Starting phenix.real_space_refine on Fri Mar 6 20:19:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4o_25683/03_2026/7t4o_25683_trim.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 17751 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 5 5.60 5 P 12 5.49 5 S 87 5.16 5 C 12684 2.51 5 N 3054 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19142 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "B" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "K" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 140} Chain breaks: 3 Chain: "F" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.22 Number of scatterers: 19142 At special positions: 0 Unit cell: (106.288, 106.288, 121.107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 5 28.99 S 87 16.00 P 12 15.00 O 3300 8.00 N 3054 7.00 C 12684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 741.7 milliseconds 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 21 sheets defined 50.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 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 381 removed outlier: 4.040A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 4.355A pdb=" N LEU C 51 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 removed outlier: 3.549A pdb=" N LEU C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 150 removed outlier: 3.686A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 4.068A pdb=" N GLU C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 199 Processing helix chain 'C' and resid 208 through 220 Proline residue: C 217 - end of helix Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'B' and resid 10 through 45 Processing helix chain 'B' and resid 45 through 51 removed outlier: 3.630A pdb=" N ASP B 49 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.681A 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 165 removed outlier: 4.194A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.942A pdb=" N VAL B 169 " --> pdb=" O PRO B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.822A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.355A pdb=" N LEU G 51 " --> pdb=" O LYS G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 removed outlier: 3.549A pdb=" N LEU G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 150 removed outlier: 3.687A pdb=" N THR G 133 " --> pdb=" O ARG G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 159 removed outlier: 4.069A pdb=" N GLU G 154 " --> pdb=" O SER G 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 199 Processing helix chain 'G' and resid 208 through 220 Proline residue: G 217 - end of helix Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 254 through 256 No H-bonds generated for 'chain 'G' and resid 254 through 256' Processing helix chain 'G' and resid 257 through 270 Processing helix chain 'K' and resid 48 through 52 removed outlier: 4.355A pdb=" N LEU K 51 " --> pdb=" O LYS K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 114 removed outlier: 3.550A pdb=" N LEU K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 150 removed outlier: 3.687A pdb=" N THR K 133 " --> pdb=" O ARG K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 159 removed outlier: 4.068A pdb=" N GLU K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 199 Processing helix chain 'K' and resid 208 through 220 Proline residue: K 217 - end of helix Processing helix chain 'K' and resid 248 through 253 Processing helix chain 'K' and resid 254 through 256 No H-bonds generated for 'chain 'K' and resid 254 through 256' Processing helix chain 'K' and resid 257 through 270 Processing helix chain 'F' and resid 10 through 45 Processing helix chain 'F' and resid 45 through 51 removed outlier: 3.630A pdb=" N ASP F 49 " --> pdb=" O MET F 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.680A 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 165 removed outlier: 4.194A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET F 150 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Processing helix chain 'F' and resid 166 through 169 removed outlier: 3.942A pdb=" N VAL F 169 " --> pdb=" O PRO F 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 166 through 169' Processing helix chain 'F' and resid 179 through 188 Processing helix chain 'F' and resid 194 through 198 Processing helix chain 'F' and resid 211 through 238 removed outlier: 3.821A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 45 Processing helix chain 'J' and resid 45 through 51 removed outlier: 3.629A pdb=" N ASP J 49 " --> pdb=" O MET J 45 " (cutoff:3.500A) removed outlier: 4.412A 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: 3.681A 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 165 removed outlier: 4.195A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET J 150 " --> pdb=" O ILE J 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Processing helix chain 'J' and resid 166 through 169 removed outlier: 3.943A pdb=" N VAL J 169 " --> pdb=" O PRO J 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 166 through 169' Processing helix chain 'J' and resid 179 through 188 Processing helix chain 'J' and resid 194 through 198 Processing helix chain 'J' and resid 211 through 238 removed outlier: 3.821A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 208 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 231 through 257 Processing helix chain 'E' and resid 337 through 339 No H-bonds generated for 'chain 'E' and resid 337 through 339' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 376 through 381 removed outlier: 4.039A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 162 through 166 Processing helix chain 'I' and resid 184 through 208 Processing helix chain 'I' and resid 212 through 221 Processing helix chain 'I' and resid 231 through 257 Processing helix chain 'I' and resid 337 through 339 No H-bonds generated for 'chain 'I' and resid 337 through 339' Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'I' and resid 376 through 381 removed outlier: 4.039A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU A 52 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 68 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP A 54 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU A 66 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP A 123 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE A 105 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG A 125 " --> pdb=" O SER A 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER A 103 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 127 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 3.968A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 3.600A pdb=" N GLY A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 removed outlier: 6.588A pdb=" N ARG A 323 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N SER A 283 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP A 406 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS A 285 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU A 287 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 284 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR A 305 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 286 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 303 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP A 288 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG A 292 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA A 297 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 360 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AA7, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AA8, first strand: chain 'G' and resid 206 through 207 Processing sheet with id=AA9, first strand: chain 'K' and resid 206 through 207 Processing sheet with id=AB1, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AB2, first strand: chain 'J' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'E' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU E 52 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS E 68 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP E 54 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU E 66 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP E 123 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E 105 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 125 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER E 103 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL E 127 " --> pdb=" O LYS E 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN E 108 " --> pdb=" O ILE E 105 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AB5, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.599A pdb=" N GLY E 148 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'E' and resid 341 through 342 removed outlier: 6.588A pdb=" N ARG E 323 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER E 283 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP E 406 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS E 285 " --> pdb=" O ASP E 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU E 287 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL E 284 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 305 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL E 286 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR E 303 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP E 288 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG E 292 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 297 " --> pdb=" O ARG E 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 360 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 47 through 54 removed outlier: 4.261A pdb=" N LEU I 52 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS I 68 " --> pdb=" O LEU I 52 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TRP I 54 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU I 66 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP I 123 " --> pdb=" O ILE I 105 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE I 105 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG I 125 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER I 103 " --> pdb=" O ARG I 125 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL I 127 " --> pdb=" O LYS I 101 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN I 108 " --> pdb=" O ILE I 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AC1, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.599A pdb=" N GLY I 148 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 169 through 171 Processing sheet with id=AC3, first strand: chain 'I' and resid 341 through 342 removed outlier: 6.587A pdb=" N ARG I 323 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N SER I 283 " --> pdb=" O GLN I 404 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N ASP I 406 " --> pdb=" O SER I 283 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS I 285 " --> pdb=" O ASP I 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLU I 287 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL I 284 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR I 305 " --> pdb=" O VAL I 284 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 286 " --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR I 303 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP I 288 " --> pdb=" O LYS I 301 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG I 292 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA I 297 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 360 " --> pdb=" O ILE I 304 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 2.21 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: 3086 1.32 - 1.45: 5668 1.45 - 1.57: 10746 1.57 - 1.69: 39 1.69 - 1.81: 168 Bond restraints: 19707 Sorted by residual: bond pdb=" C19 P1O G 302 " pdb=" O7 P1O G 302 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 P1O K 302 " pdb=" O7 P1O K 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 P1O C 302 " pdb=" O7 P1O C 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C9 P1O K 301 " pdb=" O5 P1O K 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C9 P1O C 301 " pdb=" O5 P1O C 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 19702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25724 2.16 - 4.32: 862 4.32 - 6.48: 123 6.48 - 8.63: 27 8.63 - 10.79: 21 Bond angle restraints: 26757 Sorted by residual: angle pdb=" CA PRO K 200 " pdb=" C PRO K 200 " pdb=" O PRO K 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO C 200 " pdb=" C PRO C 200 " pdb=" O PRO C 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO G 200 " pdb=" C PRO G 200 " pdb=" O PRO G 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" C GLU I 287 " pdb=" N ASP I 288 " pdb=" CA ASP I 288 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLU A 287 " pdb=" N ASP A 288 " pdb=" CA ASP A 288 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 26752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 10810 30.46 - 60.91: 536 60.91 - 91.37: 24 91.37 - 121.83: 6 121.83 - 152.28: 12 Dihedral angle restraints: 11388 sinusoidal: 4740 harmonic: 6648 Sorted by residual: dihedral pdb=" C1 P1O G 302 " pdb=" O3 P1O G 302 " pdb=" P1 P1O G 302 " pdb=" O4 P1O G 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.47 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O C 302 " pdb=" O3 P1O C 302 " pdb=" P1 P1O C 302 " pdb=" O4 P1O C 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.51 152.24 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O K 302 " pdb=" O3 P1O K 302 " pdb=" P1 P1O K 302 " pdb=" O4 P1O K 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.53 152.22 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 11385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1976 0.042 - 0.084: 558 0.084 - 0.126: 280 0.126 - 0.167: 21 0.167 - 0.209: 18 Chirality restraints: 2853 Sorted by residual: chirality pdb=" CA ILE G 193 " pdb=" N ILE G 193 " pdb=" C ILE G 193 " pdb=" CB ILE G 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE K 193 " pdb=" N ILE K 193 " pdb=" C ILE K 193 " pdb=" CB ILE K 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 193 " pdb=" N ILE C 193 " pdb=" C ILE C 193 " pdb=" CB ILE C 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2850 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 95 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO I 96 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 95 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 96 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.038 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 62 2.40 - 3.03: 11348 3.03 - 3.65: 29766 3.65 - 4.28: 45145 4.28 - 4.90: 75650 Nonbonded interactions: 161971 Sorted by model distance: nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.777 2.320 nonbonded pdb=" NE2 HIS I 139 " pdb="CU CU I 501 " model vdw 1.783 2.320 nonbonded pdb=" NE2 HIS E 139 " pdb="CU CU E 501 " model vdw 1.783 2.320 ... (remaining 161966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 501) selection = (chain 'E' and resid 33 through 501) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'F' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'J' and (resid 7 through 247 or resid 303 through 304)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.007 0.125 19707 Z= 0.366 Angle : 0.877 10.792 26757 Z= 0.474 Chirality : 0.049 0.209 2853 Planarity : 0.005 0.071 3261 Dihedral : 16.839 152.282 7134 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 1.85 % Allowed : 0.97 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2274 helix: 0.63 (0.16), residues: 951 sheet: 0.51 (0.29), residues: 348 loop : -0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 45 TYR 0.029 0.002 TYR F 37 PHE 0.026 0.001 PHE G 251 TRP 0.037 0.002 TRP J 54 HIS 0.023 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00663 (19707) covalent geometry : angle 0.87674 (26757) hydrogen bonds : bond 0.16992 ( 954) hydrogen bonds : angle 7.02098 ( 2835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6686 (pm20) REVERT: A 68 LYS cc_start: 0.7309 (mtmm) cc_final: 0.6317 (mtmt) REVERT: A 75 GLU cc_start: 0.7128 (mp0) cc_final: 0.6921 (pm20) REVERT: A 86 VAL cc_start: 0.8136 (t) cc_final: 0.7668 (t) REVERT: A 112 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7662 (ptp-170) REVERT: A 118 ILE cc_start: 0.8235 (mm) cc_final: 0.7832 (mm) REVERT: A 120 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7598 (mmtm) REVERT: A 158 THR cc_start: 0.7071 (m) cc_final: 0.6807 (m) REVERT: A 181 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 218 MET cc_start: 0.4968 (mmp) cc_final: 0.4492 (mmp) REVERT: A 237 MET cc_start: 0.6290 (mtt) cc_final: 0.5555 (mtt) REVERT: C 49 LYS cc_start: 0.5108 (OUTLIER) cc_final: 0.3944 (ptmm) REVERT: C 219 MET cc_start: 0.4543 (tmm) cc_final: 0.4315 (ppp) REVERT: C 266 PHE cc_start: 0.7410 (m-10) cc_final: 0.7068 (m-10) REVERT: B 202 LYS cc_start: 0.6585 (mttm) cc_final: 0.6207 (mtmt) REVERT: B 236 ARG cc_start: 0.5682 (tpp80) cc_final: 0.5135 (mmm160) REVERT: G 49 LYS cc_start: 0.4971 (OUTLIER) cc_final: 0.3865 (ptmt) REVERT: K 49 LYS cc_start: 0.4883 (OUTLIER) cc_final: 0.3854 (ptmt) REVERT: F 202 LYS cc_start: 0.6465 (mttm) cc_final: 0.6148 (mtmt) REVERT: F 236 ARG cc_start: 0.5715 (tpp80) cc_final: 0.5139 (mmm160) REVERT: J 202 LYS cc_start: 0.6592 (mttm) cc_final: 0.6242 (mtmt) REVERT: J 236 ARG cc_start: 0.5662 (tpp80) cc_final: 0.5110 (mmm160) REVERT: E 68 LYS cc_start: 0.7199 (mtmm) cc_final: 0.6414 (mttp) REVERT: E 86 VAL cc_start: 0.8217 (t) cc_final: 0.7953 (t) REVERT: E 120 LYS cc_start: 0.8046 (mmtm) cc_final: 0.7539 (mmtm) REVERT: E 151 ILE cc_start: 0.8280 (mm) cc_final: 0.8042 (mm) REVERT: E 181 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7236 (mm-30) REVERT: E 237 MET cc_start: 0.6237 (mtt) cc_final: 0.5805 (mtt) REVERT: E 310 SER cc_start: 0.7863 (t) cc_final: 0.7535 (t) REVERT: I 57 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6579 (pm20) REVERT: I 58 LYS cc_start: 0.7486 (ttmt) cc_final: 0.7202 (mtpp) REVERT: I 68 LYS cc_start: 0.7293 (mtmm) cc_final: 0.6367 (mtmt) REVERT: I 82 ASP cc_start: 0.6187 (m-30) cc_final: 0.5659 (m-30) REVERT: I 86 VAL cc_start: 0.8200 (t) cc_final: 0.7899 (t) REVERT: I 102 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6900 (mt-10) REVERT: I 120 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7603 (mmtm) REVERT: I 151 ILE cc_start: 0.8244 (mm) cc_final: 0.8003 (mm) REVERT: I 158 THR cc_start: 0.7167 (m) cc_final: 0.6889 (m) REVERT: I 181 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7191 (mm-30) REVERT: I 218 MET cc_start: 0.4867 (mmp) cc_final: 0.4631 (mmp) REVERT: I 237 MET cc_start: 0.6273 (mtt) cc_final: 0.5732 (mtt) REVERT: I 285 LYS cc_start: 0.6941 (tmmt) cc_final: 0.6664 (ttpt) REVERT: I 372 GLU cc_start: 0.6656 (pt0) cc_final: 0.5873 (tm-30) outliers start: 36 outliers final: 6 residues processed: 451 average time/residue: 0.1642 time to fit residues: 106.7251 Evaluate side-chains 282 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 273 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 251 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 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 = 0.3638 r_free = 0.3638 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.137979 restraints weight = 21431.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.137131 restraints weight = 27945.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.139253 restraints weight = 18893.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.139449 restraints weight = 14239.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.140020 restraints weight = 13938.613| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19707 Z= 0.203 Angle : 0.669 7.056 26757 Z= 0.347 Chirality : 0.048 0.259 2853 Planarity : 0.006 0.054 3261 Dihedral : 15.425 145.970 3009 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.75 % Favored : 94.99 % Rotamer: Outliers : 2.10 % Allowed : 9.03 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2274 helix: 0.68 (0.16), residues: 1005 sheet: 0.39 (0.30), residues: 339 loop : -0.60 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 400 TYR 0.031 0.002 TYR C 184 PHE 0.031 0.002 PHE K 251 TRP 0.035 0.002 TRP B 54 HIS 0.008 0.002 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00484 (19707) covalent geometry : angle 0.66922 (26757) hydrogen bonds : bond 0.05165 ( 954) hydrogen bonds : angle 5.46642 ( 2835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.5508 (mmp) cc_final: 0.4972 (mmp) REVERT: A 237 MET cc_start: 0.6639 (mtt) cc_final: 0.6394 (mtt) REVERT: A 269 MET cc_start: 0.7719 (mtp) cc_final: 0.7456 (mtp) REVERT: C 49 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.4924 (ptmt) REVERT: B 22 ASP cc_start: 0.8243 (m-30) cc_final: 0.7941 (m-30) REVERT: B 236 ARG cc_start: 0.6607 (tpp80) cc_final: 0.6000 (mtp85) REVERT: G 49 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.4816 (ptmt) REVERT: K 210 TYR cc_start: 0.7855 (t80) cc_final: 0.7623 (t80) REVERT: F 236 ARG cc_start: 0.6604 (tpp80) cc_final: 0.5995 (mtp85) REVERT: J 22 ASP cc_start: 0.8246 (m-30) cc_final: 0.7816 (m-30) REVERT: J 236 ARG cc_start: 0.6611 (tpp80) cc_final: 0.5978 (mtp85) REVERT: E 163 MET cc_start: 0.8224 (ttt) cc_final: 0.7948 (ttm) REVERT: E 218 MET cc_start: 0.5341 (mmp) cc_final: 0.5056 (mmp) REVERT: I 68 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7643 (mttp) REVERT: I 151 ILE cc_start: 0.8353 (mm) cc_final: 0.8089 (mm) outliers start: 41 outliers final: 23 residues processed: 312 average time/residue: 0.1510 time to fit residues: 70.0686 Evaluate side-chains 278 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 97 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN E 38 GLN I 38 GLN ** I 72 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 = 0.3579 r_free = 0.3579 target = 0.154375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.133800 restraints weight = 21405.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.134109 restraints weight = 21739.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.135524 restraints weight = 18755.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.135811 restraints weight = 15879.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.135868 restraints weight = 14856.329| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19707 Z= 0.207 Angle : 0.648 6.668 26757 Z= 0.337 Chirality : 0.047 0.172 2853 Planarity : 0.006 0.043 3261 Dihedral : 14.860 143.989 2999 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.57 % Favored : 95.16 % Rotamer: Outliers : 2.87 % Allowed : 12.21 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.07 (0.17), residues: 2274 helix: 0.75 (0.16), residues: 972 sheet: 0.08 (0.29), residues: 327 loop : -0.59 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 400 TYR 0.031 0.002 TYR K 184 PHE 0.030 0.002 PHE G 251 TRP 0.034 0.002 TRP G 253 HIS 0.008 0.002 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00467 (19707) covalent geometry : angle 0.64753 (26757) hydrogen bonds : bond 0.04811 ( 954) hydrogen bonds : angle 5.26906 ( 2835) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 0.700 Fit side-chains REVERT: A 218 MET cc_start: 0.5768 (mmp) cc_final: 0.5527 (mmp) REVERT: C 49 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.4378 (mttt) REVERT: B 22 ASP cc_start: 0.8552 (m-30) cc_final: 0.8261 (m-30) REVERT: B 236 ARG cc_start: 0.7044 (tpp80) cc_final: 0.6755 (mtt180) REVERT: B 244 LEU cc_start: 0.5931 (tp) cc_final: 0.5572 (mp) REVERT: G 49 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.4441 (ptmt) REVERT: K 210 TYR cc_start: 0.8016 (t80) cc_final: 0.7814 (t80) REVERT: F 22 ASP cc_start: 0.8462 (m-30) cc_final: 0.8227 (m-30) REVERT: F 236 ARG cc_start: 0.7076 (tpp80) cc_final: 0.6205 (mtp85) REVERT: F 244 LEU cc_start: 0.5898 (tp) cc_final: 0.5551 (mp) REVERT: J 236 ARG cc_start: 0.7024 (tpp80) cc_final: 0.6268 (mtp85) REVERT: J 244 LEU cc_start: 0.5993 (tp) cc_final: 0.5759 (mp) REVERT: E 82 ASP cc_start: 0.5898 (m-30) cc_final: 0.5685 (m-30) REVERT: E 381 TYR cc_start: 0.5876 (t80) cc_final: 0.5654 (t80) REVERT: I 56 LYS cc_start: 0.7142 (mttt) cc_final: 0.6626 (mmmm) REVERT: I 68 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7674 (mttp) REVERT: I 151 ILE cc_start: 0.8559 (mm) cc_final: 0.8318 (mm) outliers start: 56 outliers final: 35 residues processed: 326 average time/residue: 0.1493 time to fit residues: 73.3900 Evaluate side-chains 299 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 211 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN J 245 GLN I 62 ASN I 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.153148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.134037 restraints weight = 21559.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.133372 restraints weight = 24000.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.133735 restraints weight = 21620.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.133863 restraints weight = 19669.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.134033 restraints weight = 18934.948| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19707 Z= 0.169 Angle : 0.605 6.637 26757 Z= 0.315 Chirality : 0.046 0.171 2853 Planarity : 0.005 0.041 3261 Dihedral : 14.334 145.545 2999 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.84 % Favored : 94.90 % Rotamer: Outliers : 3.18 % Allowed : 14.00 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2274 helix: 0.80 (0.16), residues: 975 sheet: 0.12 (0.29), residues: 327 loop : -0.62 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 360 TYR 0.027 0.002 TYR K 184 PHE 0.023 0.002 PHE K 251 TRP 0.026 0.002 TRP G 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00401 (19707) covalent geometry : angle 0.60499 (26757) hydrogen bonds : bond 0.04415 ( 954) hydrogen bonds : angle 5.09805 ( 2835) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 281 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.4203 (mttt) REVERT: B 223 MET cc_start: 0.7768 (tpp) cc_final: 0.7148 (tpp) REVERT: B 236 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6273 (mtp85) REVERT: G 49 LYS cc_start: 0.5874 (OUTLIER) cc_final: 0.4284 (ptmt) REVERT: F 22 ASP cc_start: 0.8553 (m-30) cc_final: 0.8203 (m-30) REVERT: E 381 TYR cc_start: 0.5828 (t80) cc_final: 0.5624 (t80) REVERT: I 56 LYS cc_start: 0.7203 (mttt) cc_final: 0.6701 (mmmm) REVERT: I 151 ILE cc_start: 0.8531 (mm) cc_final: 0.8255 (mm) REVERT: I 310 SER cc_start: 0.7917 (t) cc_final: 0.7628 (m) outliers start: 62 outliers final: 39 residues processed: 322 average time/residue: 0.1489 time to fit residues: 71.6388 Evaluate side-chains 296 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 62 ASN B 245 GLN F 245 GLN J 245 GLN E 33 HIS I 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.150997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.132157 restraints weight = 21869.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130671 restraints weight = 27884.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.131579 restraints weight = 26874.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.131702 restraints weight = 22228.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.131742 restraints weight = 21337.801| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19707 Z= 0.172 Angle : 0.606 6.063 26757 Z= 0.317 Chirality : 0.046 0.163 2853 Planarity : 0.005 0.042 3261 Dihedral : 14.056 145.607 2996 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 3.54 % Allowed : 14.62 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2274 helix: 0.76 (0.16), residues: 993 sheet: -0.01 (0.27), residues: 357 loop : -0.65 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 236 TYR 0.026 0.002 TYR K 184 PHE 0.021 0.002 PHE C 251 TRP 0.029 0.002 TRP C 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00400 (19707) covalent geometry : angle 0.60622 (26757) hydrogen bonds : bond 0.04392 ( 954) hydrogen bonds : angle 5.05887 ( 2835) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 278 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8198 (tpt) cc_final: 0.7954 (tpt) REVERT: A 310 SER cc_start: 0.7956 (t) cc_final: 0.7731 (m) REVERT: C 49 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.4036 (mttt) REVERT: B 49 ASP cc_start: 0.7628 (t0) cc_final: 0.7301 (t70) REVERT: B 223 MET cc_start: 0.7746 (tpp) cc_final: 0.7135 (tpp) REVERT: B 236 ARG cc_start: 0.7326 (tpp80) cc_final: 0.6393 (mtp85) REVERT: G 49 LYS cc_start: 0.5791 (OUTLIER) cc_final: 0.4297 (ptmt) REVERT: F 22 ASP cc_start: 0.8594 (m-30) cc_final: 0.8316 (m-30) REVERT: F 229 PHE cc_start: 0.7518 (t80) cc_final: 0.6995 (t80) REVERT: I 56 LYS cc_start: 0.7249 (mttt) cc_final: 0.6687 (mmmm) REVERT: I 151 ILE cc_start: 0.8597 (mm) cc_final: 0.8341 (mm) REVERT: I 310 SER cc_start: 0.7868 (t) cc_final: 0.7614 (m) outliers start: 69 outliers final: 54 residues processed: 321 average time/residue: 0.1442 time to fit residues: 70.1704 Evaluate side-chains 319 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 245 GLN F 245 GLN J 245 GLN I 33 HIS I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.151659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.143118 restraints weight = 21663.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.129164 restraints weight = 33350.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.130189 restraints weight = 28095.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132251 restraints weight = 22882.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132261 restraints weight = 19376.840| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19707 Z= 0.149 Angle : 0.584 7.821 26757 Z= 0.305 Chirality : 0.045 0.161 2853 Planarity : 0.005 0.043 3261 Dihedral : 13.729 145.747 2993 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.79 % Favored : 95.07 % Rotamer: Outliers : 3.85 % Allowed : 15.33 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.14 (0.17), residues: 2274 helix: 0.84 (0.16), residues: 999 sheet: -0.02 (0.27), residues: 357 loop : -0.58 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 215 TYR 0.025 0.002 TYR K 184 PHE 0.018 0.001 PHE C 251 TRP 0.020 0.001 TRP G 253 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00347 (19707) covalent geometry : angle 0.58443 (26757) hydrogen bonds : bond 0.04201 ( 954) hydrogen bonds : angle 4.99749 ( 2835) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8187 (tpt) cc_final: 0.7934 (tpt) REVERT: A 310 SER cc_start: 0.8038 (t) cc_final: 0.7833 (m) REVERT: C 49 LYS cc_start: 0.5127 (OUTLIER) cc_final: 0.3396 (mttt) REVERT: C 114 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6010 (t) REVERT: B 49 ASP cc_start: 0.7640 (t0) cc_final: 0.7349 (t70) REVERT: B 223 MET cc_start: 0.7709 (tpp) cc_final: 0.7136 (tpp) REVERT: B 229 PHE cc_start: 0.7874 (t80) cc_final: 0.7446 (m-80) REVERT: B 236 ARG cc_start: 0.7383 (tpp80) cc_final: 0.6429 (mtp85) REVERT: G 49 LYS cc_start: 0.5055 (OUTLIER) cc_final: 0.3571 (ptmt) REVERT: F 22 ASP cc_start: 0.8519 (m-30) cc_final: 0.8260 (m-30) REVERT: F 178 MET cc_start: 0.8385 (mtt) cc_final: 0.7740 (mtt) REVERT: F 223 MET cc_start: 0.7652 (tpp) cc_final: 0.7114 (tpp) REVERT: F 229 PHE cc_start: 0.7548 (t80) cc_final: 0.6991 (t80) REVERT: J 223 MET cc_start: 0.7682 (tpp) cc_final: 0.7029 (tpp) REVERT: E 381 TYR cc_start: 0.5938 (t80) cc_final: 0.5663 (t80) REVERT: I 56 LYS cc_start: 0.7239 (mttt) cc_final: 0.6663 (mmmm) REVERT: I 151 ILE cc_start: 0.8618 (mm) cc_final: 0.8302 (mm) REVERT: I 310 SER cc_start: 0.7962 (t) cc_final: 0.7728 (m) outliers start: 75 outliers final: 52 residues processed: 320 average time/residue: 0.1530 time to fit residues: 73.3965 Evaluate side-chains 313 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 19 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.128337 restraints weight = 21779.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.128293 restraints weight = 20345.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.128720 restraints weight = 18326.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.129493 restraints weight = 16688.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.129813 restraints weight = 15517.908| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19707 Z= 0.173 Angle : 0.613 8.021 26757 Z= 0.320 Chirality : 0.046 0.165 2853 Planarity : 0.005 0.044 3261 Dihedral : 13.771 152.390 2990 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 4.05 % Allowed : 15.28 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.03 (0.17), residues: 2274 helix: 0.76 (0.15), residues: 999 sheet: -0.15 (0.27), residues: 357 loop : -0.61 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 323 TYR 0.025 0.002 TYR C 184 PHE 0.016 0.002 PHE C 202 TRP 0.027 0.001 TRP K 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00409 (19707) covalent geometry : angle 0.61300 (26757) hydrogen bonds : bond 0.04380 ( 954) hydrogen bonds : angle 5.03156 ( 2835) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 281 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8237 (tpt) cc_final: 0.7986 (tpt) REVERT: A 310 SER cc_start: 0.8002 (t) cc_final: 0.7784 (m) REVERT: C 49 LYS cc_start: 0.5133 (OUTLIER) cc_final: 0.3370 (mttt) REVERT: C 114 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6150 (t) REVERT: B 49 ASP cc_start: 0.7670 (t0) cc_final: 0.7351 (t70) REVERT: B 229 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: B 236 ARG cc_start: 0.7509 (tpp80) cc_final: 0.6540 (mtp85) REVERT: G 49 LYS cc_start: 0.4960 (OUTLIER) cc_final: 0.3546 (ptmt) REVERT: F 22 ASP cc_start: 0.8503 (m-30) cc_final: 0.8257 (m-30) REVERT: F 223 MET cc_start: 0.7658 (tpp) cc_final: 0.7131 (tpp) REVERT: F 229 PHE cc_start: 0.7561 (t80) cc_final: 0.6978 (t80) REVERT: J 100 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 142 MET cc_start: 0.8279 (tpt) cc_final: 0.8020 (tpt) REVERT: I 56 LYS cc_start: 0.7224 (mttt) cc_final: 0.6674 (mmmm) REVERT: I 60 LYS cc_start: 0.7468 (pttp) cc_final: 0.7063 (ptmt) REVERT: I 151 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8333 (mm) REVERT: I 310 SER cc_start: 0.7919 (t) cc_final: 0.7689 (m) outliers start: 79 outliers final: 61 residues processed: 333 average time/residue: 0.1416 time to fit residues: 71.8557 Evaluate side-chains 328 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 262 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 138 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 0.0570 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 overall best weight: 3.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.149368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.140775 restraints weight = 21601.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.128497 restraints weight = 28221.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.127245 restraints weight = 33954.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.128344 restraints weight = 25843.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.129526 restraints weight = 21563.911| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19707 Z= 0.183 Angle : 0.620 8.026 26757 Z= 0.323 Chirality : 0.046 0.166 2853 Planarity : 0.005 0.044 3261 Dihedral : 13.764 159.129 2990 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 3.95 % Allowed : 15.59 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: -0.02 (0.17), residues: 2274 helix: 0.70 (0.15), residues: 1002 sheet: -0.28 (0.27), residues: 351 loop : -0.57 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 215 TYR 0.025 0.002 TYR G 184 PHE 0.016 0.002 PHE C 202 TRP 0.018 0.001 TRP K 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00437 (19707) covalent geometry : angle 0.62013 (26757) hydrogen bonds : bond 0.04425 ( 954) hydrogen bonds : angle 5.03628 ( 2835) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 263 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8216 (tpt) cc_final: 0.8000 (tpt) REVERT: A 310 SER cc_start: 0.8002 (t) cc_final: 0.7783 (m) REVERT: C 49 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.3236 (mttt) REVERT: C 114 THR cc_start: 0.6726 (OUTLIER) cc_final: 0.6247 (t) REVERT: B 49 ASP cc_start: 0.7681 (t0) cc_final: 0.7383 (t70) REVERT: B 229 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: G 49 LYS cc_start: 0.4828 (OUTLIER) cc_final: 0.3472 (ptmt) REVERT: F 22 ASP cc_start: 0.8512 (m-30) cc_final: 0.8268 (m-30) REVERT: F 223 MET cc_start: 0.7644 (tpp) cc_final: 0.7140 (tpp) REVERT: F 229 PHE cc_start: 0.7581 (t80) cc_final: 0.6967 (t80) REVERT: E 142 MET cc_start: 0.8294 (tpt) cc_final: 0.8043 (tpt) REVERT: I 56 LYS cc_start: 0.7235 (mttt) cc_final: 0.6645 (mmmm) REVERT: I 60 LYS cc_start: 0.7519 (pttp) cc_final: 0.7097 (ptmt) REVERT: I 151 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8347 (mm) REVERT: I 310 SER cc_start: 0.7904 (t) cc_final: 0.7669 (m) outliers start: 77 outliers final: 64 residues processed: 317 average time/residue: 0.1498 time to fit residues: 71.6806 Evaluate side-chains 319 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 196 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.151249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.142518 restraints weight = 21498.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.128586 restraints weight = 31052.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.132112 restraints weight = 24943.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.132258 restraints weight = 20257.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.132380 restraints weight = 18370.833| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19707 Z= 0.141 Angle : 0.580 7.666 26757 Z= 0.303 Chirality : 0.044 0.180 2853 Planarity : 0.005 0.045 3261 Dihedral : 13.426 163.267 2990 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 3.13 % Allowed : 16.77 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2274 helix: 0.89 (0.16), residues: 1002 sheet: -0.20 (0.27), residues: 360 loop : -0.52 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 236 TYR 0.022 0.001 TYR K 184 PHE 0.011 0.001 PHE C 251 TRP 0.020 0.001 TRP K 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00328 (19707) covalent geometry : angle 0.57996 (26757) hydrogen bonds : bond 0.04116 ( 954) hydrogen bonds : angle 4.94156 ( 2835) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8191 (tpt) cc_final: 0.7972 (tpt) REVERT: C 49 LYS cc_start: 0.4957 (OUTLIER) cc_final: 0.3295 (mttt) REVERT: C 114 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6268 (t) REVERT: B 22 ASP cc_start: 0.8331 (m-30) cc_final: 0.7978 (m-30) REVERT: B 49 ASP cc_start: 0.7655 (t0) cc_final: 0.7372 (t70) REVERT: B 229 PHE cc_start: 0.7809 (t80) cc_final: 0.7381 (m-80) REVERT: G 49 LYS cc_start: 0.4738 (OUTLIER) cc_final: 0.3410 (ptmt) REVERT: G 114 THR cc_start: 0.6467 (OUTLIER) cc_final: 0.6197 (t) REVERT: G 122 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.3873 (mp) REVERT: K 114 THR cc_start: 0.6888 (OUTLIER) cc_final: 0.6480 (t) REVERT: F 178 MET cc_start: 0.8345 (mtt) cc_final: 0.7705 (mtt) REVERT: F 223 MET cc_start: 0.7559 (tpp) cc_final: 0.6828 (tpp) REVERT: J 24 MET cc_start: 0.7166 (mtp) cc_final: 0.6962 (mtm) REVERT: E 142 MET cc_start: 0.8261 (tpt) cc_final: 0.8044 (tpt) REVERT: I 56 LYS cc_start: 0.7227 (mttt) cc_final: 0.6647 (mmmm) REVERT: I 60 LYS cc_start: 0.7461 (pttp) cc_final: 0.7056 (ptmt) REVERT: I 151 ILE cc_start: 0.8643 (mm) cc_final: 0.8263 (mm) REVERT: I 310 SER cc_start: 0.7859 (t) cc_final: 0.7645 (m) outliers start: 61 outliers final: 55 residues processed: 299 average time/residue: 0.1516 time to fit residues: 68.0971 Evaluate side-chains 316 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 255 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 188 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 148 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 174 ASN F 245 GLN J 245 GLN E 143 ASN E 401 GLN I 62 ASN I 401 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.153993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134540 restraints weight = 21442.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.134118 restraints weight = 24171.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134319 restraints weight = 22291.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134319 restraints weight = 21523.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134319 restraints weight = 21522.740| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19707 Z= 0.117 Angle : 0.556 9.147 26757 Z= 0.291 Chirality : 0.044 0.212 2853 Planarity : 0.004 0.046 3261 Dihedral : 13.008 163.988 2990 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 2.41 % Allowed : 18.00 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.43 (0.17), residues: 2274 helix: 1.13 (0.16), residues: 996 sheet: 0.12 (0.28), residues: 327 loop : -0.48 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 236 TYR 0.021 0.001 TYR C 184 PHE 0.015 0.001 PHE C 251 TRP 0.019 0.001 TRP K 253 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00259 (19707) covalent geometry : angle 0.55638 (26757) hydrogen bonds : bond 0.03853 ( 954) hydrogen bonds : angle 4.85850 ( 2835) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.765 Fit side-chains REVERT: A 142 MET cc_start: 0.8145 (tpt) cc_final: 0.7938 (tpt) REVERT: C 49 LYS cc_start: 0.5009 (OUTLIER) cc_final: 0.3400 (mttt) REVERT: C 114 THR cc_start: 0.6721 (OUTLIER) cc_final: 0.6232 (t) REVERT: B 22 ASP cc_start: 0.8278 (m-30) cc_final: 0.7905 (m-30) REVERT: B 49 ASP cc_start: 0.7647 (t0) cc_final: 0.7364 (t70) REVERT: B 229 PHE cc_start: 0.7772 (t80) cc_final: 0.7439 (m-80) REVERT: B 236 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7248 (mtt180) REVERT: G 49 LYS cc_start: 0.4798 (OUTLIER) cc_final: 0.3503 (ptmt) REVERT: G 114 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.6100 (t) REVERT: K 114 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6422 (t) REVERT: F 178 MET cc_start: 0.8309 (mtt) cc_final: 0.7699 (mtt) REVERT: F 223 MET cc_start: 0.7465 (tpp) cc_final: 0.6756 (tpp) REVERT: F 236 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7409 (mtt180) REVERT: I 56 LYS cc_start: 0.7211 (mttt) cc_final: 0.6636 (mmmm) REVERT: I 151 ILE cc_start: 0.8548 (mm) cc_final: 0.8198 (mm) REVERT: I 310 SER cc_start: 0.7806 (t) cc_final: 0.7593 (m) outliers start: 47 outliers final: 39 residues processed: 292 average time/residue: 0.1489 time to fit residues: 65.5407 Evaluate side-chains 294 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 261 THR Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 205 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 224 optimal weight: 0.6980 chunk 156 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 185 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN B 174 ASN B 245 GLN F 245 GLN J 245 GLN E 401 GLN I 401 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.154021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.134612 restraints weight = 21534.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134442 restraints weight = 22397.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134440 restraints weight = 22583.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134445 restraints weight = 22328.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.134445 restraints weight = 21897.591| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19707 Z= 0.119 Angle : 0.551 9.390 26757 Z= 0.288 Chirality : 0.043 0.165 2853 Planarity : 0.004 0.046 3261 Dihedral : 12.768 164.880 2990 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 2.62 % Allowed : 18.05 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % 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: 0.55 (0.17), residues: 2274 helix: 1.23 (0.16), residues: 996 sheet: 0.15 (0.28), residues: 327 loop : -0.40 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 236 TYR 0.021 0.001 TYR C 184 PHE 0.023 0.001 PHE E 394 TRP 0.021 0.001 TRP C 253 HIS 0.003 0.001 HIS J 232 Details of bonding type rmsd covalent geometry : bond 0.00266 (19707) covalent geometry : angle 0.55136 (26757) hydrogen bonds : bond 0.03828 ( 954) hydrogen bonds : angle 4.81173 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.96 seconds wall clock time: 49 minutes 14.17 seconds (2954.17 seconds total)