002 TRP J 231 HIS 0.007 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.27 (23127) covalent geometry : angle 0.70823 / 0.37 (31293) hydrogen bonds : bond 0.06133 / 4.14 ( 1135) hydrogen bonds : angle 5.57160 / 3.99 ( 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 304 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 225 time to evaluate : 0.967 Fit side-chains REVERT: A 112 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8733 (mtm180) REVERT: A 208 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7744 (mtp180) REVERT: A 299 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7504 (ptm-80) REVERT: A 399 ASN cc_start: 0.7617 (p0) cc_final: 0.7199 (p0) REVERT: J 13 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: E 108 GLN cc_start: 0.8325 (pt0) cc_final: 0.8080 (pp30) REVERT: E 112 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8680 (mtt180) REVERT: E 299 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7327 (ptm-80) REVERT: E 399 ASN cc_start: 0.7678 (p0) cc_final: 0.7276 (p0) REVERT: E 414 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6238 (mpt) REVERT: I 108 GLN cc_start: 0.8373 (pt0) cc_final: 0.8001 (pp30) REVERT: I 112 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8657 (mtt180) REVERT: I 208 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: I 299 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7479 (ptm-80) REVERT: I 399 ASN cc_start: 0.7602 (p0) cc_final: 0.7166 (p0) REVERT: I 414 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6291 (mpt) REVERT: K 84 GLU cc_start: 0.8132 (pm20) cc_final: 0.7913 (pm20) outliers start: 79 outliers final: 30 residues processed: 284 average time/residue: 0.7338 time to fit residues: 235.7936 Evaluate side-chains 253 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 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 F residue 29 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 13 GLU 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 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 273 LYS Chi-restraints excluded: chain E residue 414 MET 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 I residue 414 MET Chi-restraints excluded: chain G residue 74 TRP 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 74 TRP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 213 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 41 optimal weight: 0.0970 chunk 153 optimal weight: 8.9990 chunk 58 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN C 161 GLN B 187 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095492 restraints weight = 23182.301| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.19 r_work: 0.3009 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23127 Z= 0.220 Angle : 0.662 8.471 31293 Z= 0.348 Chirality : 0.049 0.273 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.794 177.426 4165 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 3.80 % Allowed : 16.42 % 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: 0.73 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1227 sheet: 0.94 (0.28), residues: 339 loop : -0.17 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 9 TYR 0.022 0.002 TYR G 184 PHE 0.021 0.002 PHE J 31 TRP 0.017 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (23127) covalent geometry : angle 0.66229 / 0.35 (31293) hydrogen bonds : bond 0.05706 / 3.85 ( 1135) hydrogen bonds : angle 5.49277 / 3.93 ( 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 306 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 223 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 112 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8713 (mtm180) REVERT: A 208 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7763 (mtp180) REVERT: A 299 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7482 (ptm-80) REVERT: A 399 ASN cc_start: 0.7638 (p0) cc_final: 0.7216 (p0) REVERT: J 13 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: E 108 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: E 112 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8651 (mtt180) REVERT: E 208 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7818 (mtt180) REVERT: E 299 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7354 (ptm-80) REVERT: E 399 ASN cc_start: 0.7719 (p0) cc_final: 0.7305 (p0) REVERT: E 414 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6235 (mpt) REVERT: I 108 GLN cc_start: 0.8322 (pt0) cc_final: 0.7991 (pp30) REVERT: I 112 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8622 (mtt180) REVERT: I 208 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7643 (mtp180) REVERT: I 399 ASN cc_start: 0.7646 (p0) cc_final: 0.7227 (p0) REVERT: K 84 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7816 (pm20) outliers start: 83 outliers final: 37 residues processed: 283 average time/residue: 0.7281 time to fit residues: 232.9887 Evaluate side-chains 263 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 87 THR 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 C residue 274 LEU 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 J residue 8 VAL Chi-restraints excluded: chain J residue 13 GLU 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 108 GLN 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 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET 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 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 84 GLU Chi-restraints excluded: chain K residue 87 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 GLN J 187 ASN I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096711 restraints weight = 22976.491| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.16 r_work: 0.3027 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23127 Z= 0.188 Angle : 0.630 8.268 31293 Z= 0.331 Chirality : 0.048 0.270 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.312 178.697 4165 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.08 % Favored : 94.69 % Rotamer: Outliers : 3.02 % Allowed : 17.15 % Favored : 79.84 % 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: 0.76 (0.17), residues: 2559 helix: 0.99 (0.15), residues: 1236 sheet: 0.99 (0.28), residues: 339 loop : -0.17 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 129 TYR 0.021 0.002 TYR K 184 PHE 0.020 0.002 PHE B 31 TRP 0.016 0.002 TRP I 206 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (23127) covalent geometry : angle 0.63046 / 0.33 (31293) hydrogen bonds : bond 0.05447 / 3.68 ( 1135) hydrogen bonds : angle 5.39979 / 3.86 ( 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 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8702 (mtm180) REVERT: A 208 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: A 399 ASN cc_start: 0.7628 (p0) cc_final: 0.7199 (p0) REVERT: B 198 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.7071 (ttp-170) REVERT: J 198 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: E 108 GLN cc_start: 0.8287 (pt0) cc_final: 0.8062 (pp30) REVERT: E 112 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8626 (mtt180) REVERT: E 208 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7718 (mtt180) REVERT: E 399 ASN cc_start: 0.7691 (p0) cc_final: 0.7273 (p0) REVERT: E 414 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6184 (mpt) REVERT: I 108 GLN cc_start: 0.8324 (pt0) cc_final: 0.7975 (pp30) REVERT: I 112 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8602 (mtt180) REVERT: I 208 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7756 (mtp180) REVERT: I 299 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7493 (ptm-80) REVERT: I 363 ASP cc_start: 0.8320 (m-30) cc_final: 0.8024 (m-30) REVERT: K 84 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7742 (pm20) outliers start: 66 outliers final: 32 residues processed: 280 average time/residue: 0.7263 time to fit residues: 229.4046 Evaluate side-chains 259 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 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 274 LEU 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 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 59 LEU Chi-restraints excluded: chain J residue 198 ARG 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 E residue 414 MET 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 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 84 GLU 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: 0.7980 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 204 optimal weight: 20.0000 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3519 r_free = 0.3519 target = 0.121430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097304 restraints weight = 23136.522| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.17 r_work: 0.3037 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 moved from start: 0.1359 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= 0.170 Angle : 0.616 8.032 31293 Z= 0.323 Chirality : 0.047 0.258 3207 Planarity : 0.004 0.039 3732 Dihedral : 21.089 179.636 4165 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.00 % Favored : 94.76 % Rotamer: Outliers : 2.74 % Allowed : 17.51 % Favored : 79.74 % 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: 0.79 (0.17), residues: 2559 helix: 1.06 (0.15), residues: 1230 sheet: 0.96 (0.28), residues: 339 loop : -0.19 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 129 TYR 0.022 0.002 TYR G 184 PHE 0.019 0.002 PHE B 31 TRP 0.016 0.002 TRP I 206 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (23127) covalent geometry : angle 0.61571 / 0.32 (31293) hydrogen bonds : bond 0.05291 / 3.57 ( 1135) hydrogen bonds : angle 5.35624 / 3.83 ( 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: 60 poor density : 224 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8676 (mtm180) REVERT: A 208 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: A 399 ASN cc_start: 0.7600 (p0) cc_final: 0.7158 (p0) REVERT: B 198 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.7055 (ttp-170) REVERT: J 198 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8248 (ttp-170) REVERT: E 108 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8064 (pp30) REVERT: E 208 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7694 (mtt180) REVERT: E 399 ASN cc_start: 0.7652 (p0) cc_final: 0.7229 (p0) REVERT: E 414 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6199 (mpt) REVERT: I 108 GLN cc_start: 0.8317 (pt0) cc_final: 0.7966 (pp30) REVERT: I 112 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8580 (mtt180) REVERT: I 208 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: I 299 ARG cc_start: 0.7856 (ttp80) cc_final: 0.7498 (ptm-80) REVERT: I 363 ASP cc_start: 0.8313 (m-30) cc_final: 0.8011 (m-30) REVERT: G 86 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7731 (mm-30) REVERT: K 84 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7743 (pm20) outliers start: 60 outliers final: 27 residues processed: 271 average time/residue: 0.7640 time to fit residues: 232.6593 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 : 0.854 ------------------------------------------------------------------------------- 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 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 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 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 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN 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 E residue 414 MET 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 I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER 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: 4.9990 chunk 190 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 166 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 168 ASN C 161 GLN B 187 ASN J 187 ASN I 72 HIS 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 = 0.3538 r_free = 0.3538 target = 0.122770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098701 restraints weight = 22952.959| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.17 r_work: 0.3060 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23127 Z= 0.147 Angle : 0.593 7.668 31293 Z= 0.310 Chirality : 0.046 0.251 3207 Planarity : 0.004 0.039 3732 Dihedral : 20.616 179.971 4164 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.55 % Favored : 94.22 % Rotamer: Outliers : 2.74 % Allowed : 17.56 % 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: 0.83 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1227 sheet: 0.92 (0.28), residues: 339 loop : -0.17 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 129 TYR 0.021 0.001 TYR G 184 PHE 0.018 0.001 PHE B 31 TRP 0.017 0.002 TRP G 74 HIS 0.003 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (23127) covalent geometry : angle 0.59321 / 0.31 (31293) hydrogen bonds : bond 0.05015 / 3.39 ( 1135) hydrogen bonds : angle 5.27967 / 3.77 ( 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 284 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 224 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8322 (pt0) cc_final: 0.7934 (pp30) REVERT: A 208 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: A 316 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 399 ASN cc_start: 0.7613 (p0) cc_final: 0.7184 (p0) REVERT: B 198 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.7159 (ttp-170) REVERT: J 198 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8437 (ttp-170) REVERT: E 108 GLN cc_start: 0.8259 (pt0) cc_final: 0.8038 (pp30) REVERT: E 208 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7662 (mtt180) REVERT: E 414 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6192 (mpt) REVERT: I 108 GLN cc_start: 0.8286 (pt0) cc_final: 0.7915 (pp30) REVERT: I 208 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7708 (mtp180) REVERT: I 299 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7517 (ptm-80) REVERT: I 363 ASP cc_start: 0.8328 (m-30) cc_final: 0.8033 (m-30) REVERT: K 84 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: K 274 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5427 (tt) outliers start: 60 outliers final: 29 residues processed: 273 average time/residue: 0.7608 time to fit residues: 234.0038 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 : 0.714 ------------------------------------------------------------------------------- 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 403 VAL 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 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 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG 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 E residue 414 MET 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 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 84 GLU 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 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: 10.0000 chunk 230 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS A 168 ASN C 161 GLN B 187 ASN F 187 ASN J 187 ASN E 168 ASN I 72 HIS I 168 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095333 restraints weight = 22874.113| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.19 r_work: 0.3004 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23127 Z= 0.227 Angle : 0.669 8.510 31293 Z= 0.352 Chirality : 0.049 0.258 3207 Planarity : 0.005 0.041 3732 Dihedral : 20.814 179.109 4162 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.71 % Favored : 94.06 % Rotamer: Outliers : 2.42 % Allowed : 18.02 % 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: 0.78 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1236 sheet: 0.92 (0.28), residues: 339 loop : -0.13 (0.20), residues: 984 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 0.021 0.002 TRP K 74 HIS 0.006 0.002 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (23127) covalent geometry : angle 0.66895 / 0.35 (31293) hydrogen bonds : bond 0.05751 / 3.88 ( 1135) hydrogen bonds : angle 5.43972 / 3.90 ( 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 273 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: A 316 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: A 399 ASN cc_start: 0.7590 (p0) cc_final: 0.7144 (p0) REVERT: E 108 GLN cc_start: 0.8359 (pt0) cc_final: 0.8114 (pp30) REVERT: E 208 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7698 (mtt180) REVERT: E 288 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7962 (p0) REVERT: E 414 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6227 (mpt) REVERT: I 108 GLN cc_start: 0.8365 (pt0) cc_final: 0.8006 (pp30) REVERT: I 208 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7628 (mtp180) REVERT: I 363 ASP cc_start: 0.8350 (m-30) cc_final: 0.8093 (m-30) REVERT: K 84 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (pm20) outliers start: 53 outliers final: 30 residues processed: 263 average time/residue: 0.7282 time to fit residues: 215.6534 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 : 0.817 ------------------------------------------------------------------------------- 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 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 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU 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 J residue 137 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 288 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 64 THR 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 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 84 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 195 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 237 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 247 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3541 r_free = 0.3541 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098940 restraints weight = 22978.815| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.17 r_work: 0.3064 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23127 Z= 0.146 Angle : 0.600 7.570 31293 Z= 0.313 Chirality : 0.046 0.249 3207 Planarity : 0.004 0.039 3732 Dihedral : 20.048 179.823 4160 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 1.92 % Allowed : 18.66 % 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: 0.80 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1236 sheet: 0.87 (0.28), residues: 339 loop : -0.18 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 115 TYR 0.021 0.001 TYR K 184 PHE 0.017 0.001 PHE B 31 TRP 0.022 0.002 TRP K 74 HIS 0.003 0.001 HIS E 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (23127) covalent geometry : angle 0.59953 / 0.31 (31293) hydrogen bonds : bond 0.04980 / 3.36 ( 1135) hydrogen bonds : angle 5.28542 / 3.78 ( 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 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 1.037 Fit side-chains REVERT: A 108 GLN cc_start: 0.8327 (pt0) cc_final: 0.7939 (pp30) REVERT: A 208 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (mtp180) REVERT: A 299 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7505 (ptm-80) REVERT: A 316 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: A 404 GLN cc_start: 0.8192 (tt0) cc_final: 0.7945 (tp40) REVERT: B 198 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: E 108 GLN cc_start: 0.8260 (pt0) cc_final: 0.8043 (pp30) REVERT: E 208 ARG cc_start: 0.8073 (mtp180) cc_final: 0.7651 (mtt180) REVERT: E 299 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7378 (ptm-80) REVERT: E 414 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6185 (mpt) REVERT: I 108 GLN cc_start: 0.8255 (pt0) cc_final: 0.7913 (pp30) REVERT: I 208 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7720 (mtp180) REVERT: I 299 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7579 (ptm-80) REVERT: I 316 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: I 363 ASP cc_start: 0.8338 (m-30) cc_final: 0.8078 (m-30) REVERT: K 84 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7737 (pm20) outliers start: 42 outliers final: 26 residues processed: 256 average time/residue: 0.7327 time to fit residues: 211.0749 Evaluate side-chains 249 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 240 PHE 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 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 E residue 414 MET 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 316 GLU 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 84 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER 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: 3.9990 chunk 198 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3497 r_free = 0.3497 target = 0.119880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095217 restraints weight = 22811.404| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.18 r_work: 0.3005 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23127 Z= 0.228 Angle : 0.670 8.401 31293 Z= 0.352 Chirality : 0.049 0.254 3207 Planarity : 0.005 0.041 3732 Dihedral : 20.126 179.983 4160 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 2.10 % Allowed : 18.43 % Favored : 79.47 % 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: 0.79 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1236 sheet: 0.90 (0.28), residues: 339 loop : -0.13 (0.20), residues: 984 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 0.022 0.002 PHE B 31 TRP 0.027 0.002 TRP C 74 HIS 0.006 0.002 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (23127) covalent geometry : angle 0.67038 / 0.35 (31293) hydrogen bonds : bond 0.05693 / 3.84 ( 1135) hydrogen bonds : angle 5.41755 / 3.88 ( 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 261 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8388 (pt0) cc_final: 0.7996 (pp30) REVERT: A 208 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: A 316 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: E 108 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8131 (pp30) REVERT: E 208 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7674 (mtt180) REVERT: E 414 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6172 (mpt) REVERT: I 108 GLN cc_start: 0.8357 (pt0) cc_final: 0.8004 (pp30) REVERT: I 208 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7751 (mtp180) REVERT: I 316 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: I 363 ASP cc_start: 0.8356 (m-30) cc_final: 0.8098 (m-30) REVERT: K 84 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7796 (pm20) outliers start: 46 outliers final: 30 residues processed: 253 average time/residue: 0.7734 time to fit residues: 220.2683 Evaluate side-chains 254 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN 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 E residue 414 MET Chi-restraints excluded: chain I residue 64 THR 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 316 GLU Chi-restraints excluded: chain I residue 403 VAL 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 84 GLU 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: 8.9990 chunk 141 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 chunk 195 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3560 r_free = 0.3560 target = 0.124301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099933 restraints weight = 22851.734| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.19 r_work: 0.3084 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1641 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 : 0.591 7.928 31293 Z= 0.307 Chirality : 0.046 0.246 3207 Planarity : 0.004 0.038 3732 Dihedral : 19.334 178.636 4160 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.28 % Favored : 94.49 % Rotamer: Outliers : 1.69 % Allowed : 18.93 % Favored : 79.38 % 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: 0.83 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1233 sheet: 0.92 (0.28), residues: 336 loop : -0.18 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 115 TYR 0.021 0.001 TYR C 184 PHE 0.016 0.001 PHE B 31 TRP 0.024 0.002 TRP C 74 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (23127) covalent geometry : angle 0.59066 / 0.31 (31293) hydrogen bonds : bond 0.04771 / 3.22 ( 1135) hydrogen bonds : angle 5.24845 / 3.75 ( 3315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8713.94 seconds wall clock time: 149 minutes 4.70 seconds (8944.70 seconds total)