Starting phenix.real_space_refine on Tue Aug 26 22:20:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr1_40717/08_2025/8sr1_40717.map" } resolution = 2.18 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= 0.004 sd= 0.036 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 15042 2.51 5 N 3417 2.21 5 O 4248 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: 22854 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: "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: "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: "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: "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: "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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "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: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 323 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} 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: "J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 4.22, per 1000 atoms: 0.18 Number of scatterers: 22854 At special positions: 0 Unit cell: (107.936, 107.936, 120.635, 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 4248 8.00 N 3417 7.00 C 15042 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: 2.12 Conformation dependent library (CDL) restraints added in 692.2 milliseconds Enol-peptide restraints added in 715.3 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 52.5% 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: 3.670A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.672A 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: 3.958A 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: 3.624A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 114 Processing helix chain 'C' and resid 123 through 150 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 179 through 199 Processing helix chain 'C' and resid 207 through 230 Proline residue: C 217 - end of helix removed outlier: 3.579A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.662A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.698A 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 '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: 3.670A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.671A 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: 4.110A 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: 3.766A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (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: 3.670A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 43 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.673A 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: 3.957A 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: 4.108A 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: 3.765A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (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 161 Processing helix chain 'G' and resid 170 through 176 Processing helix chain 'G' and resid 179 through 199 Processing helix chain 'G' and resid 207 through 230 Proline residue: G 217 - end of helix removed outlier: 3.578A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.661A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.698A 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: 3.625A pdb=" N GLU K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 114 Processing helix chain 'K' and resid 123 through 150 Processing helix chain 'K' and resid 150 through 161 Processing helix chain 'K' and resid 170 through 176 Processing helix chain 'K' and resid 179 through 199 Processing helix chain 'K' and resid 207 through 230 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: 4.342A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.662A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.456A 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: 3.698A 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: 4.483A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.682A 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: 6.670A 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: 3.829A 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: 5.813A 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: 5.692A 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: 5.558A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.333A 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: 6.555A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.448A 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 'E' and resid 47 through 54 removed outlier: 4.296A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.667A 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: 6.652A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.671A pdb=" N VAL E 144 " --> pdb=" O PRO E 149 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE E 151 " --> pdb=" O MET E 142 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET E 142 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 140 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB1, first strand: chain 'E' and resid 346 through 348 removed outlier: 5.813A 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: 4.497A 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: 5.693A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.257A 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: 9.675A 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: 7.333A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.555A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AB4, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.295A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.671A 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: 6.784A 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=AB6, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'I' and resid 346 through 348 removed outlier: 5.813A 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: 4.498A 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: 5.692A 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: 5.558A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.333A 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=AB8, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.556A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.295A 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) Processing sheet with id=AB9, first strand: chain 'J' and resid 170 through 173 1107 hydrogen bonds defined for protein. 3249 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: 2.74 Time building geometry restraints manager: 2.62 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: 3312 1.32 - 1.44: 6811 1.44 - 1.57: 12712 1.57 - 1.69: 133 1.69 - 1.81: 180 Bond restraints: 23148 Sorted by residual: bond pdb=" CE1 HIS C 231 " pdb=" NE2 HIS C 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" CE1 HIS G 231 " pdb=" NE2 HIS G 231 " ideal model delta sigma weight residual 1.321 1.393 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" CE1 HIS K 231 " pdb=" NE2 HIS K 231 " ideal model delta sigma weight residual 1.321 1.392 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" CG HIS G 245 " pdb=" ND1 HIS G 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.95e+01 bond pdb=" CG HIS C 245 " pdb=" ND1 HIS C 245 " ideal model delta sigma weight residual 1.378 1.455 -0.077 1.10e-02 8.26e+03 4.91e+01 ... (remaining 23143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 30020 2.43 - 4.86: 1020 4.86 - 7.29: 167 7.29 - 9.73: 92 9.73 - 12.16: 21 Bond angle restraints: 31320 Sorted by residual: angle pdb=" CA HIS K 160 " pdb=" CB HIS K 160 " pdb=" CG HIS K 160 " ideal model delta sigma weight residual 113.80 105.68 8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA HIS G 160 " pdb=" CB HIS G 160 " pdb=" CG HIS G 160 " ideal model delta sigma weight residual 113.80 105.69 8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" CA HIS C 160 " pdb=" CB HIS C 160 " pdb=" CG HIS C 160 " ideal model delta sigma weight residual 113.80 105.71 8.09 1.00e+00 1.00e+00 6.55e+01 angle pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " pdb=" CD2 HIS K 173 " ideal model delta sigma weight residual 131.20 121.90 9.30 1.30e+00 5.92e-01 5.12e+01 angle pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " pdb=" CD2 HIS G 173 " ideal model delta sigma weight residual 131.20 121.93 9.27 1.30e+00 5.92e-01 5.09e+01 ... (remaining 31315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12587 34.45 - 68.89: 823 68.89 - 103.34: 104 103.34 - 137.79: 34 137.79 - 172.24: 12 Dihedral angle restraints: 13560 sinusoidal: 6108 harmonic: 7452 Sorted by residual: dihedral pdb=" CD ARG G 165 " pdb=" NE ARG G 165 " pdb=" CZ ARG G 165 " pdb=" NH1 ARG G 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.06e+01 dihedral pdb=" CD ARG C 165 " pdb=" NE ARG C 165 " pdb=" CZ ARG C 165 " pdb=" NH1 ARG C 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.33 -68.33 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CD ARG K 165 " pdb=" NE ARG K 165 " pdb=" CZ ARG K 165 " pdb=" NH1 ARG K 165 " ideal model delta sinusoidal sigma weight residual 0.00 68.29 -68.29 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 13557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2337 0.049 - 0.097: 635 0.097 - 0.146: 178 0.146 - 0.194: 38 0.194 - 0.243: 19 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC G 308 " pdb=" C1 PLC G 308 " pdb=" C3 PLC G 308 " pdb=" O2 PLC G 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C2 PLC K 308 " pdb=" C1 PLC K 308 " pdb=" C3 PLC K 308 " pdb=" O2 PLC K 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 165 " -0.939 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG G 165 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG C 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 165 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 165 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.09e+02 pdb=" NE ARG K 165 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG K 165 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG K 165 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 165 " -0.015 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 149 2.42 - 3.04: 14488 3.04 - 3.66: 37938 3.66 - 4.28: 61870 4.28 - 4.90: 98877 Nonbonded interactions: 213322 Sorted by model distance: nonbonded pdb=" CA GLU K 238 " pdb=" F1 WIY K 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU G 238 " pdb=" F1 WIY G 311 " model vdw 1.795 3.420 nonbonded pdb=" CA GLU C 238 " pdb=" F1 WIY C 310 " model vdw 1.795 3.420 nonbonded pdb=" NH2 ARG K 165 " pdb=" F2 WIY K 311 " model vdw 1.836 3.070 nonbonded pdb=" NH2 ARG C 165 " pdb=" F2 WIY C 310 " model vdw 1.836 3.070 ... (remaining 213317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.380 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 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 23148 Z= 0.500 Angle : 1.096 12.158 31320 Z= 0.571 Chirality : 0.052 0.243 3207 Planarity : 0.013 0.421 3732 Dihedral : 22.782 172.235 8802 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.02 % Favored : 93.51 % Rotamer: Outliers : 3.93 % Allowed : 17.60 % 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: 0.61 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1191 sheet: 1.30 (0.28), residues: 357 loop : -0.63 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 165 TYR 0.022 0.001 TYR C 184 PHE 0.015 0.002 PHE B 31 TRP 0.017 0.002 TRP I 202 HIS 0.023 0.003 HIS K 160 Details of bonding type rmsd covalent geometry : bond 0.00892 (23148) covalent geometry : angle 1.09561 (31320) hydrogen bonds : bond 0.11863 ( 1107) hydrogen bonds : angle 6.36956 ( 3249) *********************** 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 448 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 362 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7769 (mmp) cc_final: 0.7484 (mmm) REVERT: B 45 MET cc_start: 0.7151 (ppp) cc_final: 0.6480 (ppp) REVERT: B 93 VAL cc_start: 0.7692 (t) cc_final: 0.7446 (p) REVERT: B 206 ARG cc_start: 0.6551 (mmm160) cc_final: 0.6174 (mtp-110) REVERT: C 90 MET cc_start: 0.6069 (mmm) cc_final: 0.5729 (mmp) REVERT: C 155 GLN cc_start: 0.7210 (tt0) cc_final: 0.6980 (tt0) REVERT: C 165 ARG cc_start: 0.3797 (OUTLIER) cc_final: 0.3230 (ttt180) REVERT: C 207 SER cc_start: 0.7747 (OUTLIER) cc_final: 0.7479 (p) REVERT: E 145 GLN cc_start: 0.7107 (tp-100) cc_final: 0.6905 (tp40) REVERT: E 248 VAL cc_start: 0.7947 (t) cc_final: 0.7740 (m) REVERT: E 256 SER cc_start: 0.7133 (OUTLIER) cc_final: 0.6811 (p) REVERT: E 272 MET cc_start: 0.7755 (mmp) cc_final: 0.7355 (mmp) REVERT: F 93 VAL cc_start: 0.7609 (t) cc_final: 0.7340 (t) REVERT: F 223 MET cc_start: 0.8089 (mmm) cc_final: 0.7755 (mmm) REVERT: I 272 MET cc_start: 0.7688 (mmp) cc_final: 0.7435 (mmp) REVERT: J 223 MET cc_start: 0.7819 (mmm) cc_final: 0.7442 (mmm) REVERT: K 90 MET cc_start: 0.5794 (mmm) cc_final: 0.5586 (mmp) REVERT: K 97 ILE cc_start: 0.7020 (mt) cc_final: 0.6793 (mm) REVERT: K 238 GLU cc_start: 0.3372 (OUTLIER) cc_final: 0.2934 (mm-30) outliers start: 86 outliers final: 24 residues processed: 438 average time/residue: 0.5504 time to fit residues: 275.3318 Evaluate side-chains 296 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 165 ARG Chi-restraints excluded: chain G residue 238 GLU 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 164 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 238 GLU 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: 20.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 91 ASN ** G 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.193879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.167626 restraints weight = 28100.698| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.22 r_work: 0.4078 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23148 Z= 0.251 Angle : 0.788 7.886 31320 Z= 0.405 Chirality : 0.050 0.332 3207 Planarity : 0.006 0.051 3732 Dihedral : 22.221 179.791 4224 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.02 % Favored : 93.75 % Rotamer: Outliers : 4.12 % Allowed : 19.16 % Favored : 76.73 % 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: 0.54 (0.17), residues: 2559 helix: 0.78 (0.15), residues: 1254 sheet: 0.59 (0.28), residues: 381 loop : -0.15 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 299 TYR 0.021 0.003 TYR C 184 PHE 0.033 0.003 PHE F 243 TRP 0.033 0.003 TRP K 234 HIS 0.008 0.002 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00536 (23148) covalent geometry : angle 0.78800 (31320) hydrogen bonds : bond 0.05402 ( 1107) hydrogen bonds : angle 5.63571 ( 3249) *********************** 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 367 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 277 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7177 (pp30) cc_final: 0.6969 (pp30) REVERT: B 59 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 152 TRP cc_start: 0.8804 (OUTLIER) cc_final: 0.6395 (t-100) REVERT: B 206 ARG cc_start: 0.6956 (mmm160) cc_final: 0.6719 (mmm160) REVERT: C 90 MET cc_start: 0.5261 (mmm) cc_final: 0.4879 (mmp) REVERT: C 244 LEU cc_start: 0.3928 (OUTLIER) cc_final: 0.3543 (pt) REVERT: F 136 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (ttp) REVERT: F 223 MET cc_start: 0.8511 (mmm) cc_final: 0.8187 (mmm) REVERT: J 223 MET cc_start: 0.8444 (mmm) cc_final: 0.8040 (mmm) REVERT: G 165 ARG cc_start: 0.3458 (OUTLIER) cc_final: 0.2474 (mmm-85) REVERT: G 244 LEU cc_start: 0.3878 (OUTLIER) cc_final: 0.3432 (pt) REVERT: G 248 PHE cc_start: 0.6365 (m-80) cc_final: 0.5711 (m-80) REVERT: K 90 MET cc_start: 0.4973 (mmm) cc_final: 0.4707 (mmp) REVERT: K 97 ILE cc_start: 0.6496 (mt) cc_final: 0.6161 (mm) REVERT: K 156 ASP cc_start: 0.6958 (t70) cc_final: 0.6488 (t70) outliers start: 90 outliers final: 28 residues processed: 351 average time/residue: 0.5666 time to fit residues: 226.0188 Evaluate side-chains 276 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 165 ARG Chi-restraints excluded: chain G residue 166 ASP 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 164 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 241 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 174 ASN C 155 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 155 GLN K 155 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.192138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.165995 restraints weight = 28040.186| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.22 r_work: 0.4055 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23148 Z= 0.229 Angle : 0.722 9.214 31320 Z= 0.375 Chirality : 0.048 0.233 3207 Planarity : 0.005 0.051 3732 Dihedral : 21.333 179.548 4191 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 3.48 % Allowed : 19.25 % Favored : 77.27 % 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: 0.45 (0.17), residues: 2559 helix: 0.80 (0.15), residues: 1245 sheet: 0.49 (0.28), residues: 357 loop : -0.30 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 198 TYR 0.025 0.003 TYR C 184 PHE 0.025 0.002 PHE B 31 TRP 0.021 0.002 TRP J 231 HIS 0.010 0.002 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00500 (23148) covalent geometry : angle 0.72165 (31320) hydrogen bonds : bond 0.05353 ( 1107) hydrogen bonds : angle 5.58471 ( 3249) *********************** 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 341 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.844 Fit side-chains REVERT: A 108 GLN cc_start: 0.7148 (pp30) cc_final: 0.6948 (pp30) REVERT: B 152 TRP cc_start: 0.8796 (OUTLIER) cc_final: 0.6255 (t-100) REVERT: B 206 ARG cc_start: 0.6960 (mmm160) cc_final: 0.6296 (mmm160) REVERT: B 211 ASP cc_start: 0.6864 (p0) cc_final: 0.6568 (p0) REVERT: C 90 MET cc_start: 0.5332 (mmm) cc_final: 0.4839 (mmp) REVERT: C 117 ARG cc_start: 0.8279 (tpp-160) cc_final: 0.7990 (mmm160) REVERT: C 244 LEU cc_start: 0.4200 (OUTLIER) cc_final: 0.3895 (pp) REVERT: C 259 MET cc_start: 0.7902 (mtm) cc_final: 0.7531 (mtm) REVERT: F 152 TRP cc_start: 0.8738 (OUTLIER) cc_final: 0.6208 (t-100) REVERT: I 44 MET cc_start: 0.8388 (mtt) cc_final: 0.8064 (mtt) REVERT: J 152 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.6031 (t-100) REVERT: J 206 ARG cc_start: 0.6761 (mtp180) cc_final: 0.6400 (mtp180) REVERT: J 223 MET cc_start: 0.8360 (mmm) cc_final: 0.8105 (mmm) REVERT: J 226 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8535 (tp) REVERT: G 244 LEU cc_start: 0.4368 (OUTLIER) cc_final: 0.3970 (pt) REVERT: G 248 PHE cc_start: 0.6406 (m-80) cc_final: 0.5895 (m-80) REVERT: K 97 ILE cc_start: 0.6373 (mt) cc_final: 0.6106 (mm) REVERT: K 118 ASN cc_start: 0.8568 (t0) cc_final: 0.8114 (t0) REVERT: K 156 ASP cc_start: 0.7015 (t70) cc_final: 0.6586 (t70) REVERT: K 166 ASP cc_start: 0.4284 (OUTLIER) cc_final: 0.3415 (t0) outliers start: 76 outliers final: 34 residues processed: 326 average time/residue: 0.5588 time to fit residues: 208.7740 Evaluate side-chains 283 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 226 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 221 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN B 174 ASN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.195962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.172548 restraints weight = 28089.947| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.09 r_work: 0.4143 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23148 Z= 0.173 Angle : 0.664 7.197 31320 Z= 0.343 Chirality : 0.046 0.247 3207 Planarity : 0.005 0.048 3732 Dihedral : 20.782 178.051 4181 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.92 % Favored : 94.84 % Rotamer: Outliers : 3.43 % Allowed : 19.48 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1239 sheet: 0.32 (0.27), residues: 375 loop : -0.22 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 57 TYR 0.024 0.002 TYR C 184 PHE 0.023 0.002 PHE K 248 TRP 0.019 0.002 TRP E 206 HIS 0.006 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00369 (23148) covalent geometry : angle 0.66415 (31320) hydrogen bonds : bond 0.04918 ( 1107) hydrogen bonds : angle 5.42299 ( 3249) *********************** 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 333 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 0.709 Fit side-chains REVERT: B 59 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 152 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.6296 (t-100) REVERT: B 206 ARG cc_start: 0.6938 (mmm160) cc_final: 0.6539 (mmm160) REVERT: C 90 MET cc_start: 0.5466 (mmm) cc_final: 0.4964 (mmp) REVERT: C 118 ASN cc_start: 0.8432 (t0) cc_final: 0.8107 (t0) REVERT: C 259 MET cc_start: 0.7667 (mtm) cc_final: 0.7373 (mtm) REVERT: I 44 MET cc_start: 0.8303 (mtt) cc_final: 0.7993 (mtt) REVERT: I 272 MET cc_start: 0.8089 (mmp) cc_final: 0.7288 (mpp) REVERT: I 375 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7560 (mtp-110) REVERT: J 152 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.6106 (t-100) REVERT: J 206 ARG cc_start: 0.6711 (mtp180) cc_final: 0.6280 (mtp180) REVERT: J 223 MET cc_start: 0.8262 (mmm) cc_final: 0.8012 (mmm) REVERT: G 244 LEU cc_start: 0.4849 (OUTLIER) cc_final: 0.4414 (pt) REVERT: G 248 PHE cc_start: 0.6428 (m-80) cc_final: 0.5909 (m-80) REVERT: K 97 ILE cc_start: 0.6615 (mt) cc_final: 0.6347 (mm) REVERT: K 118 ASN cc_start: 0.8548 (t0) cc_final: 0.8293 (t0) REVERT: K 156 ASP cc_start: 0.7060 (t70) cc_final: 0.6686 (t70) REVERT: K 238 GLU cc_start: 0.4838 (OUTLIER) cc_final: 0.4030 (mp0) outliers start: 75 outliers final: 38 residues processed: 325 average time/residue: 0.5604 time to fit residues: 208.1055 Evaluate side-chains 288 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP 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 164 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.195019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.171687 restraints weight = 27944.020| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 1.09 r_work: 0.4132 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23148 Z= 0.187 Angle : 0.684 7.392 31320 Z= 0.353 Chirality : 0.046 0.225 3207 Planarity : 0.005 0.063 3732 Dihedral : 20.276 174.609 4181 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 3.61 % Allowed : 18.88 % Favored : 77.50 % 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: 0.56 (0.17), residues: 2559 helix: 0.90 (0.14), residues: 1239 sheet: 0.54 (0.28), residues: 357 loop : -0.25 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 57 TYR 0.025 0.002 TYR C 184 PHE 0.026 0.002 PHE C 248 TRP 0.021 0.002 TRP E 206 HIS 0.010 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00407 (23148) covalent geometry : angle 0.68384 (31320) hydrogen bonds : bond 0.04993 ( 1107) hydrogen bonds : angle 5.44634 ( 3249) *********************** 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 334 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 255 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8522 (mm) REVERT: B 152 TRP cc_start: 0.8738 (OUTLIER) cc_final: 0.6301 (t-100) REVERT: B 211 ASP cc_start: 0.6850 (p0) cc_final: 0.6556 (p0) REVERT: C 90 MET cc_start: 0.5523 (mmm) cc_final: 0.5030 (mmp) REVERT: C 118 ASN cc_start: 0.8391 (t0) cc_final: 0.8173 (t0) REVERT: C 259 MET cc_start: 0.7704 (mtm) cc_final: 0.7389 (mtm) REVERT: F 136 MET cc_start: 0.7999 (ttt) cc_final: 0.7725 (ttp) REVERT: F 152 TRP cc_start: 0.8708 (OUTLIER) cc_final: 0.6257 (t-100) REVERT: F 212 VAL cc_start: 0.8512 (t) cc_final: 0.8177 (p) REVERT: I 44 MET cc_start: 0.8321 (mtt) cc_final: 0.8045 (mtt) REVERT: I 272 MET cc_start: 0.8131 (mmp) cc_final: 0.7276 (mpp) REVERT: J 152 TRP cc_start: 0.8719 (OUTLIER) cc_final: 0.6093 (t-100) REVERT: G 244 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4242 (pt) REVERT: G 248 PHE cc_start: 0.6447 (m-80) cc_final: 0.5969 (m-80) REVERT: K 97 ILE cc_start: 0.6658 (mt) cc_final: 0.6393 (mm) REVERT: K 118 ASN cc_start: 0.8563 (t0) cc_final: 0.8340 (t0) REVERT: K 166 ASP cc_start: 0.4203 (OUTLIER) cc_final: 0.3603 (t70) REVERT: K 238 GLU cc_start: 0.4894 (OUTLIER) cc_final: 0.4447 (tp30) outliers start: 79 outliers final: 45 residues processed: 326 average time/residue: 0.5431 time to fit residues: 202.6817 Evaluate side-chains 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 241 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 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 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 238 GLU Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 68 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 233 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 33 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN G 155 GLN ** G 173 HIS ** 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 = 0.4507 r_free = 0.4507 target = 0.192994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.169466 restraints weight = 28288.452| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.14 r_work: 0.4097 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23148 Z= 0.255 Angle : 0.748 7.702 31320 Z= 0.390 Chirality : 0.049 0.228 3207 Planarity : 0.005 0.051 3732 Dihedral : 20.079 172.273 4181 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.24 % Favored : 94.53 % Rotamer: Outliers : 3.48 % Allowed : 19.84 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2559 helix: 0.72 (0.14), residues: 1263 sheet: 0.40 (0.28), residues: 366 loop : -0.29 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 208 TYR 0.026 0.003 TYR C 184 PHE 0.030 0.003 PHE C 248 TRP 0.022 0.002 TRP J 231 HIS 0.010 0.002 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00563 (23148) covalent geometry : angle 0.74805 (31320) hydrogen bonds : bond 0.05400 ( 1107) hydrogen bonds : angle 5.64119 ( 3249) *********************** 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 331 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 255 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: B 152 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.6327 (t-100) REVERT: B 211 ASP cc_start: 0.6821 (p0) cc_final: 0.6556 (p0) REVERT: C 90 MET cc_start: 0.5460 (mmm) cc_final: 0.4970 (mmp) REVERT: C 259 MET cc_start: 0.7740 (mtm) cc_final: 0.7425 (mtm) REVERT: F 136 MET cc_start: 0.8110 (ttt) cc_final: 0.7818 (ttp) REVERT: F 152 TRP cc_start: 0.8704 (OUTLIER) cc_final: 0.6241 (t-100) REVERT: I 79 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6646 (pm20) REVERT: I 272 MET cc_start: 0.8167 (mmp) cc_final: 0.7224 (mpp) REVERT: J 152 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.6027 (t-100) REVERT: G 244 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4439 (pt) REVERT: G 248 PHE cc_start: 0.6491 (m-80) cc_final: 0.6169 (m-80) REVERT: K 81 PHE cc_start: 0.7035 (m-80) cc_final: 0.6527 (m-80) REVERT: K 97 ILE cc_start: 0.6628 (mt) cc_final: 0.6374 (mm) REVERT: K 156 ASP cc_start: 0.7197 (t70) cc_final: 0.6648 (t0) REVERT: K 161 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.5809 (mp10) outliers start: 76 outliers final: 44 residues processed: 322 average time/residue: 0.5381 time to fit residues: 197.9993 Evaluate side-chains 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 161 GLN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 19 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 72 HIS I 176 GLN J 16 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.195397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.172285 restraints weight = 27890.147| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.08 r_work: 0.4140 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4039 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23148 Z= 0.160 Angle : 0.676 9.390 31320 Z= 0.346 Chirality : 0.046 0.218 3207 Planarity : 0.005 0.049 3732 Dihedral : 19.601 170.374 4181 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 3.48 % Allowed : 20.39 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1242 sheet: 0.53 (0.27), residues: 387 loop : -0.31 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 208 TYR 0.024 0.002 TYR C 184 PHE 0.033 0.002 PHE C 248 TRP 0.021 0.002 TRP E 206 HIS 0.010 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00348 (23148) covalent geometry : angle 0.67650 (31320) hydrogen bonds : bond 0.04812 ( 1107) hydrogen bonds : angle 5.42762 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 251 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8498 (mm) REVERT: B 152 TRP cc_start: 0.8688 (OUTLIER) cc_final: 0.6307 (t-100) REVERT: B 211 ASP cc_start: 0.6796 (p0) cc_final: 0.6515 (p0) REVERT: C 90 MET cc_start: 0.5496 (mmm) cc_final: 0.5021 (mmp) REVERT: C 259 MET cc_start: 0.7779 (mtm) cc_final: 0.7490 (mtm) REVERT: E 249 MET cc_start: 0.6895 (ppp) cc_final: 0.6609 (ppp) REVERT: F 136 MET cc_start: 0.8010 (ttt) cc_final: 0.7735 (ttp) REVERT: I 272 MET cc_start: 0.8104 (mmp) cc_final: 0.7117 (mpp) REVERT: J 152 TRP cc_start: 0.8701 (OUTLIER) cc_final: 0.6120 (t-100) REVERT: J 206 ARG cc_start: 0.6746 (mtp180) cc_final: 0.6291 (mtp180) REVERT: G 244 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4470 (pt) REVERT: G 248 PHE cc_start: 0.6477 (m-80) cc_final: 0.6090 (m-80) REVERT: K 81 PHE cc_start: 0.6932 (m-80) cc_final: 0.6513 (m-80) REVERT: K 97 ILE cc_start: 0.6686 (mt) cc_final: 0.6412 (mm) REVERT: K 156 ASP cc_start: 0.7100 (t70) cc_final: 0.6548 (t70) REVERT: K 166 ASP cc_start: 0.4049 (OUTLIER) cc_final: 0.3574 (t70) outliers start: 76 outliers final: 41 residues processed: 313 average time/residue: 0.5253 time to fit residues: 188.2065 Evaluate side-chains 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 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 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 221 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.196126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.168885 restraints weight = 28182.161| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.25 r_work: 0.4198 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4101 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23148 Z= 0.180 Angle : 0.694 8.348 31320 Z= 0.357 Chirality : 0.047 0.212 3207 Planarity : 0.005 0.081 3732 Dihedral : 19.336 169.431 4181 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.77 % Favored : 95.00 % Rotamer: Outliers : 3.16 % Allowed : 20.76 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2559 helix: 0.91 (0.15), residues: 1242 sheet: 0.51 (0.28), residues: 357 loop : -0.31 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 208 TYR 0.025 0.002 TYR C 184 PHE 0.027 0.002 PHE K 248 TRP 0.018 0.002 TRP I 206 HIS 0.010 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00396 (23148) covalent geometry : angle 0.69432 (31320) hydrogen bonds : bond 0.04932 ( 1107) hydrogen bonds : angle 5.44358 ( 3249) *********************** 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 317 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8516 (mm) REVERT: B 152 TRP cc_start: 0.8701 (OUTLIER) cc_final: 0.6320 (t-100) REVERT: B 211 ASP cc_start: 0.6753 (p0) cc_final: 0.6467 (p0) REVERT: C 90 MET cc_start: 0.5854 (mmm) cc_final: 0.5396 (mmp) REVERT: C 173 HIS cc_start: 0.7446 (m-70) cc_final: 0.6785 (m90) REVERT: C 243 PRO cc_start: 0.5192 (Cg_exo) cc_final: 0.4736 (Cg_endo) REVERT: C 259 MET cc_start: 0.7678 (mtm) cc_final: 0.7459 (mtm) REVERT: F 136 MET cc_start: 0.7967 (ttt) cc_final: 0.7652 (ttp) REVERT: F 152 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.6262 (t-100) REVERT: F 212 VAL cc_start: 0.8516 (t) cc_final: 0.8240 (p) REVERT: I 272 MET cc_start: 0.8057 (mmp) cc_final: 0.7044 (mpp) REVERT: J 152 TRP cc_start: 0.8697 (OUTLIER) cc_final: 0.6109 (t-100) REVERT: J 206 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6578 (mtp180) REVERT: G 244 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4852 (pt) REVERT: K 81 PHE cc_start: 0.7099 (m-80) cc_final: 0.6617 (m-80) REVERT: K 97 ILE cc_start: 0.6968 (mt) cc_final: 0.6737 (mm) REVERT: K 156 ASP cc_start: 0.7141 (t70) cc_final: 0.6631 (t70) REVERT: K 161 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5774 (mp10) REVERT: K 166 ASP cc_start: 0.4048 (OUTLIER) cc_final: 0.3672 (t70) outliers start: 69 outliers final: 43 residues processed: 308 average time/residue: 0.5163 time to fit residues: 182.8873 Evaluate side-chains 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 245 GLN Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 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 161 GLN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 173 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.194898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.171537 restraints weight = 28000.138| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.15 r_work: 0.4125 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23148 Z= 0.181 Angle : 0.700 9.228 31320 Z= 0.359 Chirality : 0.047 0.209 3207 Planarity : 0.005 0.059 3732 Dihedral : 19.113 168.234 4181 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 2.74 % Allowed : 21.17 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2559 helix: 0.91 (0.15), residues: 1242 sheet: 0.52 (0.28), residues: 357 loop : -0.31 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 208 TYR 0.026 0.002 TYR A 381 PHE 0.043 0.002 PHE G 248 TRP 0.019 0.002 TRP E 206 HIS 0.009 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00396 (23148) covalent geometry : angle 0.69965 (31320) hydrogen bonds : bond 0.04913 ( 1107) hydrogen bonds : angle 5.44134 ( 3249) *********************** 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 313 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 ARG cc_start: 0.7931 (mtp85) cc_final: 0.7709 (ptm160) REVERT: B 59 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8502 (mm) REVERT: B 152 TRP cc_start: 0.8706 (OUTLIER) cc_final: 0.6298 (t-100) REVERT: B 211 ASP cc_start: 0.6801 (p0) cc_final: 0.6510 (p0) REVERT: C 90 MET cc_start: 0.5423 (mmm) cc_final: 0.4955 (mmp) REVERT: C 173 HIS cc_start: 0.7108 (m-70) cc_final: 0.6379 (m90) REVERT: C 243 PRO cc_start: 0.4685 (Cg_exo) cc_final: 0.4218 (Cg_endo) REVERT: C 259 MET cc_start: 0.7763 (mtm) cc_final: 0.7475 (mtm) REVERT: E 249 MET cc_start: 0.6886 (ppp) cc_final: 0.6630 (ppp) REVERT: F 136 MET cc_start: 0.8051 (ttt) cc_final: 0.7742 (ttp) REVERT: F 152 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.6238 (t-100) REVERT: I 272 MET cc_start: 0.8142 (mmp) cc_final: 0.7131 (mpp) REVERT: J 152 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.6108 (t-100) REVERT: J 206 ARG cc_start: 0.6724 (mtp180) cc_final: 0.6286 (mtp180) REVERT: G 244 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4352 (pt) REVERT: K 81 PHE cc_start: 0.7043 (m-80) cc_final: 0.6578 (m-80) REVERT: K 97 ILE cc_start: 0.6627 (mt) cc_final: 0.6357 (mm) REVERT: K 156 ASP cc_start: 0.7119 (t70) cc_final: 0.6531 (t70) REVERT: K 161 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.5744 (mp10) REVERT: K 166 ASP cc_start: 0.4122 (OUTLIER) cc_final: 0.3606 (t70) REVERT: K 173 HIS cc_start: 0.6637 (m170) cc_final: 0.6268 (m170) outliers start: 60 outliers final: 41 residues processed: 303 average time/residue: 0.5313 time to fit residues: 184.1487 Evaluate side-chains 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 245 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 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 161 GLN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 179 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.195204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.171942 restraints weight = 28105.633| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.09 r_work: 0.4224 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23148 Z= 0.171 Angle : 0.702 10.826 31320 Z= 0.358 Chirality : 0.047 0.206 3207 Planarity : 0.005 0.060 3732 Dihedral : 18.904 167.253 4180 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 2.42 % Allowed : 21.72 % Favored : 75.86 % 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: 0.54 (0.17), residues: 2559 helix: 0.93 (0.15), residues: 1242 sheet: 0.53 (0.28), residues: 357 loop : -0.32 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 208 TYR 0.025 0.002 TYR C 184 PHE 0.027 0.002 PHE K 248 TRP 0.018 0.002 TRP I 206 HIS 0.009 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00376 (23148) covalent geometry : angle 0.70154 (31320) hydrogen bonds : bond 0.04854 ( 1107) hydrogen bonds : angle 5.41501 ( 3249) ********************** 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 298 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8512 (mm) REVERT: B 152 TRP cc_start: 0.8635 (OUTLIER) cc_final: 0.6303 (t-100) REVERT: B 211 ASP cc_start: 0.6716 (p0) cc_final: 0.6450 (p0) REVERT: C 90 MET cc_start: 0.5990 (mmm) cc_final: 0.5548 (mmp) REVERT: C 173 HIS cc_start: 0.7415 (m-70) cc_final: 0.6860 (m90) REVERT: C 259 MET cc_start: 0.7606 (mtm) cc_final: 0.7318 (mtm) REVERT: E 249 MET cc_start: 0.6815 (ppp) cc_final: 0.6546 (ppp) REVERT: F 136 MET cc_start: 0.7865 (ttt) cc_final: 0.7545 (ttp) REVERT: F 152 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.6269 (t-100) REVERT: I 272 MET cc_start: 0.7980 (mmp) cc_final: 0.6947 (mpp) REVERT: J 152 TRP cc_start: 0.8672 (OUTLIER) cc_final: 0.6136 (t-100) REVERT: J 206 ARG cc_start: 0.6916 (mtp180) cc_final: 0.6558 (mtp180) REVERT: G 244 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.5026 (pt) REVERT: K 81 PHE cc_start: 0.7030 (m-80) cc_final: 0.6637 (m-80) REVERT: K 97 ILE cc_start: 0.7075 (mt) cc_final: 0.6862 (mm) REVERT: K 156 ASP cc_start: 0.7137 (t70) cc_final: 0.6675 (t70) REVERT: K 161 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5716 (mp10) REVERT: K 166 ASP cc_start: 0.4110 (OUTLIER) cc_final: 0.3800 (t70) REVERT: K 173 HIS cc_start: 0.6992 (m170) cc_final: 0.6728 (m90) outliers start: 53 outliers final: 38 residues processed: 291 average time/residue: 0.5483 time to fit residues: 182.6937 Evaluate side-chains 286 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 241 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 62 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 152 TRP Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 102 ILE Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 152 TRP Chi-restraints excluded: chain J residue 193 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 164 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 161 GLN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 66 optimal weight: 1.9990 chunk 209 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.195741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.172583 restraints weight = 27971.320| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 1.14 r_work: 0.4226 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23148 Z= 0.160 Angle : 0.692 11.176 31320 Z= 0.352 Chirality : 0.046 0.202 3207 Planarity : 0.005 0.055 3732 Dihedral : 18.697 166.282 4180 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 2.51 % Allowed : 21.67 % Favored : 75.81 % 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 (0.17), residues: 2559 helix: 0.88 (0.15), residues: 1260 sheet: 0.54 (0.28), residues: 357 loop : -0.39 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 208 TYR 0.025 0.002 TYR C 184 PHE 0.041 0.002 PHE G 248 TRP 0.018 0.002 TRP E 206 HIS 0.009 0.001 HIS K 245 Details of bonding type rmsd covalent geometry : bond 0.00350 (23148) covalent geometry : angle 0.69183 (31320) hydrogen bonds : bond 0.04741 ( 1107) hydrogen bonds : angle 5.36849 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7995.74 seconds wall clock time: 136 minutes 38.25 seconds (8198.25 seconds total)