Starting phenix.real_space_refine on Mon Jul 6 22:50:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4p_25684/07_2026/7t4p_25684_trim.cif" } resolution = 3.62 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= 0.008 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 30 5.49 5 S 93 5.16 5 C 14856 2.51 5 N 3411 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s 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: 22242 Number of models: 1 Model: "" Number of chains: 18 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: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "F" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "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: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 284 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 194 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 284 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Chain: "K" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 242 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 7} Link IDs: {None: 5} Chain breaks: 1 Chain: "F" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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 Time building chain proxies: 3.96, per 1000 atoms: 0.18 Number of scatterers: 22242 At special positions: 0 Unit cell: (106.25, 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 30 15.00 O 3843 8.00 N 3411 7.00 C 14856 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: 1.80 Conformation dependent library (CDL) restraints added in 920.2 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: 96 helices and 21 sheets defined 53.1% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 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 removed outlier: 4.020A pdb=" N TRP A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) 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 380 removed outlier: 3.572A pdb=" N ASP A 378 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 380' Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.549A pdb=" N PHE C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.616A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.629A 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 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 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'B' and resid 10 through 51 removed outlier: 7.654A pdb=" N ASP B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.524A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.116A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (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 169 removed outlier: 3.835A pdb=" N VAL B 169 " --> pdb=" O PRO B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.561A pdb=" N ILE B 197 " --> pdb=" O PRO B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.756A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.549A pdb=" N PHE G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.617A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.629A 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 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 Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.548A pdb=" N PHE K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.617A pdb=" N GLU K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.630A 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 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 Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'F' and resid 10 through 51 removed outlier: 7.654A pdb=" N ASP F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.524A pdb=" N ALA F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.116A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (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 169 removed outlier: 3.834A pdb=" N VAL F 169 " --> pdb=" O PRO F 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 179 through 188 Processing helix chain 'F' and resid 194 through 198 removed outlier: 3.561A pdb=" N ILE F 197 " --> pdb=" O PRO F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.756A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 51 removed outlier: 7.654A pdb=" N ASP J 47 " --> pdb=" O LEU J 43 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.796A 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: 3.524A pdb=" N ALA J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.116A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (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 169 removed outlier: 3.834A pdb=" N VAL J 169 " --> pdb=" O PRO J 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'J' and resid 194 through 198 removed outlier: 3.561A pdb=" N ILE J 197 " --> pdb=" O PRO J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.756A 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 removed outlier: 4.020A pdb=" N TRP E 206 " --> pdb=" O TRP E 202 " (cutoff:3.500A) 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 380 removed outlier: 3.572A pdb=" N ASP E 378 " --> pdb=" O ARG E 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 375 through 380' 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 removed outlier: 4.021A pdb=" N TRP I 206 " --> pdb=" O TRP I 202 " (cutoff:3.500A) 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 380 removed outlier: 3.572A pdb=" N ASP I 378 " --> pdb=" O ARG I 375 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 375 through 380' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.321A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.844A 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: 6.824A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.600A 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 346 through 348 removed outlier: 5.579A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 removed outlier: 5.202A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 394 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AA8, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AA9, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB2, first strand: chain 'J' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.321A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.824A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB6, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.579A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.201A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.322A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.823A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC2, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.579A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.201A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) 1113 hydrogen bonds defined for protein. 3276 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: 4.16 Time building geometry restraints manager: 2.31 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: 3456 1.32 - 1.45: 6628 1.45 - 1.57: 12501 1.57 - 1.69: 134 1.69 - 1.81: 180 Bond restraints: 22899 Sorted by residual: bond pdb=" CB PLC G 303 " pdb=" O3 PLC G 303 " 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 C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC B 305 " pdb=" O3 PLC B 305 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C19 P1O B 307 " pdb=" O7 P1O B 307 " ideal model delta sigma weight residual 1.331 1.457 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CE1 HIS I 33 " pdb=" NE2 HIS I 33 " ideal model delta sigma weight residual 1.321 1.258 0.063 1.00e-02 1.00e+04 3.92e+01 ... (remaining 22894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 30311 2.80 - 5.60: 562 5.60 - 8.40: 99 8.40 - 11.20: 39 11.20 - 14.01: 6 Bond angle restraints: 31017 Sorted by residual: angle pdb=" CA PHE C 233 " pdb=" C PHE C 233 " pdb=" O PHE C 233 " ideal model delta sigma weight residual 117.94 114.33 3.61 5.80e-01 2.97e+00 3.88e+01 angle pdb=" CA PHE K 233 " pdb=" C PHE K 233 " pdb=" O PHE K 233 " ideal model delta sigma weight residual 117.94 114.33 3.61 5.80e-01 2.97e+00 3.87e+01 angle pdb=" CA PHE G 233 " pdb=" C PHE G 233 " pdb=" O PHE G 233 " ideal model delta sigma weight residual 117.94 114.36 3.58 5.80e-01 2.97e+00 3.80e+01 angle pdb=" O PHE C 233 " pdb=" C PHE C 233 " pdb=" N TRP C 234 " ideal model delta sigma weight residual 121.47 125.24 -3.77 7.50e-01 1.78e+00 2.52e+01 angle pdb=" O PHE G 233 " pdb=" C PHE G 233 " pdb=" N TRP G 234 " ideal model delta sigma weight residual 121.47 125.23 -3.76 7.50e-01 1.78e+00 2.51e+01 ... (remaining 31012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 12753 35.47 - 70.94: 489 70.94 - 106.41: 60 106.41 - 141.88: 36 141.88 - 177.35: 15 Dihedral angle restraints: 13353 sinusoidal: 5901 harmonic: 7452 Sorted by residual: dihedral pdb=" CA ARG A 45 " pdb=" C ARG A 45 " pdb=" N THR A 46 " pdb=" CA THR A 46 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ARG I 45 " pdb=" C ARG I 45 " pdb=" N THR I 46 " pdb=" CA THR I 46 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ARG E 45 " pdb=" C ARG E 45 " pdb=" N THR E 46 " pdb=" CA THR E 46 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 13350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2626 0.063 - 0.126: 508 0.126 - 0.189: 58 0.189 - 0.251: 5 0.251 - 0.314: 4 Chirality restraints: 3201 Sorted by residual: chirality pdb=" CA TRP K 234 " pdb=" N TRP K 234 " pdb=" C TRP K 234 " pdb=" CB TRP K 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA TRP C 234 " pdb=" N TRP C 234 " pdb=" C TRP C 234 " pdb=" CB TRP C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA TRP G 234 " pdb=" N TRP G 234 " pdb=" C TRP G 234 " pdb=" CB TRP G 234 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 3198 not shown) Planarity restraints: 3717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 33 " -0.003 2.00e-02 2.50e+03 2.93e-02 1.28e+01 pdb=" CG HIS E 33 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS E 33 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS E 33 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS E 33 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS E 33 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 33 " -0.003 2.00e-02 2.50e+03 2.92e-02 1.28e+01 pdb=" CG HIS A 33 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 33 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 33 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS A 33 " 0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS A 33 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS I 33 " 0.003 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS I 33 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS I 33 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS I 33 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS I 33 " -0.045 2.00e-02 2.50e+03 pdb=" NE2 HIS I 33 " 0.039 2.00e-02 2.50e+03 ... (remaining 3714 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 63 2.35 - 2.99: 11365 2.99 - 3.62: 34752 3.62 - 4.26: 57505 4.26 - 4.90: 96591 Nonbonded interactions: 200276 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.709 3.060 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.709 3.060 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.710 3.060 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 502 " model vdw 1.809 3.060 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.810 3.060 ... (remaining 200271 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)) selection = (chain 'F' and (resid 7 through 247 or resid 304)) selection = (chain 'J' and (resid 7 through 247 or resid 304)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 308)) selection = (chain 'G' and (resid 45 through 280 or resid 308)) selection = (chain 'K' and (resid 45 through 280 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 22899 Z= 0.460 Angle : 0.983 14.006 31017 Z= 0.497 Chirality : 0.051 0.314 3201 Planarity : 0.005 0.051 3717 Dihedral : 20.564 177.347 8595 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.14 % Favored : 93.51 % Rotamer: Outliers : 0.82 % Allowed : 1.23 % Favored : 97.94 % 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: 0.12 (0.17), residues: 2559 helix: 0.90 (0.15), residues: 1176 sheet: -0.29 (0.30), residues: 363 loop : -0.65 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 45 TYR 0.026 0.002 TYR K 210 PHE 0.030 0.002 PHE K 235 TRP 0.022 0.002 TRP G 234 HIS 0.047 0.003 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.46 (22899) covalent geometry : angle 0.98279 / 0.50 (31017) hydrogen bonds : bond 0.13412 / 8.63 ( 1113) hydrogen bonds : angle 7.03153 / 5.04 ( 3276) *********************** 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 332 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 314 time to evaluate : 0.541 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8330 (tpp) cc_final: 0.7932 (tpt) REVERT: A 414 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5540 (mtp) REVERT: G 210 TYR cc_start: 0.8675 (t80) cc_final: 0.8142 (t80) REVERT: G 214 VAL cc_start: 0.8348 (t) cc_final: 0.7928 (m) REVERT: G 228 GLU cc_start: 0.7078 (mp0) cc_final: 0.6708 (mp0) REVERT: K 214 VAL cc_start: 0.8422 (t) cc_final: 0.7948 (m) REVERT: E 414 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5697 (mtp) REVERT: I 142 MET cc_start: 0.8290 (tpp) cc_final: 0.7623 (tpt) REVERT: I 381 TYR cc_start: 0.6684 (t80) cc_final: 0.6344 (t80) outliers start: 18 outliers final: 9 residues processed: 319 average time/residue: 0.1388 time to fit residues: 70.2794 Evaluate side-chains 281 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 414 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 overall best weight: 0.6502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS A 145 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS B 240 ASN G 245 HIS K 245 HIS F 160 ASN F 240 ASN J 160 ASN J 240 ASN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 145 GLN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS I 145 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.122467 restraints weight = 23168.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.121130 restraints weight = 29210.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.121561 restraints weight = 28858.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.121748 restraints weight = 25781.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.121803 restraints weight = 23338.298| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22899 Z= 0.146 Angle : 0.634 8.019 31017 Z= 0.325 Chirality : 0.046 0.215 3201 Planarity : 0.005 0.060 3717 Dihedral : 21.253 168.818 3987 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.61 % Favored : 95.04 % Rotamer: Outliers : 1.37 % Allowed : 6.58 % Favored : 92.04 % 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: 0.25 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1170 sheet: -0.46 (0.28), residues: 390 loop : -0.62 (0.21), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 375 TYR 0.038 0.002 TYR G 184 PHE 0.027 0.001 PHE C 92 TRP 0.018 0.001 TRP F 237 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (22899) covalent geometry : angle 0.63384 / 0.33 (31017) hydrogen bonds : bond 0.04370 / 2.82 ( 1113) hydrogen bonds : angle 5.75331 / 4.13 ( 3276) *********************** 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 323 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 293 time to evaluate : 0.720 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8392 (tpp) cc_final: 0.8042 (tpt) REVERT: A 414 MET cc_start: 0.5976 (mpp) cc_final: 0.5688 (mtp) REVERT: G 88 TYR cc_start: 0.7835 (m-80) cc_final: 0.7455 (m-80) REVERT: G 210 TYR cc_start: 0.8695 (t80) cc_final: 0.8435 (t80) REVERT: G 228 GLU cc_start: 0.7053 (mp0) cc_final: 0.6811 (mp0) REVERT: F 236 ARG cc_start: 0.7670 (mmt90) cc_final: 0.7316 (ttm-80) REVERT: E 62 ASN cc_start: 0.8430 (m-40) cc_final: 0.8228 (m-40) REVERT: E 375 ARG cc_start: 0.7819 (mtp-110) cc_final: 0.7594 (mtp85) REVERT: E 414 MET cc_start: 0.6028 (mpp) cc_final: 0.5676 (mtp) outliers start: 30 outliers final: 12 residues processed: 306 average time/residue: 0.1490 time to fit residues: 71.5830 Evaluate side-chains 263 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 24 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 221 optimal weight: 0.4980 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 ASN J 160 ASN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116232 restraints weight = 23185.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.114578 restraints weight = 29880.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.115459 restraints weight = 28509.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.115547 restraints weight = 25337.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.115680 restraints weight = 23219.598| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22899 Z= 0.202 Angle : 0.637 8.032 31017 Z= 0.330 Chirality : 0.048 0.213 3201 Planarity : 0.005 0.065 3717 Dihedral : 20.443 165.858 3977 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.63 % Favored : 94.14 % Rotamer: Outliers : 1.83 % Allowed : 9.10 % Favored : 89.07 % 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: 0.07 (0.17), residues: 2559 helix: 1.02 (0.15), residues: 1179 sheet: -0.83 (0.27), residues: 393 loop : -0.66 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 375 TYR 0.032 0.002 TYR K 184 PHE 0.020 0.002 PHE B 31 TRP 0.017 0.002 TRP A 77 HIS 0.007 0.002 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (22899) covalent geometry : angle 0.63679 / 0.33 (31017) hydrogen bonds : bond 0.04464 / 2.90 ( 1113) hydrogen bonds : angle 5.55422 / 4.01 ( 3276) *********************** 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 307 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 267 time to evaluate : 0.813 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8366 (tpp) cc_final: 0.8140 (ttm) REVERT: A 375 ARG cc_start: 0.7721 (mtp-110) cc_final: 0.7468 (mtm110) REVERT: C 169 PHE cc_start: 0.7167 (m-10) cc_final: 0.6936 (m-10) REVERT: B 236 ARG cc_start: 0.7919 (mmt90) cc_final: 0.7534 (ttm-80) REVERT: K 72 TYR cc_start: 0.8085 (m-80) cc_final: 0.7813 (m-80) REVERT: F 178 MET cc_start: 0.8718 (mtt) cc_final: 0.8364 (mtt) REVERT: F 236 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7467 (ttm-80) REVERT: J 236 ARG cc_start: 0.7883 (mmt90) cc_final: 0.7551 (ttm-80) REVERT: E 375 ARG cc_start: 0.7682 (mtp-110) cc_final: 0.7403 (mtp85) REVERT: E 406 ASP cc_start: 0.7793 (p0) cc_final: 0.7548 (p0) REVERT: E 414 MET cc_start: 0.6154 (mpp) cc_final: 0.5876 (mtp) outliers start: 40 outliers final: 27 residues processed: 287 average time/residue: 0.1456 time to fit residues: 66.4970 Evaluate side-chains 272 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 49 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 254 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN C 161 GLN G 161 GLN K 161 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN ** I 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.133565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.113810 restraints weight = 22944.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112596 restraints weight = 29293.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.112950 restraints weight = 28549.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113259 restraints weight = 26798.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.113399 restraints weight = 23765.058| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22899 Z= 0.204 Angle : 0.629 8.004 31017 Z= 0.326 Chirality : 0.048 0.224 3201 Planarity : 0.005 0.059 3717 Dihedral : 19.850 162.265 3975 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.24 % Favored : 94.53 % Rotamer: Outliers : 2.42 % Allowed : 11.34 % Favored : 86.24 % 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: -0.05 (0.17), residues: 2559 helix: 0.92 (0.15), residues: 1185 sheet: -0.91 (0.26), residues: 387 loop : -0.71 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 131 TYR 0.029 0.002 TYR C 184 PHE 0.030 0.002 PHE K 248 TRP 0.019 0.002 TRP A 77 HIS 0.007 0.002 HIS I 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (22899) covalent geometry : angle 0.62885 / 0.33 (31017) hydrogen bonds : bond 0.04369 / 2.85 ( 1113) hydrogen bonds : angle 5.46198 / 3.93 ( 3276) *********************** 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 312 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 0.752 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8319 (tpp) cc_final: 0.8023 (ttm) REVERT: A 231 THR cc_start: 0.8063 (p) cc_final: 0.7862 (p) REVERT: B 236 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7579 (ttm-80) REVERT: F 178 MET cc_start: 0.8720 (mtt) cc_final: 0.8473 (mtt) REVERT: F 236 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7579 (ttm-80) REVERT: J 236 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7575 (ttm-80) REVERT: E 375 ARG cc_start: 0.7573 (mtp-110) cc_final: 0.7365 (mtp85) outliers start: 53 outliers final: 39 residues processed: 288 average time/residue: 0.1480 time to fit residues: 67.5006 Evaluate side-chains 281 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 359 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 137 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN J 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.137130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.118951 restraints weight = 22611.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.117207 restraints weight = 29397.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.117685 restraints weight = 28853.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.118039 restraints weight = 24806.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.118133 restraints weight = 23186.290| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22899 Z= 0.130 Angle : 0.569 8.320 31017 Z= 0.294 Chirality : 0.045 0.223 3201 Planarity : 0.005 0.056 3717 Dihedral : 19.144 159.739 3973 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.16 % Favored : 94.61 % Rotamer: Outliers : 2.70 % Allowed : 12.12 % Favored : 85.19 % 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: 0.13 (0.17), residues: 2559 helix: 1.14 (0.15), residues: 1170 sheet: -0.95 (0.26), residues: 405 loop : -0.64 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 375 TYR 0.026 0.001 TYR C 184 PHE 0.026 0.001 PHE K 248 TRP 0.016 0.001 TRP G 234 HIS 0.004 0.001 HIS G 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (22899) covalent geometry : angle 0.56859 / 0.29 (31017) hydrogen bonds : bond 0.03926 / 2.54 ( 1113) hydrogen bonds : angle 5.30498 / 3.81 ( 3276) *********************** 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 322 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 263 time to evaluate : 0.773 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8315 (tpp) cc_final: 0.8030 (ttm) REVERT: A 231 THR cc_start: 0.8061 (p) cc_final: 0.7850 (p) REVERT: A 375 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7104 (mmp80) REVERT: B 236 ARG cc_start: 0.7906 (mmt90) cc_final: 0.7573 (ttm-80) REVERT: G 163 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8046 (tp) REVERT: K 163 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8091 (tp) REVERT: K 248 PHE cc_start: 0.7565 (m-80) cc_final: 0.7354 (m-80) REVERT: F 178 MET cc_start: 0.8723 (mtt) cc_final: 0.8441 (mtt) REVERT: F 236 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7559 (ttm-80) REVERT: J 236 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7565 (ttm-80) REVERT: E 375 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.7231 (mtp85) REVERT: I 381 TYR cc_start: 0.6938 (t80) cc_final: 0.6333 (t80) outliers start: 59 outliers final: 40 residues processed: 301 average time/residue: 0.1388 time to fit residues: 66.5497 Evaluate side-chains 285 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 243 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 168 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN J 160 ASN E 401 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.132251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.111366 restraints weight = 23251.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.111281 restraints weight = 24082.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.111601 restraints weight = 24634.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.112286 restraints weight = 22857.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.112388 restraints weight = 20724.520| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22899 Z= 0.213 Angle : 0.642 7.964 31017 Z= 0.332 Chirality : 0.048 0.219 3201 Planarity : 0.005 0.057 3717 Dihedral : 19.132 160.760 3971 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 3.20 % Allowed : 12.12 % Favored : 84.68 % 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: -0.06 (0.17), residues: 2559 helix: 0.97 (0.15), residues: 1179 sheet: -0.99 (0.26), residues: 375 loop : -0.77 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 242 TYR 0.027 0.002 TYR K 184 PHE 0.024 0.002 PHE K 248 TRP 0.020 0.002 TRP A 77 HIS 0.007 0.002 HIS I 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (22899) covalent geometry : angle 0.64207 / 0.33 (31017) hydrogen bonds : bond 0.04353 / 2.84 ( 1113) hydrogen bonds : angle 5.38004 / 3.88 ( 3276) *********************** 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 319 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 0.814 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8319 (tpp) cc_final: 0.8054 (ttm) REVERT: A 231 THR cc_start: 0.8151 (p) cc_final: 0.7914 (p) REVERT: A 375 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7216 (mmp80) REVERT: B 236 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7630 (ttm-80) REVERT: G 163 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.7992 (tp) REVERT: F 236 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7635 (ttm-80) REVERT: J 236 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7590 (ttm-80) REVERT: E 375 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7193 (mtp85) REVERT: I 227 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8804 (mt) outliers start: 70 outliers final: 53 residues processed: 293 average time/residue: 0.1474 time to fit residues: 69.0179 Evaluate side-chains 291 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 14 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 118 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 186 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN A 404 GLN J 160 ASN E 401 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.111261 restraints weight = 23091.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111024 restraints weight = 24342.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111590 restraints weight = 25646.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.112516 restraints weight = 22826.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.114110 restraints weight = 20609.363| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22899 Z= 0.216 Angle : 0.638 8.009 31017 Z= 0.330 Chirality : 0.048 0.212 3201 Planarity : 0.005 0.055 3717 Dihedral : 18.961 162.347 3971 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.47 % Favored : 94.29 % Rotamer: Outliers : 3.16 % Allowed : 12.76 % Favored : 84.09 % 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: -0.19 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1179 sheet: -1.15 (0.26), residues: 375 loop : -0.83 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 375 TYR 0.026 0.002 TYR C 184 PHE 0.028 0.002 PHE C 248 TRP 0.020 0.002 TRP A 77 HIS 0.007 0.002 HIS I 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (22899) covalent geometry : angle 0.63829 / 0.33 (31017) hydrogen bonds : bond 0.04343 / 2.84 ( 1113) hydrogen bonds : angle 5.41079 / 3.90 ( 3276) *********************** 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 327 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 0.843 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8311 (tpp) cc_final: 0.8042 (ttm) REVERT: A 231 THR cc_start: 0.8149 (p) cc_final: 0.7905 (p) REVERT: A 375 ARG cc_start: 0.7476 (mtm110) cc_final: 0.7185 (mmp80) REVERT: B 236 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7638 (ttm-80) REVERT: G 163 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8059 (tp) REVERT: K 240 PHE cc_start: 0.6054 (OUTLIER) cc_final: 0.4466 (t80) REVERT: F 236 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7673 (ttm-80) REVERT: J 236 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7603 (ttm-80) REVERT: E 375 ARG cc_start: 0.7456 (mtp-110) cc_final: 0.7220 (mtp85) REVERT: E 381 TYR cc_start: 0.7202 (t80) cc_final: 0.6331 (t80) REVERT: I 227 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8743 (mt) outliers start: 69 outliers final: 61 residues processed: 301 average time/residue: 0.1531 time to fit residues: 73.8045 Evaluate side-chains 313 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 249 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 248 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN E 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116960 restraints weight = 22954.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.115836 restraints weight = 28233.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.117061 restraints weight = 23109.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.117113 restraints weight = 19273.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.117235 restraints weight = 18512.980| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22899 Z= 0.142 Angle : 0.587 8.142 31017 Z= 0.304 Chirality : 0.046 0.216 3201 Planarity : 0.005 0.054 3717 Dihedral : 18.506 163.030 3971 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 3.11 % Allowed : 13.35 % Favored : 83.54 % 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: -0.00 (0.17), residues: 2559 helix: 1.06 (0.15), residues: 1176 sheet: -0.97 (0.26), residues: 381 loop : -0.78 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 360 TYR 0.025 0.001 TYR C 184 PHE 0.026 0.001 PHE C 248 TRP 0.028 0.001 TRP E 206 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (22899) covalent geometry : angle 0.58725 / 0.30 (31017) hydrogen bonds : bond 0.03994 / 2.60 ( 1113) hydrogen bonds : angle 5.30269 / 3.81 ( 3276) *********************** 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 324 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 256 time to evaluate : 0.730 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8296 (tpp) cc_final: 0.8037 (ttm) REVERT: A 231 THR cc_start: 0.8126 (p) cc_final: 0.7861 (p) REVERT: A 375 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7143 (mmp80) REVERT: B 236 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7612 (ttm-80) REVERT: G 163 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8077 (tp) REVERT: K 240 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.4464 (t80) REVERT: J 236 ARG cc_start: 0.7835 (mmt90) cc_final: 0.7579 (ttm-80) REVERT: E 381 TYR cc_start: 0.7006 (t80) cc_final: 0.6223 (t80) REVERT: I 227 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8770 (mt) REVERT: I 375 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7541 (mtp180) outliers start: 68 outliers final: 53 residues processed: 293 average time/residue: 0.1526 time to fit residues: 71.8019 Evaluate side-chains 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN E 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.141677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124932 restraints weight = 22639.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125611 restraints weight = 20691.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.125789 restraints weight = 18996.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125753 restraints weight = 18449.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125761 restraints weight = 18778.011| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22899 Z= 0.134 Angle : 0.580 8.296 31017 Z= 0.299 Chirality : 0.045 0.220 3201 Planarity : 0.005 0.054 3717 Dihedral : 18.060 165.024 3969 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 2.83 % Allowed : 13.72 % Favored : 83.45 % 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: 0.09 (0.17), residues: 2559 helix: 1.15 (0.15), residues: 1173 sheet: -0.92 (0.27), residues: 381 loop : -0.76 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 242 TYR 0.025 0.001 TYR C 184 PHE 0.025 0.001 PHE C 248 TRP 0.019 0.001 TRP B 54 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (22899) covalent geometry : angle 0.58008 / 0.30 (31017) hydrogen bonds : bond 0.03893 / 2.53 ( 1113) hydrogen bonds : angle 5.21520 / 3.74 ( 3276) *********************** 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 324 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 0.791 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8318 (tpp) cc_final: 0.8023 (ttm) REVERT: A 231 THR cc_start: 0.8056 (p) cc_final: 0.7803 (p) REVERT: A 375 ARG cc_start: 0.7334 (mtm110) cc_final: 0.7107 (mmp80) REVERT: B 236 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7562 (ttm-80) REVERT: G 163 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8119 (tp) REVERT: K 240 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4441 (t80) REVERT: J 236 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7570 (ttm-80) REVERT: E 381 TYR cc_start: 0.6990 (t80) cc_final: 0.6286 (t80) REVERT: I 321 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8299 (p) outliers start: 62 outliers final: 52 residues processed: 297 average time/residue: 0.1439 time to fit residues: 69.9951 Evaluate side-chains 309 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 151 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 242 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN E 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.124765 restraints weight = 22644.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.124001 restraints weight = 26264.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124442 restraints weight = 26985.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124442 restraints weight = 24709.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.124442 restraints weight = 24709.432| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22899 Z= 0.127 Angle : 0.576 7.847 31017 Z= 0.297 Chirality : 0.045 0.222 3201 Planarity : 0.005 0.054 3717 Dihedral : 17.740 166.403 3969 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 2.74 % Allowed : 14.13 % Favored : 83.13 % 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: 0.13 (0.17), residues: 2559 helix: 1.20 (0.15), residues: 1173 sheet: -0.98 (0.27), residues: 375 loop : -0.72 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 375 TYR 0.025 0.001 TYR C 184 PHE 0.025 0.001 PHE C 248 TRP 0.016 0.001 TRP A 77 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22899) covalent geometry : angle 0.57560 / 0.30 (31017) hydrogen bonds : bond 0.03831 / 2.48 ( 1113) hydrogen bonds : angle 5.19849 / 3.73 ( 3276) ********************** 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 315 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 0.825 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 142 MET cc_start: 0.8311 (tpp) cc_final: 0.8009 (ttm) REVERT: A 231 THR cc_start: 0.8038 (p) cc_final: 0.7784 (p) REVERT: A 375 ARG cc_start: 0.7350 (mtm110) cc_final: 0.7148 (mmp80) REVERT: B 236 ARG cc_start: 0.7855 (mmt90) cc_final: 0.7566 (ttm-80) REVERT: G 88 TYR cc_start: 0.7570 (m-80) cc_final: 0.7324 (t80) REVERT: G 163 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8054 (tp) REVERT: K 240 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.4548 (t80) REVERT: J 236 ARG cc_start: 0.7791 (mmt90) cc_final: 0.7561 (ttm-80) REVERT: E 381 TYR cc_start: 0.6951 (t80) cc_final: 0.6306 (t80) outliers start: 60 outliers final: 53 residues processed: 288 average time/residue: 0.1426 time to fit residues: 67.2619 Evaluate side-chains 303 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 248 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 234 TRP Chi-restraints excluded: chain K residue 219 MET Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 62 THR Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 100 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN E 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.135514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115922 restraints weight = 22950.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.115009 restraints weight = 26040.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.115232 restraints weight = 26646.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.115751 restraints weight = 24684.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115983 restraints weight = 22607.157| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22899 Z= 0.156 Angle : 0.597 7.769 31017 Z= 0.307 Chirality : 0.046 0.219 3201 Planarity : 0.005 0.053 3717 Dihedral : 17.531 167.973 3969 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.55 % Favored : 94.22 % Rotamer: Outliers : 2.83 % Allowed : 13.90 % Favored : 83.26 % 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: 0.06 (0.17), residues: 2559 helix: 1.16 (0.15), residues: 1173 sheet: -1.07 (0.27), residues: 375 loop : -0.78 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 400 TYR 0.025 0.002 TYR C 184 PHE 0.024 0.002 PHE C 248 TRP 0.015 0.001 TRP B 54 HIS 0.005 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (22899) covalent geometry : angle 0.59709 / 0.31 (31017) hydrogen bonds : bond 0.03967 / 2.58 ( 1113) hydrogen bonds : angle 5.20127 / 3.73 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.15 seconds wall clock time: 56 minutes 23.79 seconds (3383.79 seconds total)