Starting phenix.real_space_refine on Sat Mar 7 08:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4p_25684/03_2026/7t4p_25684_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4p_25684/03_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_25684/03_2026/7t4p_25684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4p_25684/03_2026/7t4p_25684.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4p_25684/03_2026/7t4p_25684_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4p_25684/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 285 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} 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, 285 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 243 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 1, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.76, per 1000 atoms: 0.21 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: 1.83 Conformation dependent library (CDL) restraints added in 899.5 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: 0.69 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: 3.62 Time building geometry restraints manager: 2.43 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 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.709 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.710 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 502 " model vdw 1.809 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.810 2.320 ... (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: 6.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.830 Find NCS groups from input model: 0.530 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 covalent geometry : bond 0.00882 (22899) covalent geometry : angle 0.98279 (31017) hydrogen bonds : bond 0.13412 ( 1113) hydrogen bonds : angle 7.03153 ( 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 : 0.636 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: 0.1470 time to fit residues: 74.7028 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 : 0.688 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 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: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN K 245 HIS F 160 ASN F 240 ASN J 160 ASN J 240 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.138110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119743 restraints weight = 23256.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118451 restraints weight = 26545.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.118564 restraints weight = 25519.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.119003 restraints weight = 24770.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.119185 restraints weight = 22551.493| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22899 Z= 0.156 Angle : 0.637 7.687 31017 Z= 0.327 Chirality : 0.046 0.201 3201 Planarity : 0.005 0.059 3717 Dihedral : 21.355 169.044 3987 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.69 % Favored : 94.96 % Rotamer: Outliers : 1.37 % Allowed : 6.68 % Favored : 91.95 % 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: 0.20 (0.17), residues: 2559 helix: 1.09 (0.15), residues: 1167 sheet: -0.52 (0.28), residues: 390 loop : -0.64 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 375 TYR 0.038 0.002 TYR G 184 PHE 0.027 0.002 PHE C 92 TRP 0.017 0.001 TRP F 237 HIS 0.004 0.001 HIS F 38 Details of bonding type rmsd covalent geometry : bond 0.00343 (22899) covalent geometry : angle 0.63656 (31017) hydrogen bonds : bond 0.04501 ( 1113) hydrogen bonds : angle 5.78165 ( 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 320 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 0.786 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: 0.8368 (tpp) cc_final: 0.8045 (tpt) REVERT: A 414 MET cc_start: 0.5990 (mpp) cc_final: 0.5732 (mtp) REVERT: G 88 TYR cc_start: 0.7854 (m-80) cc_final: 0.7507 (m-80) REVERT: G 210 TYR cc_start: 0.8709 (t80) cc_final: 0.8482 (t80) REVERT: G 228 GLU cc_start: 0.7077 (mp0) cc_final: 0.6817 (mp0) REVERT: F 236 ARG cc_start: 0.7692 (mmt90) cc_final: 0.7353 (ttm-80) REVERT: E 375 ARG cc_start: 0.7864 (mtp-110) cc_final: 0.7469 (mtp85) REVERT: E 414 MET cc_start: 0.6036 (mpp) cc_final: 0.5703 (mtp) REVERT: I 375 ARG cc_start: 0.7799 (mtp-110) cc_final: 0.7597 (mtp85) outliers start: 30 outliers final: 14 residues processed: 303 average time/residue: 0.1514 time to fit residues: 72.4640 Evaluate side-chains 260 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 246 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 Chi-restraints excluded: chain E residue 300 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 24 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 161 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3345 r_free = 0.3345 target = 0.131094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111705 restraints weight = 23898.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110359 restraints weight = 31037.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.110802 restraints weight = 29791.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.111102 restraints weight = 27754.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.111211 restraints weight = 24902.323| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22899 Z= 0.252 Angle : 0.696 8.165 31017 Z= 0.360 Chirality : 0.050 0.223 3201 Planarity : 0.005 0.064 3717 Dihedral : 20.609 164.598 3977 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.10 % Favored : 93.67 % Rotamer: Outliers : 2.33 % Allowed : 9.42 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2559 helix: 0.84 (0.15), residues: 1179 sheet: -1.03 (0.26), residues: 393 loop : -0.81 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 375 TYR 0.034 0.002 TYR K 184 PHE 0.025 0.002 PHE K 240 TRP 0.020 0.002 TRP A 77 HIS 0.009 0.002 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00608 (22899) covalent geometry : angle 0.69628 (31017) hydrogen bonds : bond 0.04759 ( 1113) hydrogen bonds : angle 5.64306 ( 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 326 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 275 time to evaluate : 0.834 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: 0.8327 (tpp) cc_final: 0.8043 (ttm) REVERT: A 375 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7522 (mtm110) REVERT: C 169 PHE cc_start: 0.7284 (m-10) cc_final: 0.7076 (m-10) REVERT: B 236 ARG cc_start: 0.7951 (mmt90) cc_final: 0.7624 (ttm-80) REVERT: F 178 MET cc_start: 0.8776 (mtt) cc_final: 0.8387 (mtt) REVERT: F 236 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7566 (ttm-80) REVERT: J 236 ARG cc_start: 0.7922 (mmt90) cc_final: 0.7589 (ttm-80) REVERT: E 375 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7432 (mtp85) outliers start: 51 outliers final: 35 residues processed: 304 average time/residue: 0.1476 time to fit residues: 71.9711 Evaluate side-chains 280 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 288 ASP Chi-restraints excluded: chain A residue 373 VAL 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 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 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 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 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 373 VAL Chi-restraints excluded: chain I residue 65 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: 1.9990 chunk 109 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 chunk 230 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN C 161 GLN G 161 GLN K 271 GLN E 401 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.139843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.122201 restraints weight = 23262.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.123199 restraints weight = 21806.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.123184 restraints weight = 20680.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.123396 restraints weight = 20282.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.123428 restraints weight = 19700.246| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1908 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= 0.147 Angle : 0.586 8.207 31017 Z= 0.305 Chirality : 0.046 0.222 3201 Planarity : 0.005 0.059 3717 Dihedral : 19.773 161.035 3975 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.92 % Favored : 94.84 % Rotamer: Outliers : 2.15 % Allowed : 11.80 % Favored : 86.05 % 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: 0.04 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1176 sheet: -0.88 (0.26), residues: 387 loop : -0.66 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 58 TYR 0.027 0.002 TYR C 184 PHE 0.022 0.001 PHE K 248 TRP 0.021 0.001 TRP C 234 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00340 (22899) covalent geometry : angle 0.58642 (31017) hydrogen bonds : bond 0.04136 ( 1113) hydrogen bonds : angle 5.42948 ( 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 300 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 0.492 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: 0.8272 (tpp) cc_final: 0.8000 (ttm) REVERT: B 141 TYR cc_start: 0.8496 (m-80) cc_final: 0.8129 (m-80) REVERT: B 236 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7572 (ttm-80) REVERT: K 90 MET cc_start: 0.8125 (mmm) cc_final: 0.7639 (tpp) REVERT: F 178 MET cc_start: 0.8741 (mtt) cc_final: 0.8398 (mtt) REVERT: F 236 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7557 (ttm-80) REVERT: J 236 ARG cc_start: 0.7870 (mmt90) cc_final: 0.7558 (ttm-80) REVERT: E 375 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.7253 (mtp85) outliers start: 47 outliers final: 35 residues processed: 280 average time/residue: 0.1481 time to fit residues: 66.4159 Evaluate side-chains 277 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 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 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 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 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 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 362 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 359 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 137 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN J 160 ASN E 401 GLN I 404 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 = 0.132486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113100 restraints weight = 23692.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.111752 restraints weight = 29392.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.112870 restraints weight = 27960.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.113402 restraints weight = 24726.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.113481 restraints weight = 22310.572| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2105 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= 0.194 Angle : 0.619 8.197 31017 Z= 0.321 Chirality : 0.047 0.222 3201 Planarity : 0.005 0.061 3717 Dihedral : 19.427 160.236 3973 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.78 % Favored : 93.98 % Rotamer: Outliers : 3.29 % Allowed : 11.43 % Favored : 85.28 % 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: 0.99 (0.15), residues: 1173 sheet: -0.93 (0.27), residues: 375 loop : -0.78 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 375 TYR 0.027 0.002 TYR C 184 PHE 0.026 0.002 PHE K 248 TRP 0.018 0.002 TRP K 234 HIS 0.005 0.002 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00464 (22899) covalent geometry : angle 0.61884 (31017) hydrogen bonds : bond 0.04282 ( 1113) hydrogen bonds : angle 5.41328 ( 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 321 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 249 time to evaluate : 0.552 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: 0.8289 (tpp) cc_final: 0.8038 (ttm) REVERT: A 231 THR cc_start: 0.8019 (p) cc_final: 0.7808 (p) REVERT: B 236 ARG cc_start: 0.7946 (mmt90) cc_final: 0.7625 (ttm-80) REVERT: G 163 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.7904 (tp) REVERT: K 240 PHE cc_start: 0.5969 (OUTLIER) cc_final: 0.4658 (t80) REVERT: F 178 MET cc_start: 0.8739 (mtt) cc_final: 0.8449 (mtt) REVERT: F 236 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7633 (ttm-80) REVERT: J 150 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6997 (mtp) REVERT: J 236 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7592 (ttm-80) REVERT: E 375 ARG cc_start: 0.7516 (mtp-110) cc_final: 0.7310 (mtp85) REVERT: I 227 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8789 (mt) outliers start: 72 outliers final: 50 residues processed: 296 average time/residue: 0.1479 time to fit residues: 70.5227 Evaluate side-chains 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 348 VAL 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 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 245 GLN Chi-restraints excluded: chain G residue 163 ILE 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 K residue 248 PHE Chi-restraints excluded: chain F residue 29 VAL 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 17 VAL 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 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain E residue 114 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 E residue 373 VAL 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 168 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 36 optimal weight: 0.0270 chunk 240 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 overall best weight: 1.2440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3440 r_free = 0.3440 target = 0.139976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.122274 restraints weight = 23435.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.122833 restraints weight = 22583.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.122982 restraints weight = 21212.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.122982 restraints weight = 20918.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.122982 restraints weight = 20918.717| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2220 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= 0.138 Angle : 0.571 7.926 31017 Z= 0.297 Chirality : 0.045 0.220 3201 Planarity : 0.005 0.058 3717 Dihedral : 18.922 158.191 3971 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.35 % Favored : 94.41 % Rotamer: Outliers : 3.06 % Allowed : 12.39 % Favored : 84.55 % 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: 0.10 (0.17), residues: 2559 helix: 1.12 (0.15), residues: 1173 sheet: -0.89 (0.27), residues: 375 loop : -0.70 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 242 TYR 0.025 0.001 TYR K 184 PHE 0.028 0.001 PHE K 248 TRP 0.015 0.001 TRP A 77 HIS 0.004 0.001 HIS C 160 Details of bonding type rmsd covalent geometry : bond 0.00319 (22899) covalent geometry : angle 0.57126 (31017) hydrogen bonds : bond 0.03965 ( 1113) hydrogen bonds : angle 5.29370 ( 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 326 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 0.803 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: 0.8270 (tpp) cc_final: 0.8034 (ttm) REVERT: A 231 THR cc_start: 0.8038 (p) cc_final: 0.7828 (p) REVERT: B 236 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7603 (ttm-80) REVERT: G 163 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.7894 (tp) REVERT: K 240 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.4659 (t80) REVERT: F 178 MET cc_start: 0.8756 (mtt) cc_final: 0.8467 (mtt) REVERT: F 236 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7627 (ttm-80) REVERT: J 150 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6956 (mtp) REVERT: J 236 ARG cc_start: 0.7844 (mmt90) cc_final: 0.7573 (ttm-80) outliers start: 67 outliers final: 49 residues processed: 299 average time/residue: 0.1492 time to fit residues: 71.6465 Evaluate side-chains 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 LEU 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 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 234 TRP 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 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 150 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 227 LEU Chi-restraints excluded: chain E residue 288 ASP 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 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 359 THR 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: 10.0000 chunk 94 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 118 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 44 optimal weight: 0.0670 chunk 186 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3403 r_free = 0.3403 target = 0.136235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116943 restraints weight = 23534.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.117191 restraints weight = 23154.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.117183 restraints weight = 23594.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.117947 restraints weight = 22162.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.118106 restraints weight = 20965.510| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2307 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= 0.128 Angle : 0.564 7.897 31017 Z= 0.292 Chirality : 0.045 0.219 3201 Planarity : 0.005 0.056 3717 Dihedral : 18.578 159.179 3971 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.24 % Favored : 94.53 % Rotamer: Outliers : 2.97 % Allowed : 12.80 % Favored : 84.22 % 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: 0.17 (0.17), residues: 2559 helix: 1.21 (0.15), residues: 1170 sheet: -0.79 (0.27), residues: 381 loop : -0.75 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 375 TYR 0.025 0.001 TYR C 184 PHE 0.026 0.001 PHE K 248 TRP 0.017 0.001 TRP A 77 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00294 (22899) covalent geometry : angle 0.56400 (31017) hydrogen bonds : bond 0.03859 ( 1113) hydrogen bonds : angle 5.23702 ( 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 322 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 0.829 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: 0.8274 (tpp) cc_final: 0.8007 (ttm) REVERT: A 231 THR cc_start: 0.8045 (p) cc_final: 0.7824 (p) REVERT: B 150 MET cc_start: 0.7336 (mmm) cc_final: 0.6952 (mtp) REVERT: B 236 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7579 (ttm-80) REVERT: G 163 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.7886 (tp) REVERT: K 240 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.4644 (t80) REVERT: F 178 MET cc_start: 0.8780 (mtt) cc_final: 0.8492 (mtt) REVERT: J 236 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7554 (ttm-80) outliers start: 65 outliers final: 50 residues processed: 294 average time/residue: 0.1466 time to fit residues: 69.8059 Evaluate side-chains 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR 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 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 245 GLN Chi-restraints excluded: chain G residue 45 LEU 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 248 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 HIS ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.130184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.110590 restraints weight = 23789.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.109541 restraints weight = 28530.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.110320 restraints weight = 26875.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.110577 restraints weight = 25132.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.110931 restraints weight = 23309.406| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22899 Z= 0.248 Angle : 0.678 8.601 31017 Z= 0.350 Chirality : 0.049 0.209 3201 Planarity : 0.005 0.055 3717 Dihedral : 18.775 162.010 3971 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.06 % Favored : 93.71 % Rotamer: Outliers : 3.38 % Allowed : 12.85 % Favored : 83.77 % 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: 0.91 (0.15), residues: 1176 sheet: -1.12 (0.26), residues: 378 loop : -0.88 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 100 TYR 0.027 0.002 TYR K 184 PHE 0.025 0.002 PHE K 248 TRP 0.018 0.002 TRP A 77 HIS 0.007 0.002 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00597 (22899) covalent geometry : angle 0.67836 (31017) hydrogen bonds : bond 0.04551 ( 1113) hydrogen bonds : angle 5.43848 ( 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 340 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 266 time to evaluate : 0.793 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: 0.8281 (tpp) cc_final: 0.8007 (ttm) REVERT: A 231 THR cc_start: 0.8122 (p) cc_final: 0.7892 (p) REVERT: C 236 MET cc_start: 0.6034 (mtp) cc_final: 0.5594 (mtp) REVERT: B 150 MET cc_start: 0.7416 (mmm) cc_final: 0.7102 (mtp) REVERT: B 236 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7660 (ttm-80) REVERT: G 163 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.7955 (tp) REVERT: K 240 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.4629 (t80) REVERT: F 45 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7265 (ppp) REVERT: J 236 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7617 (ttm-80) REVERT: E 381 TYR cc_start: 0.7207 (t80) cc_final: 0.6400 (t80) REVERT: I 227 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8822 (mt) outliers start: 74 outliers final: 54 residues processed: 311 average time/residue: 0.1407 time to fit residues: 71.4216 Evaluate side-chains 313 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 180 LEU 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 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 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 45 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 17 VAL 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 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 288 ASP Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 373 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: 4.9990 chunk 20 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN I 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.135414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.116322 restraints weight = 23536.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116935 restraints weight = 22852.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.117068 restraints weight = 21486.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.119156 restraints weight = 20917.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.119042 restraints weight = 19712.914| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2553 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= 0.133 Angle : 0.585 8.275 31017 Z= 0.302 Chirality : 0.045 0.216 3201 Planarity : 0.005 0.054 3717 Dihedral : 18.133 161.261 3969 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 2.93 % Allowed : 13.72 % Favored : 83.36 % 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: 1.13 (0.15), residues: 1173 sheet: -0.97 (0.26), residues: 381 loop : -0.76 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 375 TYR 0.024 0.001 TYR C 184 PHE 0.027 0.001 PHE K 248 TRP 0.019 0.001 TRP A 77 HIS 0.004 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00305 (22899) covalent geometry : angle 0.58482 (31017) hydrogen bonds : bond 0.03944 ( 1113) hydrogen bonds : angle 5.28877 ( 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 316 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 0.795 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: 0.8270 (tpp) cc_final: 0.8014 (ttm) REVERT: A 231 THR cc_start: 0.8090 (p) cc_final: 0.7835 (p) REVERT: C 236 MET cc_start: 0.5833 (mtp) cc_final: 0.5382 (mtp) REVERT: B 236 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7600 (ttm-80) REVERT: G 163 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.7915 (tp) REVERT: K 240 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.4619 (t80) REVERT: F 45 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7399 (ppp) REVERT: J 226 LEU cc_start: 0.8561 (mm) cc_final: 0.8303 (mt) REVERT: J 236 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7558 (ttm-80) REVERT: E 381 TYR cc_start: 0.7017 (t80) cc_final: 0.6297 (t80) outliers start: 64 outliers final: 55 residues processed: 291 average time/residue: 0.1398 time to fit residues: 67.0199 Evaluate side-chains 299 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 180 LEU 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 245 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G 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 45 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 17 VAL 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 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 80 THR 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 387 PHE Chi-restraints excluded: chain I residue 404 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 151 optimal weight: 0.0030 chunk 8 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN I 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.133807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116369 restraints weight = 23760.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114614 restraints weight = 30305.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.115538 restraints weight = 29384.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.115929 restraints weight = 25132.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.115979 restraints weight = 23131.858| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22899 Z= 0.163 Angle : 0.607 7.947 31017 Z= 0.312 Chirality : 0.047 0.216 3201 Planarity : 0.005 0.061 3717 Dihedral : 17.952 162.312 3969 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.55 % Favored : 94.22 % Rotamer: Outliers : 3.06 % Allowed : 13.76 % Favored : 83.17 % 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: 0.04 (0.17), residues: 2559 helix: 1.13 (0.15), residues: 1173 sheet: -1.10 (0.27), residues: 372 loop : -0.74 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.025 0.002 TYR C 184 PHE 0.027 0.002 PHE K 248 TRP 0.020 0.001 TRP B 54 HIS 0.005 0.001 HIS F 232 Details of bonding type rmsd covalent geometry : bond 0.00386 (22899) covalent geometry : angle 0.60664 (31017) hydrogen bonds : bond 0.04049 ( 1113) hydrogen bonds : angle 5.26820 ( 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 317 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.848 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: 0.8307 (tpp) cc_final: 0.8044 (ttm) REVERT: A 231 THR cc_start: 0.8052 (p) cc_final: 0.7809 (p) REVERT: B 236 ARG cc_start: 0.7898 (mmt90) cc_final: 0.7614 (ttm-80) REVERT: G 163 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.7954 (tp) REVERT: K 240 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.4638 (t80) REVERT: F 45 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7432 (ppp) REVERT: J 236 ARG cc_start: 0.7811 (mmt90) cc_final: 0.7567 (ttm-80) REVERT: E 381 TYR cc_start: 0.7053 (t80) cc_final: 0.6345 (t80) outliers start: 67 outliers final: 60 residues processed: 289 average time/residue: 0.1451 time to fit residues: 69.1707 Evaluate side-chains 309 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 180 LEU 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 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 17 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 42 MET Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain J residue 17 VAL 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 124 LEU Chi-restraints excluded: chain J residue 136 MET Chi-restraints excluded: chain J residue 176 MET Chi-restraints excluded: chain J residue 207 THR 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 80 THR 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 Chi-restraints excluded: chain I residue 404 GLN 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: 0.9990 chunk 146 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN E 401 GLN I 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.136230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.117964 restraints weight = 23396.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.116694 restraints weight = 29782.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.118163 restraints weight = 27171.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.118450 restraints weight = 22681.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.118678 restraints weight = 21410.014| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22899 Z= 0.132 Angle : 0.587 7.772 31017 Z= 0.302 Chirality : 0.045 0.220 3201 Planarity : 0.005 0.054 3717 Dihedral : 17.646 162.536 3969 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.45 % Rotamer: Outliers : 3.02 % Allowed : 13.85 % 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: 0.12 (0.17), residues: 2559 helix: 1.19 (0.15), residues: 1173 sheet: -1.03 (0.27), residues: 375 loop : -0.70 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 375 TYR 0.025 0.001 TYR C 184 PHE 0.026 0.001 PHE K 248 TRP 0.017 0.001 TRP B 54 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00305 (22899) covalent geometry : angle 0.58716 (31017) hydrogen bonds : bond 0.03888 ( 1113) hydrogen bonds : angle 5.23428 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3094.57 seconds wall clock time: 54 minutes 43.23 seconds (3283.23 seconds total)