Starting phenix.real_space_refine on Tue Aug 26 22:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oyi_17287/08_2025/8oyi_17287.map" } resolution = 2.19 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= 0.003 sd= 0.033 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 20898 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: 7 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15036 2.51 5 N 3417 2.21 5 O 4249 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22849 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: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "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: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 279 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 4.94, per 1000 atoms: 0.22 Number of scatterers: 22849 At special positions: 0 Unit cell: (107.407, 106.878, 119.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 F 9 9.00 O 4249 8.00 N 3417 7.00 C 15036 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: 1.71 Conformation dependent library (CDL) restraints added in 770.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 18 sheets defined 53.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 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 376 through 382 removed outlier: 3.672A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.674A 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: 3.956A 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: 4.110A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 180 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 239 removed outlier: 3.764A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 73 removed outlier: 3.906A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.623A 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 163 Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 181 through 199 Processing helix chain 'C' and resid 207 through 233 Proline residue: C 217 - end of helix removed outlier: 3.580A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.663A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) 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: 3.696A 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 'F' and resid 10 through 43 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.673A 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: 3.958A 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: 4.109A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 165 Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 180 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 239 removed outlier: 3.764A 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: 3.672A 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: 3.959A 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: 4.110A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 165 Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 180 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 239 removed outlier: 3.763A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 376 through 382 removed outlier: 3.672A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.631A 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 376 through 382 removed outlier: 3.672A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 73 removed outlier: 3.906A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.623A 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 163 Processing helix chain 'G' and resid 170 through 177 Processing helix chain 'G' and resid 181 through 199 Processing helix chain 'G' and resid 207 through 233 Proline residue: G 217 - end of helix removed outlier: 3.580A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.662A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) 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: 3.697A 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: 3.906A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.623A 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 163 Processing helix chain 'K' and resid 170 through 177 Processing helix chain 'K' and resid 181 through 199 Processing helix chain 'K' and resid 207 through 233 Proline residue: K 217 - end of helix removed outlier: 3.579A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.663A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) 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: 3.697A pdb=" N LEU K 254 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.295A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.684A 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: 6.669A pdb=" N VAL A 144 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE A 151 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A 142 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 3.828A 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: 5.814A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.253A 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: 6.554A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 173 Processing sheet with id=AA7, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AA8, first strand: chain 'J' and resid 170 through 173 Processing sheet with id=AA9, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.295A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.670A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB3, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.814A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.554A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.294A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.670A pdb=" N VAL I 144 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE I 151 " --> pdb=" O MET I 142 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET I 142 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR I 140 " --> pdb=" O PRO I 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.815A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.554A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 3285 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: 3.75 Time building geometry restraints manager: 2.18 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: 3350 1.32 - 1.44: 6774 1.44 - 1.57: 12699 1.57 - 1.69: 139 1.69 - 1.81: 180 Bond restraints: 23142 Sorted by residual: bond pdb=" CB PLC C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC G 302 " pdb=" O3 PLC G 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CB PLC K 302 " pdb=" O3 PLC K 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C9 P1O B 307 " pdb=" O5 P1O B 307 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CB PLC F 301 " pdb=" O3 PLC F 301 " ideal model delta sigma weight residual 1.327 1.452 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 29615 2.13 - 4.26: 1319 4.26 - 6.38: 257 6.38 - 8.51: 45 8.51 - 10.64: 78 Bond angle restraints: 31314 Sorted by residual: angle pdb=" N HIS C 231 " pdb=" CA HIS C 231 " pdb=" C HIS C 231 " ideal model delta sigma weight residual 112.12 104.45 7.67 1.34e+00 5.57e-01 3.27e+01 angle pdb=" N HIS G 231 " pdb=" CA HIS G 231 " pdb=" C HIS G 231 " ideal model delta sigma weight residual 112.12 104.46 7.66 1.34e+00 5.57e-01 3.27e+01 angle pdb=" N HIS K 231 " pdb=" CA HIS K 231 " pdb=" C HIS K 231 " ideal model delta sigma weight residual 112.12 104.47 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C PHE K 177 " pdb=" CA PHE K 177 " pdb=" CB PHE K 177 " ideal model delta sigma weight residual 110.79 101.36 9.43 1.66e+00 3.63e-01 3.23e+01 angle pdb=" C PHE C 177 " pdb=" CA PHE C 177 " pdb=" CB PHE C 177 " ideal model delta sigma weight residual 110.79 101.40 9.39 1.66e+00 3.63e-01 3.20e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 12602 34.43 - 68.86: 799 68.86 - 103.29: 99 103.29 - 137.73: 36 137.73 - 172.16: 12 Dihedral angle restraints: 13548 sinusoidal: 6096 harmonic: 7452 Sorted by residual: dihedral pdb=" O2 PLC F 301 " pdb=" C1 PLC F 301 " pdb=" C2 PLC F 301 " pdb=" O3P PLC F 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.45 -172.16 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC J 308 " pdb=" C1 PLC J 308 " pdb=" C2 PLC J 308 " pdb=" O3P PLC J 308 " ideal model delta sinusoidal sigma weight residual -55.71 116.44 -172.15 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC B 308 " pdb=" C1 PLC B 308 " pdb=" C2 PLC B 308 " pdb=" O3P PLC B 308 " ideal model delta sinusoidal sigma weight residual -55.71 116.41 -172.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2371 0.052 - 0.103: 633 0.103 - 0.155: 142 0.155 - 0.207: 40 0.207 - 0.258: 21 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA HIS K 173 " pdb=" N HIS K 173 " pdb=" C HIS K 173 " pdb=" CB HIS K 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA HIS C 173 " pdb=" N HIS C 173 " pdb=" C HIS C 173 " pdb=" CB HIS C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA HIS G 173 " pdb=" N HIS G 173 " pdb=" C HIS G 173 " pdb=" CB HIS G 173 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 245 " 0.027 2.00e-02 2.50e+03 3.57e-02 1.91e+01 pdb=" CG HIS K 245 " 0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS K 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS K 245 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS K 245 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS K 245 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 245 " 0.027 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" CG HIS G 245 " 0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS G 245 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS G 245 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS G 245 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS G 245 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 245 " -0.027 2.00e-02 2.50e+03 3.55e-02 1.90e+01 pdb=" CG HIS C 245 " -0.004 2.00e-02 2.50e+03 pdb=" ND1 HIS C 245 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 HIS C 245 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 HIS C 245 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS C 245 " -0.055 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 248 2.55 - 3.13: 18310 3.13 - 3.72: 40037 3.72 - 4.31: 59536 4.31 - 4.90: 95069 Nonbonded interactions: 213200 Sorted by model distance: nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.958 2.320 nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 301 " model vdw 1.958 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 301 " model vdw 1.959 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 502 " model vdw 1.967 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.967 2.320 ... (remaining 213195 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 414 or resid 502)) selection = (chain 'E' and (resid 33 through 414 or resid 502)) selection = (chain 'I' and (resid 33 through 414 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 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' selection = chain 'G' selection = chain 'K' } 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: 8.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.860 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 0.126 23142 Z= 0.474 Angle : 1.051 10.641 31314 Z= 0.529 Chirality : 0.054 0.258 3207 Planarity : 0.005 0.036 3732 Dihedral : 22.696 172.158 8790 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.55 % Favored : 93.63 % Rotamer: Outliers : 4.53 % Allowed : 17.19 % Favored : 78.28 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1203 sheet: 1.30 (0.28), residues: 357 loop : -0.62 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 375 TYR 0.040 0.002 TYR G 178 PHE 0.053 0.002 PHE K 248 TRP 0.017 0.002 TRP I 202 HIS 0.046 0.004 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00874 (23142) covalent geometry : angle 1.05107 (31314) hydrogen bonds : bond 0.12193 ( 1119) hydrogen bonds : angle 6.62117 ( 3285) *********************** 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 487 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 388 time to evaluate : 0.989 Fit side-chains REVERT: B 39 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8063 (tp) REVERT: C 57 ILE cc_start: 0.8272 (tp) cc_final: 0.7986 (tp) REVERT: C 240 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: F 39 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (tp) REVERT: G 57 ILE cc_start: 0.8299 (tp) cc_final: 0.8097 (tp) REVERT: G 74 TRP cc_start: 0.6111 (OUTLIER) cc_final: 0.5888 (m-90) REVERT: G 240 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: K 240 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6994 (m-80) outliers start: 99 outliers final: 27 residues processed: 459 average time/residue: 0.6844 time to fit residues: 355.1967 Evaluate side-chains 301 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 268 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 231 HIS Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K 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: 0.3980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN F 187 ASN J 240 ASN E 38 GLN E 108 GLN E 168 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119942 restraints weight = 25586.851| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.43 r_work: 0.3445 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23142 Z= 0.154 Angle : 0.655 9.295 31314 Z= 0.334 Chirality : 0.046 0.265 3207 Planarity : 0.005 0.038 3732 Dihedral : 22.424 177.379 4208 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.81 % Favored : 94.88 % Rotamer: Outliers : 4.07 % Allowed : 17.15 % 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 aren not related in a simple way. whole: 0.69 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1212 sheet: 1.05 (0.29), residues: 339 loop : -0.31 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.017 0.002 TYR K 184 PHE 0.021 0.002 PHE G 177 TRP 0.019 0.002 TRP I 206 HIS 0.004 0.001 HIS G 245 Details of bonding type rmsd covalent geometry : bond 0.00328 (23142) covalent geometry : angle 0.65501 (31314) hydrogen bonds : bond 0.04956 ( 1119) hydrogen bonds : angle 5.47096 ( 3285) *********************** 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 355 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 266 time to evaluate : 0.702 Fit side-chains REVERT: C 57 ILE cc_start: 0.8470 (tp) cc_final: 0.8192 (tp) REVERT: C 156 ASP cc_start: 0.8315 (t70) cc_final: 0.8068 (t70) REVERT: F 39 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8351 (tp) REVERT: I 225 ASP cc_start: 0.6196 (m-30) cc_final: 0.5912 (m-30) REVERT: I 316 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: G 240 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: K 101 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8320 (mp) REVERT: K 129 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7854 (mtm-85) outliers start: 89 outliers final: 34 residues processed: 336 average time/residue: 0.6108 time to fit residues: 233.7389 Evaluate side-chains 288 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 186 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 216 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 107 ASN C 276 GLN F 187 ASN J 107 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.142296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115034 restraints weight = 25234.373| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.44 r_work: 0.3357 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23142 Z= 0.276 Angle : 0.728 6.581 31314 Z= 0.384 Chirality : 0.051 0.244 3207 Planarity : 0.006 0.047 3732 Dihedral : 21.527 179.433 4190 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.81 % Favored : 94.92 % Rotamer: Outliers : 4.66 % Allowed : 16.55 % 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 aren not related in a simple way. whole: 0.35 (0.16), residues: 2559 helix: 0.63 (0.14), residues: 1224 sheet: 0.77 (0.28), residues: 336 loop : -0.32 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 57 TYR 0.021 0.003 TYR E 374 PHE 0.022 0.003 PHE C 152 TRP 0.027 0.003 TRP I 206 HIS 0.009 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00630 (23142) covalent geometry : angle 0.72779 (31314) hydrogen bonds : bond 0.05761 ( 1119) hydrogen bonds : angle 5.69539 ( 3285) *********************** 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 357 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 255 time to evaluate : 0.888 Fit side-chains REVERT: A 112 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8650 (mtt180) REVERT: A 344 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7751 (m-30) REVERT: F 39 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (tp) REVERT: E 112 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8663 (mtt180) REVERT: E 276 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: E 406 ASP cc_start: 0.7748 (p0) cc_final: 0.7429 (p0) REVERT: I 112 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (mtt180) REVERT: I 227 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.5651 (mp) REVERT: I 316 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: I 404 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: G 84 GLU cc_start: 0.7771 (tt0) cc_final: 0.7552 (tt0) REVERT: G 115 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8282 (ptp90) REVERT: G 145 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8972 (mm) REVERT: K 101 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8213 (mp) REVERT: K 156 ASP cc_start: 0.8611 (t70) cc_final: 0.8366 (t70) outliers start: 102 outliers final: 35 residues processed: 328 average time/residue: 0.7672 time to fit residues: 282.3020 Evaluate side-chains 286 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 72 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN E 38 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116534 restraints weight = 24959.300| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.43 r_work: 0.3380 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23142 Z= 0.188 Angle : 0.646 7.055 31314 Z= 0.338 Chirality : 0.047 0.235 3207 Planarity : 0.005 0.046 3732 Dihedral : 20.909 179.500 4176 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.42 % Favored : 95.35 % Rotamer: Outliers : 4.25 % Allowed : 16.83 % Favored : 78.92 % 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 aren not related in a simple way. whole: 0.39 (0.16), residues: 2559 helix: 0.72 (0.14), residues: 1224 sheet: 0.74 (0.28), residues: 336 loop : -0.35 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.018 0.002 TYR K 184 PHE 0.016 0.002 PHE J 31 TRP 0.023 0.002 TRP E 206 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00418 (23142) covalent geometry : angle 0.64572 (31314) hydrogen bonds : bond 0.05090 ( 1119) hydrogen bonds : angle 5.48518 ( 3285) *********************** 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 343 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 250 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: B 172 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8305 (tm-30) REVERT: E 45 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.6284 (mtp85) REVERT: I 227 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.5671 (mp) REVERT: I 316 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7800 (tm-30) REVERT: I 344 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: I 404 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7054 (tt0) REVERT: I 406 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7566 (p0) REVERT: G 84 GLU cc_start: 0.7770 (tt0) cc_final: 0.7432 (tt0) REVERT: K 101 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8182 (mp) REVERT: K 156 ASP cc_start: 0.8587 (t70) cc_final: 0.8371 (t70) outliers start: 93 outliers final: 42 residues processed: 317 average time/residue: 0.6976 time to fit residues: 249.2206 Evaluate side-chains 289 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 175 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.117342 restraints weight = 24776.451| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.42 r_work: 0.3390 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23142 Z= 0.167 Angle : 0.624 6.530 31314 Z= 0.326 Chirality : 0.046 0.227 3207 Planarity : 0.005 0.045 3732 Dihedral : 20.428 178.628 4174 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 3.75 % Allowed : 17.42 % Favored : 78.83 % 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 aren not related in a simple way. whole: 0.47 (0.16), residues: 2559 helix: 0.88 (0.14), residues: 1206 sheet: 0.71 (0.28), residues: 336 loop : -0.40 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 9 TYR 0.018 0.002 TYR K 184 PHE 0.016 0.002 PHE J 31 TRP 0.022 0.002 TRP E 206 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00369 (23142) covalent geometry : angle 0.62445 (31314) hydrogen bonds : bond 0.04908 ( 1119) hydrogen bonds : angle 5.40105 ( 3285) *********************** 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 325 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 243 time to evaluate : 0.777 Fit side-chains REVERT: A 45 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.6212 (mtp85) REVERT: A 249 MET cc_start: 0.8460 (mtp) cc_final: 0.8083 (mtp) REVERT: A 344 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: B 172 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 236 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7236 (mmp) REVERT: E 45 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.6273 (mtp85) REVERT: E 276 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: I 227 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.5718 (mp) REVERT: I 316 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: I 344 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: I 404 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: I 406 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7565 (p0) REVERT: G 101 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8458 (mp) REVERT: K 101 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8233 (mp) REVERT: K 196 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.7972 (ttmm) outliers start: 82 outliers final: 39 residues processed: 307 average time/residue: 0.7553 time to fit residues: 261.6274 Evaluate side-chains 287 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 235 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 133 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 75 optimal weight: 0.0770 chunk 136 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 404 GLN B 16 GLN J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118497 restraints weight = 25441.104| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.45 r_work: 0.3412 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23142 Z= 0.147 Angle : 0.600 8.252 31314 Z= 0.312 Chirality : 0.045 0.213 3207 Planarity : 0.005 0.045 3732 Dihedral : 19.649 173.767 4174 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.53 % Favored : 95.23 % Rotamer: Outliers : 3.98 % Allowed : 17.15 % Favored : 78.88 % 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 aren not related in a simple way. whole: 0.57 (0.16), residues: 2559 helix: 0.97 (0.14), residues: 1206 sheet: 0.69 (0.28), residues: 336 loop : -0.34 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 115 TYR 0.018 0.002 TYR K 184 PHE 0.015 0.001 PHE F 31 TRP 0.020 0.002 TRP A 206 HIS 0.004 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00320 (23142) covalent geometry : angle 0.60032 (31314) hydrogen bonds : bond 0.04704 ( 1119) hydrogen bonds : angle 5.29477 ( 3285) *********************** 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 338 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 251 time to evaluate : 0.826 Fit side-chains REVERT: A 45 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.6114 (mtp85) REVERT: A 145 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7114 (tp40) REVERT: A 249 MET cc_start: 0.8436 (mtp) cc_final: 0.8038 (mtp) REVERT: A 344 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: B 13 GLU cc_start: 0.8550 (tt0) cc_final: 0.8286 (tt0) REVERT: B 172 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8280 (tm-30) REVERT: C 236 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6887 (mmp) REVERT: F 22 ASP cc_start: 0.8231 (m-30) cc_final: 0.7977 (m-30) REVERT: J 13 GLU cc_start: 0.8335 (tt0) cc_final: 0.8085 (tt0) REVERT: E 45 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.6152 (mtp85) REVERT: I 227 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5782 (mp) REVERT: I 316 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: I 404 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7429 (tp40) REVERT: I 406 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7555 (p0) REVERT: G 101 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8439 (mp) REVERT: G 240 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: K 48 LYS cc_start: 0.6673 (ptpt) cc_final: 0.6370 (pmtt) REVERT: K 101 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8212 (mp) REVERT: K 196 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8031 (tttm) outliers start: 87 outliers final: 42 residues processed: 313 average time/residue: 0.7464 time to fit residues: 263.3823 Evaluate side-chains 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 240 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 155 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115564 restraints weight = 25012.845| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.44 r_work: 0.3374 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23142 Z= 0.203 Angle : 0.642 8.075 31314 Z= 0.337 Chirality : 0.047 0.213 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.595 172.037 4174 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 3.84 % Allowed : 17.06 % Favored : 79.10 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2559 helix: 0.82 (0.14), residues: 1224 sheet: 0.69 (0.28), residues: 336 loop : -0.29 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 9 TYR 0.019 0.002 TYR B 188 PHE 0.018 0.002 PHE F 31 TRP 0.021 0.002 TRP I 206 HIS 0.006 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00455 (23142) covalent geometry : angle 0.64219 (31314) hydrogen bonds : bond 0.05114 ( 1119) hydrogen bonds : angle 5.40226 ( 3285) *********************** 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 323 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 239 time to evaluate : 0.829 Fit side-chains REVERT: A 45 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6225 (mtp85) REVERT: A 112 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8647 (mtt180) REVERT: A 145 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7094 (tp40) REVERT: A 249 MET cc_start: 0.8476 (mtp) cc_final: 0.8067 (mtp) REVERT: A 344 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: B 172 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 101 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 236 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6993 (mmp) REVERT: F 22 ASP cc_start: 0.8215 (m-30) cc_final: 0.7945 (m-30) REVERT: E 45 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6265 (mtp85) REVERT: E 112 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8668 (mtt180) REVERT: E 276 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: I 112 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8568 (mtt180) REVERT: I 227 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5739 (mp) REVERT: I 316 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: I 344 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: I 404 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: I 406 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7592 (p0) REVERT: G 101 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (mp) REVERT: G 240 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: K 101 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8179 (mp) REVERT: K 196 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8001 (ttmm) outliers start: 84 outliers final: 41 residues processed: 303 average time/residue: 0.7112 time to fit residues: 243.6427 Evaluate side-chains 289 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG 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 227 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115528 restraints weight = 24846.730| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.43 r_work: 0.3377 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23142 Z= 0.191 Angle : 0.637 11.449 31314 Z= 0.334 Chirality : 0.047 0.205 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.474 169.854 4174 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 3.57 % Allowed : 17.60 % Favored : 78.83 % 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 aren not related in a simple way. whole: 0.48 (0.16), residues: 2559 helix: 0.80 (0.14), residues: 1224 sheet: 0.68 (0.28), residues: 336 loop : -0.28 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 9 TYR 0.018 0.002 TYR K 184 PHE 0.017 0.002 PHE F 31 TRP 0.021 0.002 TRP E 206 HIS 0.005 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00428 (23142) covalent geometry : angle 0.63731 (31314) hydrogen bonds : bond 0.05055 ( 1119) hydrogen bonds : angle 5.39650 ( 3285) *********************** 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 313 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 235 time to evaluate : 0.904 Fit side-chains REVERT: A 45 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6217 (mtp85) REVERT: A 112 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8641 (mtt180) REVERT: A 145 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7094 (tp40) REVERT: A 249 MET cc_start: 0.8489 (mtp) cc_final: 0.8076 (mtp) REVERT: A 406 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7490 (p0) REVERT: B 172 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8285 (tm-30) REVERT: C 101 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 236 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6860 (mmp) REVERT: F 22 ASP cc_start: 0.8224 (m-30) cc_final: 0.7970 (m-30) REVERT: J 13 GLU cc_start: 0.8392 (tt0) cc_final: 0.8138 (tt0) REVERT: E 45 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6246 (mtp85) REVERT: E 79 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: E 112 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8663 (mtt180) REVERT: E 276 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: I 112 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8567 (mtt180) REVERT: I 227 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.5729 (mp) REVERT: I 316 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: I 344 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: I 404 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: I 406 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7552 (p0) REVERT: G 101 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8456 (mp) REVERT: G 240 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: K 101 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8186 (mp) REVERT: K 196 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8003 (ttmm) outliers start: 78 outliers final: 40 residues processed: 296 average time/residue: 0.7273 time to fit residues: 242.1210 Evaluate side-chains 288 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 228 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG 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 227 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 195 GLU 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 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 344 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 16 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119199 restraints weight = 25498.074| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.45 r_work: 0.3421 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23142 Z= 0.135 Angle : 0.594 12.690 31314 Z= 0.308 Chirality : 0.045 0.185 3207 Planarity : 0.004 0.045 3732 Dihedral : 18.920 168.147 4174 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.34 % Favored : 95.43 % Rotamer: Outliers : 3.02 % Allowed : 18.06 % Favored : 78.92 % 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 aren not related in a simple way. whole: 0.62 (0.17), residues: 2559 helix: 0.99 (0.14), residues: 1215 sheet: 0.73 (0.28), residues: 336 loop : -0.31 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 9 TYR 0.018 0.001 TYR K 184 PHE 0.014 0.001 PHE J 31 TRP 0.019 0.002 TRP E 206 HIS 0.003 0.001 HIS I 33 Details of bonding type rmsd covalent geometry : bond 0.00291 (23142) covalent geometry : angle 0.59436 (31314) hydrogen bonds : bond 0.04583 ( 1119) hydrogen bonds : angle 5.24302 ( 3285) *********************** 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 312 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 246 time to evaluate : 0.895 Fit side-chains REVERT: A 45 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.6147 (mtp85) REVERT: A 112 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8593 (mtt180) REVERT: A 249 MET cc_start: 0.8433 (mtp) cc_final: 0.8039 (mtp) REVERT: A 406 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7456 (p0) REVERT: B 172 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 101 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (mp) REVERT: C 236 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6761 (mmp) REVERT: J 13 GLU cc_start: 0.8297 (tt0) cc_final: 0.8068 (tt0) REVERT: E 79 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: E 112 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8668 (mtt180) REVERT: I 227 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.5830 (mp) REVERT: I 316 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: I 406 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7521 (p0) REVERT: G 101 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8466 (mp) REVERT: G 240 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: K 48 LYS cc_start: 0.6671 (ptpt) cc_final: 0.6370 (pmtt) REVERT: K 101 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8254 (mp) REVERT: K 196 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8027 (tttm) REVERT: K 240 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7261 (m-80) outliers start: 66 outliers final: 29 residues processed: 302 average time/residue: 0.7837 time to fit residues: 266.2693 Evaluate side-chains 276 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 165 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 226 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 205 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118897 restraints weight = 25364.290| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.45 r_work: 0.3417 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23142 Z= 0.141 Angle : 0.601 12.046 31314 Z= 0.312 Chirality : 0.045 0.186 3207 Planarity : 0.005 0.045 3732 Dihedral : 18.657 169.669 4172 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.47 % Rotamer: Outliers : 2.38 % Allowed : 19.16 % Favored : 78.46 % 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 aren not related in a simple way. whole: 0.64 (0.16), residues: 2559 helix: 1.04 (0.14), residues: 1209 sheet: 0.72 (0.28), residues: 336 loop : -0.33 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 57 TYR 0.019 0.002 TYR K 184 PHE 0.014 0.001 PHE B 31 TRP 0.017 0.002 TRP I 206 HIS 0.003 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00307 (23142) covalent geometry : angle 0.60123 (31314) hydrogen bonds : bond 0.04655 ( 1119) hydrogen bonds : angle 5.24072 ( 3285) ********************** 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 291 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 239 time to evaluate : 0.913 Fit side-chains REVERT: A 45 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6111 (mtp85) REVERT: A 79 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: A 112 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8618 (mtt180) REVERT: A 249 MET cc_start: 0.8420 (mtp) cc_final: 0.8018 (mtp) REVERT: B 172 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 101 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8279 (mp) REVERT: C 236 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6635 (mmp) REVERT: J 13 GLU cc_start: 0.8335 (tt0) cc_final: 0.8075 (tt0) REVERT: E 79 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: I 45 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.6108 (mtp85) REVERT: I 227 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5822 (mp) REVERT: I 316 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7811 (tm-30) REVERT: I 406 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7467 (p0) REVERT: G 101 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8435 (mp) REVERT: G 240 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: K 48 LYS cc_start: 0.6649 (ptpt) cc_final: 0.6355 (pmtt) REVERT: K 101 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8209 (mp) REVERT: K 196 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8022 (tttm) REVERT: K 240 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7210 (m-80) outliers start: 52 outliers final: 31 residues processed: 281 average time/residue: 0.7353 time to fit residues: 232.5349 Evaluate side-chains 277 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 231 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 195 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 283 SER Chi-restraints excluded: chain I residue 316 GLU Chi-restraints excluded: chain I residue 406 ASP Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 204 optimal weight: 5.9990 chunk 252 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 16 GLN ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN E 108 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.115368 restraints weight = 25162.564| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.44 r_work: 0.3370 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23142 Z= 0.211 Angle : 0.655 12.140 31314 Z= 0.344 Chirality : 0.048 0.195 3207 Planarity : 0.005 0.046 3732 Dihedral : 18.839 177.891 4172 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.49 % Favored : 95.27 % Rotamer: Outliers : 2.65 % Allowed : 18.84 % Favored : 78.51 % 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 aren not related in a simple way. whole: 0.49 (0.16), residues: 2559 helix: 0.83 (0.14), residues: 1218 sheet: 0.70 (0.28), residues: 336 loop : -0.31 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 57 TYR 0.020 0.002 TYR J 188 PHE 0.018 0.002 PHE F 31 TRP 0.022 0.002 TRP I 206 HIS 0.006 0.001 HIS E 192 Details of bonding type rmsd covalent geometry : bond 0.00475 (23142) covalent geometry : angle 0.65462 (31314) hydrogen bonds : bond 0.05205 ( 1119) hydrogen bonds : angle 5.41673 ( 3285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9000.36 seconds wall clock time: 153 minutes 55.59 seconds (9235.59 seconds total)