Starting phenix.real_space_refine on Sat Mar 7 09:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s4j_24828/03_2026/7s4j_24828.map" } resolution = 2.16 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= 0.005 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 19419 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 22780 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 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: "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: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 4.94, per 1000 atoms: 0.22 Number of scatterers: 22780 At special positions: 0 Unit cell: (107.194, 108.139, 118.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 O 4195 8.00 N 3417 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 728.9 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 21 sheets defined 53.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 184 through 208 Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 231 through 257 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 382 removed outlier: 3.547A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.986A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.539A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (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 161 removed outlier: 3.614A pdb=" N GLN C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 208 through 220 Proline residue: C 217 - end of helix removed outlier: 3.548A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.510A pdb=" N VAL C 249 " --> pdb=" O HIS C 245 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.727A 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: 3.932A 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: 4.217A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.743A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 382 removed outlier: 3.547A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 375 through 382 removed outlier: 3.547A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.987A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.539A pdb=" N GLU G 86 " --> pdb=" O ALA G 82 " (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 161 removed outlier: 3.614A pdb=" N GLN G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 177 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 208 through 220 Proline residue: G 217 - end of helix removed outlier: 3.548A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 233 Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 245 through 254 removed outlier: 3.510A pdb=" N VAL G 249 " --> pdb=" O HIS G 245 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU G 254 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 49 through 73 removed outlier: 3.986A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.539A pdb=" N GLU K 86 " --> pdb=" O ALA K 82 " (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 161 removed outlier: 3.614A pdb=" N GLN K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 177 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 208 through 220 Proline residue: K 217 - end of helix removed outlier: 3.547A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 233 Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 245 through 254 removed outlier: 3.510A pdb=" N VAL K 249 " --> pdb=" O HIS K 245 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'F' and resid 10 through 43 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.727A 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: 3.931A 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: 4.217A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.744A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.727A 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: 3.932A 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: 4.217A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 208 through 210 No H-bonds generated for 'chain 'J' and resid 208 through 210' Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.743A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.322A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.547A 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: 6.767A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.850A 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: 5.839A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.276A 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: 5.337A pdb=" N LEU A 314 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.262A 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 170 through 173 Processing sheet with id=AA8, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.323A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.766A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB2, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.839A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 10.232A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 341 through 342 removed outlier: 5.337A pdb=" N LEU E 314 " --> pdb=" O PHE E 394 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE E 394 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing sheet with id=AB4, 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: 6.632A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.767A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.839A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 341 through 342 removed outlier: 5.338A pdb=" N LEU I 314 " --> pdb=" O PHE I 394 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE I 394 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AC1, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AC2, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AC3, first strand: chain 'J' and resid 170 through 173 1122 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: 3.39 Time building geometry restraints manager: 2.07 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: 3288 1.32 - 1.44: 6821 1.44 - 1.56: 12706 1.56 - 1.69: 129 1.69 - 1.81: 180 Bond restraints: 23124 Sorted by residual: bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC C 310 " pdb=" O3 PLC C 310 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PLC J 303 " pdb=" O3 PLC J 303 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 23119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 30953 4.33 - 8.65: 264 8.65 - 12.98: 67 12.98 - 17.30: 0 17.30 - 21.63: 3 Bond angle restraints: 31287 Sorted by residual: angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.59 -21.63 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C9' PLC B 301 " pdb=" CA' PLC B 301 " pdb=" CB' PLC B 301 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C9' PLC J 303 " pdb=" CA' PLC J 303 " pdb=" CB' PLC J 303 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" CA HIS G 160 " pdb=" CB HIS G 160 " pdb=" CG HIS G 160 " ideal model delta sigma weight residual 113.80 106.85 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" CA HIS C 160 " pdb=" CB HIS C 160 " pdb=" CG HIS C 160 " ideal model delta sigma weight residual 113.80 106.86 6.94 1.00e+00 1.00e+00 4.82e+01 ... (remaining 31282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12528 34.45 - 68.90: 870 68.90 - 103.35: 93 103.35 - 137.81: 36 137.81 - 172.26: 18 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" CA GLN J 245 " pdb=" C GLN J 245 " pdb=" N SER J 246 " pdb=" CA SER J 246 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLN B 245 " pdb=" C GLN B 245 " pdb=" N SER B 246 " pdb=" CA SER B 246 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLN F 245 " pdb=" C GLN F 245 " pdb=" N SER F 246 " pdb=" CA SER F 246 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2368 0.054 - 0.108: 682 0.108 - 0.162: 124 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA ILE K 174 " pdb=" N ILE K 174 " pdb=" C ILE K 174 " pdb=" CB ILE K 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE G 174 " pdb=" N ILE G 174 " pdb=" C ILE G 174 " pdb=" CB ILE G 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE C 174 " pdb=" N ILE C 174 " pdb=" C ILE C 174 " pdb=" CB ILE C 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3204 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 173 " -0.017 2.00e-02 2.50e+03 2.08e-02 6.51e+00 pdb=" CG HIS K 173 " -0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS K 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS K 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS K 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 173 " -0.017 2.00e-02 2.50e+03 2.08e-02 6.48e+00 pdb=" CG HIS C 173 " -0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS C 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS C 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 173 " -0.017 2.00e-02 2.50e+03 2.07e-02 6.42e+00 pdb=" CG HIS G 173 " -0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS G 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS G 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS G 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS G 173 " -0.030 2.00e-02 2.50e+03 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 222 2.54 - 3.13: 17227 3.13 - 3.72: 38983 3.72 - 4.31: 59458 4.31 - 4.90: 93945 Nonbonded interactions: 209835 Sorted by model distance: nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.948 2.320 nonbonded pdb=" ND1 HIS I 48 " pdb="CU CU I 502 " model vdw 1.948 2.320 nonbonded pdb=" ND1 HIS E 48 " pdb="CU CU E 502 " model vdw 1.949 2.320 nonbonded pdb=" ND1 HIS E 72 " pdb="CU CU E 502 " model vdw 1.971 2.320 nonbonded pdb=" ND1 HIS A 72 " pdb="CU CU A 502 " model vdw 1.972 2.320 ... (remaining 209830 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 305 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.760 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 23124 Z= 0.480 Angle : 1.074 21.629 31287 Z= 0.527 Chirality : 0.054 0.270 3207 Planarity : 0.005 0.041 3729 Dihedral : 22.909 172.257 8787 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.16 % Favored : 94.33 % Rotamer: Outliers : 4.30 % Allowed : 18.88 % Favored : 76.82 % Cbeta Deviations : 0.04 % 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: 0.65 (0.17), residues: 2559 helix: 0.91 (0.15), residues: 1242 sheet: 0.35 (0.27), residues: 405 loop : -0.01 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 117 TYR 0.022 0.002 TYR K 184 PHE 0.021 0.002 PHE F 31 TRP 0.018 0.002 TRP E 206 HIS 0.026 0.002 HIS K 173 Details of bonding type rmsd covalent geometry : bond 0.00913 (23124) covalent geometry : angle 1.07411 (31287) hydrogen bonds : bond 0.13085 ( 1122) hydrogen bonds : angle 6.26311 ( 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 359 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 265 time to evaluate : 0.728 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. revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 288 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7593 (p0) REVERT: B 47 ASP cc_start: 0.7419 (m-30) cc_final: 0.7216 (m-30) REVERT: E 245 LEU cc_start: 0.8822 (mm) cc_final: 0.8549 (tt) REVERT: I 245 LEU cc_start: 0.8809 (mm) cc_final: 0.8527 (tt) REVERT: G 116 ASP cc_start: 0.8398 (t70) cc_final: 0.7922 (t0) REVERT: G 119 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8709 (mt) REVERT: K 233 PHE cc_start: 0.7508 (t80) cc_final: 0.7303 (t80) REVERT: F 113 TYR cc_start: 0.8360 (m-80) cc_final: 0.8132 (m-80) REVERT: F 150 MET cc_start: 0.7894 (tpt) cc_final: 0.7493 (tpt) outliers start: 94 outliers final: 47 residues processed: 340 average time/residue: 0.6500 time to fit residues: 249.6134 Evaluate side-chains 299 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 244 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN I 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091001 restraints weight = 24256.946| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.55 r_work: 0.2929 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23124 Z= 0.140 Angle : 0.624 8.638 31287 Z= 0.319 Chirality : 0.046 0.330 3207 Planarity : 0.004 0.041 3729 Dihedral : 22.658 176.974 4228 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 4.62 % Allowed : 17.79 % Favored : 77.59 % 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: 0.84 (0.17), residues: 2559 helix: 1.10 (0.15), residues: 1224 sheet: 0.47 (0.27), residues: 399 loop : 0.03 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 117 TYR 0.021 0.001 TYR K 184 PHE 0.021 0.001 PHE G 248 TRP 0.016 0.002 TRP I 206 HIS 0.003 0.001 HIS E 139 Details of bonding type rmsd covalent geometry : bond 0.00294 (23124) covalent geometry : angle 0.62411 (31287) hydrogen bonds : bond 0.04988 ( 1122) hydrogen bonds : angle 5.35977 ( 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 359 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 258 time to evaluate : 0.799 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 112 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8867 (mtt180) REVERT: A 401 GLN cc_start: 0.8799 (mt0) cc_final: 0.8596 (mt0) REVERT: E 112 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8841 (mtt180) REVERT: E 245 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8593 (tt) REVERT: I 112 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8615 (mtt90) REVERT: I 245 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8542 (tt) REVERT: G 116 ASP cc_start: 0.8500 (t70) cc_final: 0.7853 (t0) REVERT: F 150 MET cc_start: 0.8700 (tpt) cc_final: 0.8351 (tpt) outliers start: 101 outliers final: 41 residues processed: 332 average time/residue: 0.7111 time to fit residues: 264.4153 Evaluate side-chains 286 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 276 GLN E 176 GLN I 176 GLN G 276 GLN K 231 HIS K 276 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089481 restraints weight = 24005.733| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.54 r_work: 0.2903 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23124 Z= 0.167 Angle : 0.621 8.378 31287 Z= 0.323 Chirality : 0.047 0.264 3207 Planarity : 0.005 0.043 3729 Dihedral : 21.222 179.663 4190 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 3.84 % Allowed : 17.79 % Favored : 78.37 % 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: 0.87 (0.17), residues: 2559 helix: 1.12 (0.15), residues: 1233 sheet: 0.46 (0.26), residues: 423 loop : 0.06 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 117 TYR 0.023 0.002 TYR K 184 PHE 0.020 0.002 PHE K 248 TRP 0.013 0.001 TRP E 206 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00366 (23124) covalent geometry : angle 0.62128 (31287) hydrogen bonds : bond 0.05287 ( 1122) hydrogen bonds : angle 5.26770 ( 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 339 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 255 time to evaluate : 0.707 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 112 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8898 (mtt90) REVERT: A 285 LYS cc_start: 0.8896 (tmtm) cc_final: 0.8587 (tttp) REVERT: E 112 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8869 (mtt90) REVERT: E 145 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7499 (tp40) REVERT: E 245 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8597 (tt) REVERT: I 112 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8792 (mtt90) REVERT: I 245 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8594 (tt) REVERT: I 285 LYS cc_start: 0.9109 (tttm) cc_final: 0.8848 (tttm) REVERT: G 116 ASP cc_start: 0.8542 (t70) cc_final: 0.7860 (t0) REVERT: G 214 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8626 (p) REVERT: K 63 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9098 (mp) REVERT: J 47 ASP cc_start: 0.8337 (m-30) cc_final: 0.8084 (m-30) outliers start: 84 outliers final: 40 residues processed: 315 average time/residue: 0.7018 time to fit residues: 247.9703 Evaluate side-chains 290 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 106 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 404 GLN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 176 GLN I 401 GLN G 223 ASN K 223 ASN ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089374 restraints weight = 23901.010| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.53 r_work: 0.2903 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23124 Z= 0.171 Angle : 0.617 6.989 31287 Z= 0.321 Chirality : 0.047 0.276 3207 Planarity : 0.004 0.045 3729 Dihedral : 20.319 179.569 4182 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 3.52 % Allowed : 18.11 % Favored : 78.37 % 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: 0.88 (0.17), residues: 2559 helix: 1.13 (0.15), residues: 1236 sheet: 0.41 (0.26), residues: 423 loop : 0.09 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 117 TYR 0.022 0.002 TYR K 184 PHE 0.024 0.002 PHE K 248 TRP 0.013 0.002 TRP E 206 HIS 0.005 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00380 (23124) covalent geometry : angle 0.61716 (31287) hydrogen bonds : bond 0.05227 ( 1122) hydrogen bonds : angle 5.24736 ( 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 336 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 0.931 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 112 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8908 (mtt90) REVERT: A 145 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7734 (tp40) REVERT: E 45 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7820 (mtp85) REVERT: E 112 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8866 (mtt90) REVERT: E 245 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8587 (tt) REVERT: I 112 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8841 (mtt90) REVERT: I 145 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: I 245 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8597 (tt) REVERT: I 288 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8174 (p0) REVERT: G 116 ASP cc_start: 0.8572 (t70) cc_final: 0.7891 (t0) REVERT: K 223 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7315 (t0) REVERT: J 47 ASP cc_start: 0.8308 (m-30) cc_final: 0.8048 (m-30) outliers start: 77 outliers final: 41 residues processed: 307 average time/residue: 0.7112 time to fit residues: 244.6108 Evaluate side-chains 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 184 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 187 optimal weight: 0.0050 chunk 154 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 145 GLN I 176 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087849 restraints weight = 23730.393| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.52 r_work: 0.2876 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23124 Z= 0.205 Angle : 0.653 7.454 31287 Z= 0.340 Chirality : 0.048 0.281 3207 Planarity : 0.005 0.051 3729 Dihedral : 20.088 179.347 4177 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.57 % Favored : 95.31 % Rotamer: Outliers : 3.89 % Allowed : 17.33 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2559 helix: 1.04 (0.15), residues: 1236 sheet: 0.42 (0.26), residues: 387 loop : 0.09 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 375 TYR 0.022 0.002 TYR K 184 PHE 0.025 0.002 PHE G 248 TRP 0.013 0.002 TRP J 231 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00465 (23124) covalent geometry : angle 0.65263 (31287) hydrogen bonds : bond 0.05553 ( 1122) hydrogen bonds : angle 5.30605 ( 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 336 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 251 time to evaluate : 0.740 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 112 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8571 (mtt90) REVERT: A 145 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7708 (tp40) REVERT: E 112 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8695 (mtt90) REVERT: E 163 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8620 (ttp) REVERT: E 245 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8587 (tt) REVERT: I 112 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8808 (mtt90) REVERT: I 245 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8598 (tt) REVERT: I 288 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8208 (p0) REVERT: G 116 ASP cc_start: 0.8544 (t70) cc_final: 0.7861 (t0) REVERT: G 161 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.7739 (mm-40) REVERT: K 63 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9220 (mp) REVERT: F 13 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: F 150 MET cc_start: 0.8800 (tpt) cc_final: 0.8481 (tpt) REVERT: J 47 ASP cc_start: 0.8319 (m-30) cc_final: 0.8072 (m-30) outliers start: 85 outliers final: 49 residues processed: 305 average time/residue: 0.7188 time to fit residues: 245.1881 Evaluate side-chains 303 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 161 GLN Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 167 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 0.1980 chunk 163 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 168 ASN I 176 GLN I 404 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 ASN J 187 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091191 restraints weight = 23892.549| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.52 r_work: 0.2936 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23124 Z= 0.127 Angle : 0.587 7.603 31287 Z= 0.303 Chirality : 0.046 0.267 3207 Planarity : 0.004 0.063 3729 Dihedral : 19.451 176.816 4177 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 3.70 % Allowed : 17.74 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.17), residues: 2559 helix: 1.20 (0.15), residues: 1209 sheet: 0.39 (0.26), residues: 393 loop : -0.01 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 375 TYR 0.021 0.001 TYR C 184 PHE 0.018 0.001 PHE G 248 TRP 0.016 0.001 TRP A 206 HIS 0.004 0.001 HIS K 231 Details of bonding type rmsd covalent geometry : bond 0.00267 (23124) covalent geometry : angle 0.58653 (31287) hydrogen bonds : bond 0.04732 ( 1122) hydrogen bonds : angle 5.16277 ( 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 337 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 256 time to evaluate : 0.625 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 45 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7500 (mtp85) REVERT: A 112 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8909 (mtt90) REVERT: A 225 ASP cc_start: 0.6542 (m-30) cc_final: 0.5794 (p0) REVERT: A 245 LEU cc_start: 0.8963 (mm) cc_final: 0.8556 (tt) REVERT: C 161 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8024 (mm-40) REVERT: B 137 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8276 (mt) REVERT: E 45 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7827 (mtp85) REVERT: E 112 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8861 (mtt90) REVERT: E 245 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8598 (tt) REVERT: I 45 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7940 (mtp85) REVERT: I 112 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8883 (mtt90) REVERT: I 145 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7597 (tp40) REVERT: I 245 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8572 (tt) REVERT: I 288 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8159 (p0) REVERT: G 116 ASP cc_start: 0.8510 (t70) cc_final: 0.7831 (t0) REVERT: G 214 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8546 (p) REVERT: F 13 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8125 (tt0) REVERT: F 150 MET cc_start: 0.8723 (tpt) cc_final: 0.8435 (tpt) REVERT: J 47 ASP cc_start: 0.8285 (m-30) cc_final: 0.8029 (m-30) outliers start: 81 outliers final: 37 residues processed: 309 average time/residue: 0.7237 time to fit residues: 250.4884 Evaluate side-chains 297 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 187 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 145 GLN I 168 ASN I 176 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088199 restraints weight = 23858.781| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.53 r_work: 0.2881 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23124 Z= 0.196 Angle : 0.644 8.574 31287 Z= 0.334 Chirality : 0.048 0.273 3207 Planarity : 0.005 0.062 3729 Dihedral : 19.426 177.652 4177 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.69 % Favored : 95.15 % Rotamer: Outliers : 3.66 % Allowed : 17.92 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2559 helix: 1.06 (0.15), residues: 1245 sheet: 0.41 (0.26), residues: 387 loop : 0.08 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 375 TYR 0.023 0.002 TYR K 184 PHE 0.027 0.002 PHE K 248 TRP 0.013 0.002 TRP E 206 HIS 0.006 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00446 (23124) covalent geometry : angle 0.64433 (31287) hydrogen bonds : bond 0.05409 ( 1122) hydrogen bonds : angle 5.25875 ( 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 325 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 245 time to evaluate : 0.846 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 112 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8600 (mtt90) REVERT: A 145 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: C 279 CYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5734 (p) REVERT: B 137 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (mt) REVERT: E 102 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: E 112 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8739 (mtt90) REVERT: E 145 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: E 245 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8599 (tt) REVERT: I 112 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8834 (mtt90) REVERT: I 245 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8604 (tt) REVERT: I 288 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (p0) REVERT: G 279 CYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5701 (p) REVERT: K 223 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7409 (t0) REVERT: K 279 CYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5552 (p) REVERT: F 13 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: F 150 MET cc_start: 0.8793 (tpt) cc_final: 0.8438 (tpt) REVERT: J 47 ASP cc_start: 0.8304 (m-30) cc_final: 0.8063 (m-30) outliers start: 80 outliers final: 43 residues processed: 298 average time/residue: 0.7299 time to fit residues: 243.4933 Evaluate side-chains 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 238 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 227 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 176 GLN G 223 ASN K 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.086833 restraints weight = 23780.320| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.51 r_work: 0.2858 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23124 Z= 0.247 Angle : 0.692 8.545 31287 Z= 0.361 Chirality : 0.050 0.281 3207 Planarity : 0.005 0.063 3729 Dihedral : 19.501 179.222 4177 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.73 % Favored : 95.12 % Rotamer: Outliers : 3.80 % Allowed : 17.51 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1230 sheet: 0.31 (0.25), residues: 393 loop : 0.10 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 375 TYR 0.022 0.002 TYR K 184 PHE 0.029 0.002 PHE K 248 TRP 0.014 0.002 TRP E 206 HIS 0.008 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00569 (23124) covalent geometry : angle 0.69158 (31287) hydrogen bonds : bond 0.05836 ( 1122) hydrogen bonds : angle 5.36405 ( 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 326 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 243 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 112 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.7843 (mtt90) REVERT: A 145 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7678 (tp40) REVERT: C 279 CYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5786 (p) REVERT: B 137 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (mt) REVERT: E 112 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.7921 (mtt90) REVERT: E 145 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: E 245 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8579 (tt) REVERT: I 112 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8894 (mtt90) REVERT: I 245 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8612 (tt) REVERT: I 288 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8248 (p0) REVERT: G 279 CYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5725 (p) REVERT: K 223 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7471 (t0) REVERT: K 279 CYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5570 (p) REVERT: F 13 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: F 137 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8240 (mt) REVERT: J 47 ASP cc_start: 0.8316 (m-30) cc_final: 0.8096 (m-30) outliers start: 83 outliers final: 48 residues processed: 297 average time/residue: 0.7307 time to fit residues: 242.8184 Evaluate side-chains 298 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 131 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 108 optimal weight: 0.0470 chunk 170 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 145 GLN G 223 ASN K 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089102 restraints weight = 23799.487| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.53 r_work: 0.2896 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23124 Z= 0.153 Angle : 0.624 9.383 31287 Z= 0.323 Chirality : 0.047 0.266 3207 Planarity : 0.005 0.069 3729 Dihedral : 19.121 179.317 4177 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer: Outliers : 3.34 % Allowed : 17.88 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.17), residues: 2559 helix: 1.07 (0.15), residues: 1224 sheet: 0.40 (0.26), residues: 387 loop : -0.04 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 117 TYR 0.021 0.002 TYR K 184 PHE 0.027 0.002 PHE K 248 TRP 0.016 0.002 TRP A 206 HIS 0.003 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00334 (23124) covalent geometry : angle 0.62426 (31287) hydrogen bonds : bond 0.05132 ( 1122) hydrogen bonds : angle 5.23303 ( 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 317 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 0.621 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 112 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.7690 (mtt90) REVERT: A 145 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: C 279 CYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5734 (p) REVERT: B 137 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8313 (mt) REVERT: E 102 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8642 (mt-10) REVERT: E 112 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8556 (mtt90) REVERT: E 245 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8591 (tt) REVERT: I 112 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8958 (mtt90) REVERT: I 245 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8575 (tt) REVERT: I 288 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (p0) REVERT: G 214 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8596 (p) REVERT: G 279 CYS cc_start: 0.5886 (OUTLIER) cc_final: 0.5674 (p) REVERT: K 223 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7230 (t0) REVERT: K 279 CYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5532 (p) REVERT: F 13 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: F 150 MET cc_start: 0.8754 (tpt) cc_final: 0.8448 (tpt) REVERT: J 47 ASP cc_start: 0.8294 (m-30) cc_final: 0.8059 (m-30) REVERT: J 137 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8407 (mt) outliers start: 73 outliers final: 39 residues processed: 298 average time/residue: 0.7356 time to fit residues: 244.5762 Evaluate side-chains 299 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 223 ASN Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 212 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 158 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.0470 chunk 201 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 168 ASN E 176 GLN E 401 GLN I 168 ASN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 ASN F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092006 restraints weight = 23965.861| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.54 r_work: 0.2953 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 23124 Z= 0.118 Angle : 0.585 9.738 31287 Z= 0.300 Chirality : 0.045 0.255 3207 Planarity : 0.004 0.076 3729 Dihedral : 18.558 176.198 4177 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Rotamer: Outliers : 2.56 % Allowed : 18.79 % Favored : 78.65 % 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: 0.88 (0.17), residues: 2559 helix: 1.23 (0.15), residues: 1206 sheet: 0.42 (0.26), residues: 393 loop : -0.03 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 117 TYR 0.021 0.001 TYR C 184 PHE 0.023 0.001 PHE K 248 TRP 0.018 0.001 TRP E 202 HIS 0.003 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00244 (23124) covalent geometry : angle 0.58456 (31287) hydrogen bonds : bond 0.04516 ( 1122) hydrogen bonds : angle 5.09664 ( 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 304 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.912 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 112 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.7689 (mtt90) REVERT: A 225 ASP cc_start: 0.6492 (m-30) cc_final: 0.5776 (p0) REVERT: C 279 CYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5654 (p) REVERT: E 45 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7744 (mtp85) REVERT: E 102 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8645 (mt-10) REVERT: E 112 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8612 (mtt90) REVERT: E 225 ASP cc_start: 0.6371 (m-30) cc_final: 0.5701 (p0) REVERT: E 245 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8582 (tt) REVERT: I 112 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8864 (mtt90) REVERT: I 145 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7577 (tp40) REVERT: I 225 ASP cc_start: 0.6447 (m-30) cc_final: 0.5654 (p0) REVERT: I 245 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8561 (tt) REVERT: I 288 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8212 (p0) REVERT: G 116 ASP cc_start: 0.8504 (t70) cc_final: 0.7818 (t0) REVERT: G 214 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8540 (p) REVERT: K 279 CYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5500 (p) REVERT: F 13 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: F 150 MET cc_start: 0.8710 (tpt) cc_final: 0.8442 (tpt) REVERT: J 47 ASP cc_start: 0.8264 (m-30) cc_final: 0.8015 (m-30) REVERT: J 137 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8389 (mt) outliers start: 56 outliers final: 30 residues processed: 289 average time/residue: 0.7474 time to fit residues: 241.2126 Evaluate side-chains 283 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 137 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 141 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 401 GLN E 168 ASN E 176 GLN E 401 GLN I 145 GLN I 168 ASN I 176 GLN I 404 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091024 restraints weight = 23997.138| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.55 r_work: 0.2934 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23124 Z= 0.131 Angle : 0.599 9.423 31287 Z= 0.306 Chirality : 0.046 0.254 3207 Planarity : 0.004 0.075 3729 Dihedral : 18.308 174.622 4177 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.51 % Rotamer: Outliers : 2.51 % Allowed : 19.11 % Favored : 78.37 % 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: 0.98 (0.17), residues: 2559 helix: 1.31 (0.15), residues: 1221 sheet: 0.47 (0.26), residues: 387 loop : -0.00 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 117 TYR 0.021 0.001 TYR C 184 PHE 0.021 0.001 PHE G 248 TRP 0.013 0.001 TRP J 231 HIS 0.003 0.001 HIS K 231 Details of bonding type rmsd covalent geometry : bond 0.00281 (23124) covalent geometry : angle 0.59865 (31287) hydrogen bonds : bond 0.04686 ( 1122) hydrogen bonds : angle 5.08739 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10109.60 seconds wall clock time: 172 minutes 7.05 seconds (10327.05 seconds total)