Starting phenix.real_space_refine on Tue Jul 7 02:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr1_40717/07_2026/8sr1_40717_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr1_40717/07_2026/8sr1_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_40717/07_2026/8sr1_40717_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr1_40717/07_2026/8sr1_40717_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr1_40717/07_2026/8sr1_40717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr1_40717/07_2026/8sr1_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 322 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "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, 10 Ad-hoc single atom residues: {' CU': 2} Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 322 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 Chain: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 322 Ad-hoc single atom residues: {' CU': 1} Unusual residues: {'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4, 'WIY': 1} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 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: 4.79, per 1000 atoms: 0.21 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: 2.05 Conformation dependent library (CDL) restraints added in 991.7 milliseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 18 sheets defined 52.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 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: 4.79 Time building geometry restraints manager: 2.63 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: 0.02 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.910 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 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 are 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/Z covalent geometry : bond 0.00892 / 0.50 (23148) covalent geometry : angle 1.09561 / 0.57 (31320) hydrogen bonds : bond 0.11863 / 7.77 ( 1107) hydrogen bonds : angle 6.36956 / 4.51 ( 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 : 0.790 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: 0.7447 (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: 0.5730 (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: 0.6906 (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: 27 residues processed: 438 average time/residue: 0.6155 time to fit residues: 307.9320 Evaluate side-chains 299 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS 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 33 HIS Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 33 HIS 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: 6.9990 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: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 HIS ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 HIS I 176 GLN G 91 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 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 = 0.4519 r_free = 0.4519 target = 0.193139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166898 restraints weight = 28090.635| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.22 r_work: 0.4081 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2753 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= 0.241 Angle : 0.779 7.710 31320 Z= 0.401 Chirality : 0.050 0.317 3207 Planarity : 0.006 0.048 3732 Dihedral : 22.197 179.588 4230 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.06 % Favored : 93.79 % Rotamer: Outliers : 4.21 % Allowed : 18.98 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2559 helix: 0.77 (0.15), residues: 1254 sheet: 0.57 (0.28), residues: 381 loop : -0.18 (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 0.032 0.003 PHE F 243 TRP 0.034 0.003 TRP K 234 HIS 0.012 0.002 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (23148) covalent geometry : angle 0.77853 / 0.40 (31320) hydrogen bonds : bond 0.05471 / 3.73 ( 1107) hydrogen bonds : angle 5.64071 / 4.01 ( 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 369 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 277 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 108 GLN cc_start: 0.7184 (pp30) cc_final: 0.6971 (pp30) REVERT: B 9 ARG cc_start: 0.7482 (mmp-170) cc_final: 0.7263 (mmp80) REVERT: B 59 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8474 (mm) REVERT: B 152 TRP cc_start: 0.8806 (OUTLIER) cc_final: 0.6425 (t-100) REVERT: B 206 ARG cc_start: 0.6969 (mmm160) cc_final: 0.6731 (mmm160) REVERT: F 136 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (ttp) REVERT: F 223 MET cc_start: 0.8501 (mmm) cc_final: 0.8161 (mmm) REVERT: J 223 MET cc_start: 0.8438 (mmm) cc_final: 0.7984 (mmm) REVERT: G 227 ASN cc_start: 0.4857 (t0) cc_final: 0.4620 (t0) REVERT: G 244 LEU cc_start: 0.4012 (OUTLIER) cc_final: 0.3519 (pt) REVERT: G 248 PHE cc_start: 0.6322 (m-80) cc_final: 0.5545 (m-80) REVERT: K 90 MET cc_start: 0.4951 (mmm) cc_final: 0.4688 (mmp) REVERT: K 97 ILE cc_start: 0.6475 (mt) cc_final: 0.6139 (mm) outliers start: 92 outliers final: 29 residues processed: 351 average time/residue: 0.6049 time to fit residues: 241.9697 Evaluate side-chains 276 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 300 MET 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 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: 9.9990 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 HIS A 145 GLN C 155 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN E 72 HIS E 145 GLN F 174 ASN I 72 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN K 161 GLN ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.195715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168108 restraints weight = 28367.932| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.24 r_work: 0.4094 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23148 Z= 0.243 Angle : 0.742 9.525 31320 Z= 0.386 Chirality : 0.049 0.232 3207 Planarity : 0.005 0.049 3732 Dihedral : 21.320 178.503 4185 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.92 % Favored : 94.84 % Rotamer: Outliers : 3.48 % Allowed : 18.98 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2559 helix: 0.75 (0.15), residues: 1245 sheet: 0.37 (0.27), residues: 384 loop : -0.31 (0.21), residues: 930 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 0.027 0.003 PHE K 248 TRP 0.023 0.002 TRP J 231 HIS 0.012 0.002 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (23148) covalent geometry : angle 0.74236 / 0.39 (31320) hydrogen bonds : bond 0.05437 / 3.71 ( 1107) hydrogen bonds : angle 5.62890 / 3.99 ( 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 348 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 272 time to evaluate : 0.839 Fit side-chains REVERT: A 108 GLN cc_start: 0.7081 (pp30) cc_final: 0.6867 (pp30) REVERT: B 152 TRP cc_start: 0.8769 (OUTLIER) cc_final: 0.6234 (t-100) REVERT: B 206 ARG cc_start: 0.7021 (mmm160) cc_final: 0.6439 (mmm160) REVERT: C 90 MET cc_start: 0.5384 (mmm) cc_final: 0.5050 (mmp) REVERT: C 117 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8001 (mmm160) REVERT: F 49 ASP cc_start: 0.7767 (t0) cc_final: 0.7500 (t0) REVERT: F 152 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.6237 (t-100) REVERT: J 152 TRP cc_start: 0.8747 (OUTLIER) cc_final: 0.6018 (t-100) REVERT: J 206 ARG cc_start: 0.6950 (mtp180) cc_final: 0.6635 (mtp180) REVERT: J 223 MET cc_start: 0.8363 (mmm) cc_final: 0.8098 (mmm) REVERT: J 226 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8505 (tp) REVERT: G 118 ASN cc_start: 0.8234 (t0) cc_final: 0.7972 (t0) REVERT: G 248 PHE cc_start: 0.6614 (m-80) cc_final: 0.6094 (m-80) REVERT: K 90 MET cc_start: 0.5079 (mmm) cc_final: 0.4764 (mmp) REVERT: K 97 ILE cc_start: 0.6575 (mt) cc_final: 0.6320 (mm) REVERT: K 118 ASN cc_start: 0.8529 (t0) cc_final: 0.8160 (t0) REVERT: K 156 ASP cc_start: 0.7141 (t70) cc_final: 0.6411 (t70) REVERT: K 166 ASP cc_start: 0.4152 (OUTLIER) cc_final: 0.3452 (t0) outliers start: 76 outliers final: 36 residues processed: 331 average time/residue: 0.5764 time to fit residues: 219.0950 Evaluate side-chains 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 253 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 117 ARG Chi-restraints excluded: chain C residue 164 VAL 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 E residue 300 MET 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 I residue 381 TYR Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 59 LEU 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 87 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 221 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN I 33 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.196830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.169557 restraints weight = 28494.172| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.25 r_work: 0.4113 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23148 Z= 0.178 Angle : 0.672 7.165 31320 Z= 0.347 Chirality : 0.046 0.225 3207 Planarity : 0.005 0.046 3732 Dihedral : 20.748 176.612 4177 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 3.43 % Allowed : 19.25 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2559 helix: 0.87 (0.14), residues: 1242 sheet: 0.29 (0.27), residues: 375 loop : -0.25 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 167 TYR 0.024 0.002 TYR C 184 PHE 0.030 0.002 PHE C 248 TRP 0.019 0.002 TRP A 206 HIS 0.009 0.002 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (23148) covalent geometry : angle 0.67189 / 0.35 (31320) hydrogen bonds : bond 0.04954 / 3.39 ( 1107) hydrogen bonds : angle 5.45055 / 3.87 ( 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 338 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 263 time to evaluate : 0.856 Fit side-chains REVERT: B 59 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8521 (mm) REVERT: B 152 TRP cc_start: 0.8744 (OUTLIER) cc_final: 0.6352 (t-100) REVERT: C 90 MET cc_start: 0.5265 (mmm) cc_final: 0.4903 (mmp) REVERT: C 117 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8079 (mmm160) REVERT: C 118 ASN cc_start: 0.8426 (t0) cc_final: 0.8129 (t0) REVERT: I 272 MET cc_start: 0.8180 (mmp) cc_final: 0.7247 (mpp) REVERT: J 152 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.6094 (t-100) REVERT: J 206 ARG cc_start: 0.6758 (mtp180) cc_final: 0.6423 (mtp180) REVERT: J 223 MET cc_start: 0.8259 (mmm) cc_final: 0.8004 (mmm) REVERT: G 189 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7345 (m-10) REVERT: G 244 LEU cc_start: 0.4962 (OUTLIER) cc_final: 0.4503 (pt) REVERT: G 248 PHE cc_start: 0.6444 (m-80) cc_final: 0.5914 (m-80) REVERT: K 81 PHE cc_start: 0.6914 (m-80) cc_final: 0.6664 (m-80) REVERT: K 97 ILE cc_start: 0.6543 (mt) cc_final: 0.6272 (mm) REVERT: K 118 ASN cc_start: 0.8615 (t0) cc_final: 0.8353 (t0) REVERT: K 160 HIS cc_start: 0.7216 (m-70) cc_final: 0.6980 (m90) REVERT: K 238 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.4078 (mp0) outliers start: 75 outliers final: 36 residues processed: 328 average time/residue: 0.5760 time to fit residues: 216.5433 Evaluate side-chains 293 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 152 TRP Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 117 ARG 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 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 I residue 381 TYR 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 52 THR Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 189 PHE Chi-restraints excluded: chain G residue 240 PHE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 174 ASN F 187 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 227 ASN K 245 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.197063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.174185 restraints weight = 28112.906| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 1.07 r_work: 0.4169 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23148 Z= 0.141 Angle : 0.639 7.110 31320 Z= 0.326 Chirality : 0.045 0.217 3207 Planarity : 0.004 0.050 3732 Dihedral : 20.014 173.872 4177 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 3.16 % Allowed : 19.48 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.17), residues: 2559 helix: 0.95 (0.14), residues: 1239 sheet: 0.58 (0.28), residues: 357 loop : -0.24 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 57 TYR 0.023 0.002 TYR C 184 PHE 0.025 0.002 PHE C 248 TRP 0.020 0.001 TRP E 206 HIS 0.008 0.001 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (23148) covalent geometry : angle 0.63906 / 0.33 (31320) hydrogen bonds : bond 0.04584 / 3.15 ( 1107) hydrogen bonds : angle 5.30580 / 3.77 ( 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 340 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.6232 (t-100) REVERT: C 90 MET cc_start: 0.5122 (mmm) cc_final: 0.4803 (mmp) REVERT: F 136 MET cc_start: 0.7869 (ttt) cc_final: 0.7532 (ttp) REVERT: F 212 VAL cc_start: 0.8473 (t) cc_final: 0.8140 (p) REVERT: I 272 MET cc_start: 0.8083 (mmp) cc_final: 0.7136 (mpp) REVERT: J 59 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8531 (mm) REVERT: J 206 ARG cc_start: 0.6693 (mtp180) cc_final: 0.6355 (mtp180) REVERT: J 223 MET cc_start: 0.8149 (mmm) cc_final: 0.7849 (mmm) REVERT: G 244 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4418 (pt) REVERT: K 81 PHE cc_start: 0.6864 (m-80) cc_final: 0.6627 (m-80) REVERT: K 97 ILE cc_start: 0.6569 (mt) cc_final: 0.6279 (mm) REVERT: K 118 ASN cc_start: 0.8574 (t0) cc_final: 0.8370 (t0) REVERT: K 259 MET cc_start: 0.7690 (mtm) cc_final: 0.7471 (mtm) outliers start: 69 outliers final: 36 residues processed: 327 average time/residue: 0.5869 time to fit residues: 220.3192 Evaluate side-chains 291 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE 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 130 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 300 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL 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 I residue 298 MET Chi-restraints excluded: chain I residue 381 TYR 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 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 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: 2.9990 chunk 252 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 245 optimal weight: 0.4980 chunk 132 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 233 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 401 GLN B 174 ASN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 HIS E 168 ASN F 174 ASN F 187 ASN G 91 ASN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN ** K 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.197428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.170404 restraints weight = 28596.840| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.25 r_work: 0.4127 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23148 Z= 0.160 Angle : 0.661 7.810 31320 Z= 0.338 Chirality : 0.046 0.214 3207 Planarity : 0.005 0.047 3732 Dihedral : 19.649 172.236 4174 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 3.20 % Allowed : 19.80 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1242 sheet: 0.57 (0.28), residues: 357 loop : -0.24 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 208 TYR 0.024 0.002 TYR C 184 PHE 0.020 0.002 PHE K 248 TRP 0.018 0.001 TRP J 152 HIS 0.006 0.001 HIS K 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (23148) covalent geometry : angle 0.66063 / 0.34 (31320) hydrogen bonds : bond 0.04699 / 3.22 ( 1107) hydrogen bonds : angle 5.32488 / 3.78 ( 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 325 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 152 TRP cc_start: 0.8691 (OUTLIER) cc_final: 0.6235 (t-100) REVERT: C 90 MET cc_start: 0.5107 (mmm) cc_final: 0.4788 (mmp) REVERT: C 244 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.3980 (pt) REVERT: F 136 MET cc_start: 0.8044 (ttt) cc_final: 0.7776 (ttp) REVERT: F 152 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.6222 (t-100) REVERT: F 212 VAL cc_start: 0.8515 (t) cc_final: 0.8162 (p) REVERT: I 272 MET cc_start: 0.8138 (mmp) cc_final: 0.7216 (mpp) REVERT: J 59 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8579 (mm) REVERT: J 223 MET cc_start: 0.8192 (mmm) cc_final: 0.7880 (mmm) REVERT: G 244 LEU cc_start: 0.4646 (OUTLIER) cc_final: 0.4214 (pt) REVERT: K 81 PHE cc_start: 0.6848 (m-80) cc_final: 0.6486 (m-80) REVERT: K 97 ILE cc_start: 0.6508 (mt) cc_final: 0.6220 (mm) REVERT: K 118 ASN cc_start: 0.8691 (t0) cc_final: 0.8447 (t0) REVERT: K 168 ASP cc_start: 0.4768 (m-30) cc_final: 0.4295 (m-30) REVERT: K 259 MET cc_start: 0.7818 (mtm) cc_final: 0.7541 (mtm) outliers start: 70 outliers final: 37 residues processed: 313 average time/residue: 0.5800 time to fit residues: 209.0123 Evaluate side-chains 292 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain B residue 33 ILE 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 130 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 E residue 300 MET Chi-restraints excluded: chain F residue 59 LEU 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 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 193 THR 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 74 TRP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 19 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 160 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 = 0.4547 r_free = 0.4547 target = 0.196313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.172874 restraints weight = 28473.931| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.11 r_work: 0.4150 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23148 Z= 0.154 Angle : 0.659 8.302 31320 Z= 0.336 Chirality : 0.045 0.210 3207 Planarity : 0.005 0.046 3732 Dihedral : 19.255 170.628 4174 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 3.02 % Allowed : 20.48 % Favored : 76.50 % 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 are not related in a simple way. whole: 0.64 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1242 sheet: 0.59 (0.28), residues: 357 loop : -0.27 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.023 0.002 TYR C 184 PHE 0.030 0.002 PHE C 248 TRP 0.017 0.001 TRP E 206 HIS 0.007 0.001 HIS K 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23148) covalent geometry : angle 0.65856 / 0.34 (31320) hydrogen bonds : bond 0.04656 / 3.19 ( 1107) hydrogen bonds : angle 5.30223 / 3.76 ( 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 323 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 257 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8622 (mm) REVERT: B 152 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.6253 (t-100) REVERT: B 211 ASP cc_start: 0.6759 (p0) cc_final: 0.6458 (p0) REVERT: C 90 MET cc_start: 0.5163 (mmm) cc_final: 0.4832 (mmp) REVERT: C 244 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4333 (pt) REVERT: E 249 MET cc_start: 0.6861 (ppp) cc_final: 0.6588 (ppp) REVERT: F 136 MET cc_start: 0.8005 (ttt) cc_final: 0.7734 (ttp) REVERT: I 272 MET cc_start: 0.8097 (mmp) cc_final: 0.7167 (mpp) REVERT: J 42 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7755 (ptm) REVERT: J 59 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8552 (mm) REVERT: J 206 ARG cc_start: 0.6757 (mtp180) cc_final: 0.6362 (mtp180) REVERT: J 223 MET cc_start: 0.8167 (mmm) cc_final: 0.7855 (mmm) REVERT: G 244 LEU cc_start: 0.4925 (OUTLIER) cc_final: 0.4466 (pt) REVERT: K 81 PHE cc_start: 0.6812 (m-80) cc_final: 0.6500 (m-80) REVERT: K 97 ILE cc_start: 0.6629 (mt) cc_final: 0.6338 (mm) REVERT: K 156 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6887 (t70) REVERT: K 166 ASP cc_start: 0.3882 (OUTLIER) cc_final: 0.3299 (t0) outliers start: 66 outliers final: 38 residues processed: 309 average time/residue: 0.5792 time to fit residues: 204.8981 Evaluate side-chains 295 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 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 E residue 300 MET Chi-restraints excluded: chain F residue 59 LEU 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 298 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 42 MET 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 193 THR 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 74 TRP Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 221 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN J 16 GLN G 91 ASN G 155 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN ** K 160 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 = 0.4521 r_free = 0.4521 target = 0.193994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.170463 restraints weight = 28339.092| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.09 r_work: 0.4121 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23148 Z= 0.218 Angle : 0.722 8.409 31320 Z= 0.373 Chirality : 0.047 0.212 3207 Planarity : 0.005 0.045 3732 Dihedral : 19.178 169.212 4174 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.81 % Favored : 94.96 % Rotamer: Outliers : 2.79 % Allowed : 20.67 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2559 helix: 0.88 (0.15), residues: 1248 sheet: 0.54 (0.28), residues: 357 loop : -0.26 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 208 TYR 0.026 0.002 TYR C 184 PHE 0.033 0.002 PHE C 248 TRP 0.020 0.002 TRP J 231 HIS 0.007 0.002 HIS C 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (23148) covalent geometry : angle 0.72237 / 0.37 (31320) hydrogen bonds : bond 0.05124 / 3.50 ( 1107) hydrogen bonds : angle 5.49906 / 3.89 ( 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 315 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 152 TRP cc_start: 0.8767 (OUTLIER) cc_final: 0.6354 (t-100) REVERT: B 211 ASP cc_start: 0.6831 (p0) cc_final: 0.6531 (p0) REVERT: C 90 MET cc_start: 0.5282 (mmm) cc_final: 0.4943 (mmp) REVERT: C 244 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4406 (pt) REVERT: F 136 MET cc_start: 0.8123 (ttt) cc_final: 0.7825 (ttp) REVERT: F 152 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.6268 (t-100) REVERT: I 79 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: I 272 MET cc_start: 0.8154 (mmp) cc_final: 0.7216 (mpp) REVERT: J 152 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.6126 (t-100) REVERT: J 206 ARG cc_start: 0.6981 (mtp180) cc_final: 0.6661 (mtp180) REVERT: G 244 LEU cc_start: 0.4804 (OUTLIER) cc_final: 0.4337 (pt) REVERT: K 81 PHE cc_start: 0.6956 (m-80) cc_final: 0.6573 (m-80) REVERT: K 97 ILE cc_start: 0.6632 (mt) cc_final: 0.6370 (mm) REVERT: K 156 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6718 (t70) REVERT: K 161 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5702 (mp10) REVERT: K 166 ASP cc_start: 0.4099 (OUTLIER) cc_final: 0.3586 (t70) outliers start: 61 outliers final: 40 residues processed: 307 average time/residue: 0.5623 time to fit residues: 198.0146 Evaluate side-chains 302 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL 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 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 E residue 300 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 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 39 ILE Chi-restraints excluded: chain J residue 42 MET 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 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 156 ASP 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 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 173 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 chunk 201 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** K 160 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 = 0.4548 r_free = 0.4548 target = 0.197373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.170263 restraints weight = 28747.151| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.26 r_work: 0.4126 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23148 Z= 0.154 Angle : 0.675 10.920 31320 Z= 0.343 Chirality : 0.046 0.205 3207 Planarity : 0.005 0.045 3732 Dihedral : 18.881 167.944 4174 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 2.70 % Allowed : 21.03 % Favored : 76.27 % 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 are not related in a simple way. whole: 0.58 (0.17), residues: 2559 helix: 0.95 (0.15), residues: 1242 sheet: 0.57 (0.28), residues: 357 loop : -0.30 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 208 TYR 0.024 0.002 TYR C 184 PHE 0.037 0.002 PHE C 248 TRP 0.019 0.001 TRP I 206 HIS 0.007 0.001 HIS K 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (23148) covalent geometry : angle 0.67528 / 0.34 (31320) hydrogen bonds : bond 0.04701 / 3.22 ( 1107) hydrogen bonds : angle 5.35904 / 3.80 ( 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 311 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: B 59 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8627 (mm) REVERT: B 152 TRP cc_start: 0.8677 (OUTLIER) cc_final: 0.6267 (t-100) REVERT: B 211 ASP cc_start: 0.6873 (p0) cc_final: 0.6559 (p0) REVERT: C 90 MET cc_start: 0.5119 (mmm) cc_final: 0.4778 (mmp) REVERT: C 173 HIS cc_start: 0.7137 (m-70) cc_final: 0.6464 (m90) REVERT: C 244 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4236 (pt) REVERT: I 272 MET cc_start: 0.8105 (mmp) cc_final: 0.7162 (mpp) REVERT: J 42 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7720 (ptm) REVERT: J 59 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8547 (mm) REVERT: J 206 ARG cc_start: 0.6776 (mtp180) cc_final: 0.6434 (mtp180) REVERT: G 244 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4403 (pt) REVERT: K 81 PHE cc_start: 0.6862 (m-80) cc_final: 0.6523 (m-80) REVERT: K 97 ILE cc_start: 0.6495 (mt) cc_final: 0.6208 (mm) REVERT: K 117 ARG cc_start: 0.8385 (mpt90) cc_final: 0.8167 (mmm160) REVERT: K 156 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6704 (t70) REVERT: K 166 ASP cc_start: 0.4012 (OUTLIER) cc_final: 0.3393 (t0) REVERT: K 168 ASP cc_start: 0.4847 (m-30) cc_final: 0.4381 (m-30) outliers start: 59 outliers final: 35 residues processed: 301 average time/residue: 0.5770 time to fit residues: 199.1974 Evaluate side-chains 289 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 130 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 E residue 300 MET Chi-restraints excluded: chain F residue 59 LEU 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 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 42 MET 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 193 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 156 ASP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP 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: 0.5980 chunk 214 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 235 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 187 ASN J 16 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.197854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.174879 restraints weight = 28651.745| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 1.11 r_work: 0.4177 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23148 Z= 0.135 Angle : 0.660 11.901 31320 Z= 0.333 Chirality : 0.045 0.210 3207 Planarity : 0.004 0.044 3732 Dihedral : 18.494 166.660 4174 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.69 % Favored : 95.08 % Rotamer: Outliers : 2.24 % Allowed : 21.81 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2559 helix: 1.02 (0.15), residues: 1230 sheet: 0.64 (0.28), residues: 357 loop : -0.29 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 9 TYR 0.025 0.002 TYR J 196 PHE 0.029 0.002 PHE G 248 TRP 0.017 0.001 TRP E 206 HIS 0.008 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23148) covalent geometry : angle 0.65957 / 0.33 (31320) hydrogen bonds : bond 0.04452 / 3.05 ( 1107) hydrogen bonds : angle 5.25694 / 3.74 ( 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 311 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 211 ASP cc_start: 0.6703 (p0) cc_final: 0.6367 (p0) REVERT: C 90 MET cc_start: 0.5158 (mmm) cc_final: 0.4846 (mmp) REVERT: C 113 LYS cc_start: 0.8198 (tttt) cc_final: 0.7954 (tptt) REVERT: C 173 HIS cc_start: 0.7122 (m-70) cc_final: 0.6479 (m90) REVERT: C 244 LEU cc_start: 0.4489 (OUTLIER) cc_final: 0.4233 (pt) REVERT: F 136 MET cc_start: 0.7919 (ttt) cc_final: 0.7637 (ttp) REVERT: I 272 MET cc_start: 0.8007 (mmp) cc_final: 0.7054 (mpp) REVERT: J 42 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7758 (ptm) REVERT: J 206 ARG cc_start: 0.6781 (mtp180) cc_final: 0.6423 (mtp180) REVERT: G 244 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4403 (pt) REVERT: K 97 ILE cc_start: 0.6604 (mt) cc_final: 0.6320 (mm) REVERT: K 117 ARG cc_start: 0.8448 (mpt90) cc_final: 0.8247 (mmm160) REVERT: K 156 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6914 (t70) REVERT: K 166 ASP cc_start: 0.3992 (OUTLIER) cc_final: 0.3439 (t0) REVERT: K 168 ASP cc_start: 0.4678 (m-30) cc_final: 0.4300 (m-30) outliers start: 49 outliers final: 32 residues processed: 297 average time/residue: 0.5798 time to fit residues: 198.0414 Evaluate side-chains 290 residues out of total 2187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain B residue 33 ILE 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 130 ILE 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 227 LEU Chi-restraints excluded: chain E residue 300 MET Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL 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 256 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 300 MET Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 42 MET 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 193 THR 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 74 TRP Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 166 ASP 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: 5.9990 chunk 209 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 200 optimal weight: 0.0670 chunk 199 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN F 187 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.196518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.173218 restraints weight = 28350.625| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 1.11 r_work: 0.4154 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.4050 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23148 Z= 0.157 Angle : 0.683 11.329 31320 Z= 0.345 Chirality : 0.046 0.198 3207 Planarity : 0.005 0.044 3732 Dihedral : 18.329 165.734 4172 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.65 % Favored : 95.12 % Rotamer: Outliers : 2.01 % Allowed : 22.13 % 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 are not related in a simple way. whole: 0.66 (0.17), residues: 2559 helix: 1.02 (0.15), residues: 1242 sheet: 0.61 (0.28), residues: 357 loop : -0.27 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 208 TYR 0.024 0.002 TYR C 184 PHE 0.038 0.002 PHE G 248 TRP 0.018 0.001 TRP J 152 HIS 0.007 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (23148) covalent geometry : angle 0.68325 / 0.35 (31320) hydrogen bonds : bond 0.04664 / 3.20 ( 1107) hydrogen bonds : angle 5.30211 / 3.77 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9004.94 seconds wall clock time: 153 minutes 50.23 seconds (9230.23 seconds total)