Starting phenix.real_space_refine on Mon Jul 6 08:47:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4o_25683/07_2026/7t4o_25683_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4o_25683/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t4o_25683/07_2026/7t4o_25683_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4o_25683/07_2026/7t4o_25683_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t4o_25683/07_2026/7t4o_25683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4o_25683/07_2026/7t4o_25683.map" } 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-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CU': 2} Chain breaks: 2 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, 0 Ad-hoc single atom residues: {' CU': 2} Chain breaks: 2 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 1 Time building chain proxies: 3.57, per 1000 atoms: 0.19 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: 1.75 Conformation dependent library (CDL) restraints added in 756.8 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: 0.55 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: 3.14 Time building geometry restraints manager: 2.32 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 3.060 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.776 3.060 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.777 3.060 nonbonded pdb=" NE2 HIS I 139 " pdb="CU CU I 501 " model vdw 1.783 3.060 nonbonded pdb=" NE2 HIS E 139 " pdb="CU CU E 501 " model vdw 1.783 3.060 ... (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: 1.820 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: 0.540 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.070 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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/Z covalent geometry : bond 0.00663 / 0.37 (19707) covalent geometry : angle 0.87674 / 0.47 (26757) hydrogen bonds : bond 0.16992 / 11.16 ( 954) hydrogen bonds : angle 7.02098 / 4.87 ( 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 : 0.710 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: 0.1703 time to fit residues: 111.4705 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 : 0.442 ------------------------------------------------------------------------------- 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: 5.9990 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... ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** 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 11 HIS ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 72 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.159526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.141881 restraints weight = 21108.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.139695 restraints weight = 36423.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.140355 restraints weight = 33718.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.140280 restraints weight = 26176.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.140982 restraints weight = 22334.050| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19707 Z= 0.210 Angle : 0.689 7.893 26757 Z= 0.357 Chirality : 0.048 0.215 2853 Planarity : 0.006 0.055 3261 Dihedral : 15.455 144.015 3009 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.75 % Favored : 94.99 % Rotamer: Outliers : 2.15 % Allowed : 8.82 % Favored : 89.03 % 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: 0.11 (0.17), residues: 2274 helix: 0.67 (0.16), residues: 1005 sheet: 0.38 (0.31), residues: 339 loop : -0.60 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 100 TYR 0.032 0.002 TYR C 184 PHE 0.030 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/Z covalent geometry : bond 0.00501 / 0.21 (19707) covalent geometry : angle 0.68929 / 0.36 (26757) hydrogen bonds : bond 0.04904 / 3.20 ( 954) hydrogen bonds : angle 5.41401 / 3.78 ( 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 334 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.5524 (mmp) cc_final: 0.5040 (mmp) REVERT: A 269 MET cc_start: 0.7682 (mtp) cc_final: 0.7408 (mtp) REVERT: C 49 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.5152 (ptmt) REVERT: B 22 ASP cc_start: 0.8306 (m-30) cc_final: 0.8015 (m-30) REVERT: B 236 ARG cc_start: 0.6630 (tpp80) cc_final: 0.6061 (mtp85) REVERT: G 49 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5057 (ptmt) REVERT: K 210 TYR cc_start: 0.7879 (t80) cc_final: 0.7604 (t80) REVERT: F 230 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7267 (ttt) REVERT: F 236 ARG cc_start: 0.6650 (tpp80) cc_final: 0.6054 (mtp85) REVERT: J 22 ASP cc_start: 0.8289 (m-30) cc_final: 0.7855 (m-30) REVERT: J 236 ARG cc_start: 0.6630 (tpp80) cc_final: 0.6050 (mtp85) REVERT: E 218 MET cc_start: 0.5392 (mmp) cc_final: 0.5141 (mmp) REVERT: I 68 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7689 (mttp) REVERT: I 151 ILE cc_start: 0.8357 (mm) cc_final: 0.8103 (mm) outliers start: 42 outliers final: 24 residues processed: 314 average time/residue: 0.1551 time to fit residues: 72.5925 Evaluate side-chains 278 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 B residue 230 MET 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 F residue 230 MET 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: 2.9990 chunk 205 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 210 optimal weight: 0.0370 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN I 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.157907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.137268 restraints weight = 21140.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.137792 restraints weight = 21137.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.139198 restraints weight = 18121.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.139491 restraints weight = 15143.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.139640 restraints weight = 14387.613| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2867 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= 0.162 Angle : 0.598 6.804 26757 Z= 0.311 Chirality : 0.045 0.166 2853 Planarity : 0.005 0.040 3261 Dihedral : 14.591 143.338 2999 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.53 % Favored : 95.21 % Rotamer: Outliers : 2.51 % Allowed : 11.79 % Favored : 85.69 % 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: 0.19 (0.17), residues: 2274 helix: 0.84 (0.16), residues: 990 sheet: 0.18 (0.29), residues: 345 loop : -0.56 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 400 TYR 0.028 0.002 TYR K 184 PHE 0.020 0.002 PHE C 251 TRP 0.021 0.002 TRP G 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (19707) covalent geometry : angle 0.59751 / 0.31 (26757) hydrogen bonds : bond 0.04493 / 2.95 ( 954) hydrogen bonds : angle 5.17165 / 3.62 ( 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 341 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.760 Fit side-chains REVERT: A 218 MET cc_start: 0.5683 (mmp) cc_final: 0.5462 (mmp) REVERT: C 49 LYS cc_start: 0.6418 (OUTLIER) cc_final: 0.4544 (mttt) REVERT: B 22 ASP cc_start: 0.8550 (m-30) cc_final: 0.8232 (m-30) REVERT: B 236 ARG cc_start: 0.6921 (tpp80) cc_final: 0.6286 (mtp85) REVERT: G 49 LYS cc_start: 0.6068 (OUTLIER) cc_final: 0.4485 (ptmt) REVERT: F 22 ASP cc_start: 0.8404 (m-30) cc_final: 0.8029 (m-30) REVERT: F 236 ARG cc_start: 0.6917 (tpp80) cc_final: 0.6241 (mtp85) REVERT: J 22 ASP cc_start: 0.8431 (m-30) cc_final: 0.7969 (m-30) REVERT: J 45 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7914 (ttp) REVERT: J 236 ARG cc_start: 0.6860 (tpp80) cc_final: 0.6171 (mtp85) REVERT: E 82 ASP cc_start: 0.5812 (m-30) cc_final: 0.5598 (m-30) REVERT: E 372 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7025 (tm-30) outliers start: 49 outliers final: 28 residues processed: 321 average time/residue: 0.1476 time to fit residues: 72.5011 Evaluate side-chains 297 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 ARG 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 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 F residue 47 ASP Chi-restraints excluded: chain J residue 45 MET 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 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 80 THR Chi-restraints excluded: chain I residue 82 ASP 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: 0.5980 chunk 226 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 38 optimal weight: 0.0270 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN 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 = 0.159498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.138710 restraints weight = 21068.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.139542 restraints weight = 26271.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.141045 restraints weight = 18960.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.141193 restraints weight = 15696.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.141283 restraints weight = 14512.215| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19707 Z= 0.120 Angle : 0.557 7.043 26757 Z= 0.290 Chirality : 0.044 0.175 2853 Planarity : 0.005 0.039 3261 Dihedral : 14.038 143.173 2999 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.71 % Favored : 95.03 % Rotamer: Outliers : 2.92 % Allowed : 13.03 % Favored : 84.05 % 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: 0.40 (0.17), residues: 2274 helix: 1.09 (0.16), residues: 990 sheet: 0.17 (0.29), residues: 345 loop : -0.49 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.024 0.001 TYR C 184 PHE 0.024 0.001 PHE C 251 TRP 0.029 0.001 TRP G 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (19707) covalent geometry : angle 0.55720 / 0.29 (26757) hydrogen bonds : bond 0.03961 / 2.60 ( 954) hydrogen bonds : angle 4.99473 / 3.49 ( 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 344 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 0.726 Fit side-chains REVERT: A 310 SER cc_start: 0.7997 (t) cc_final: 0.7737 (m) REVERT: C 49 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.4357 (mttt) REVERT: B 22 ASP cc_start: 0.8486 (m-30) cc_final: 0.8226 (m-30) REVERT: B 223 MET cc_start: 0.7646 (tpp) cc_final: 0.7090 (tpp) REVERT: B 236 ARG cc_start: 0.6986 (tpp80) cc_final: 0.6347 (mtp85) REVERT: G 49 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.4470 (ptmt) REVERT: F 236 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6184 (mtp85) REVERT: J 22 ASP cc_start: 0.8488 (m-30) cc_final: 0.8005 (m-30) REVERT: J 244 LEU cc_start: 0.6064 (tp) cc_final: 0.5623 (mp) REVERT: E 82 ASP cc_start: 0.5824 (m-30) cc_final: 0.5586 (m-30) REVERT: E 323 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7506 (mtp180) REVERT: E 372 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7022 (tm-30) REVERT: I 310 SER cc_start: 0.7935 (t) cc_final: 0.7666 (m) outliers start: 57 outliers final: 33 residues processed: 320 average time/residue: 0.1503 time to fit residues: 73.8462 Evaluate side-chains 299 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 251 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 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 145 ILE Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU 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 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 321 SER 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 65 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 251 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: 0.9980 chunk 113 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 28 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.156673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.136588 restraints weight = 20983.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.136753 restraints weight = 27047.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.138128 restraints weight = 20162.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.138423 restraints weight = 16970.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.138610 restraints weight = 15334.895| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3450 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= 0.144 Angle : 0.582 6.168 26757 Z= 0.301 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.039 3261 Dihedral : 13.563 141.056 2999 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 2.72 % Allowed : 14.67 % Favored : 82.62 % 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: 0.38 (0.17), residues: 2274 helix: 1.03 (0.16), residues: 996 sheet: 0.31 (0.29), residues: 327 loop : -0.52 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 100 TYR 0.025 0.002 TYR K 184 PHE 0.022 0.001 PHE C 251 TRP 0.025 0.001 TRP C 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (19707) covalent geometry : angle 0.58185 / 0.30 (26757) hydrogen bonds : bond 0.04113 / 2.69 ( 954) hydrogen bonds : angle 4.97050 / 3.48 ( 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 322 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.744 Fit side-chains REVERT: A 310 SER cc_start: 0.7964 (t) cc_final: 0.7727 (m) REVERT: C 49 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.4178 (mttt) REVERT: C 114 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.5862 (t) REVERT: B 22 ASP cc_start: 0.8475 (m-30) cc_final: 0.8209 (m-30) REVERT: B 223 MET cc_start: 0.7669 (tpp) cc_final: 0.7085 (tpp) REVERT: B 236 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6304 (mtp85) REVERT: G 49 LYS cc_start: 0.5862 (OUTLIER) cc_final: 0.4338 (ptmt) REVERT: J 22 ASP cc_start: 0.8525 (m-30) cc_final: 0.8181 (m-30) REVERT: E 323 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7558 (mtp180) REVERT: I 56 LYS cc_start: 0.7127 (mttt) cc_final: 0.6656 (mmmm) REVERT: I 218 MET cc_start: 0.5565 (mmp) cc_final: 0.5260 (mmp) REVERT: I 310 SER cc_start: 0.7924 (t) cc_final: 0.7665 (m) outliers start: 53 outliers final: 40 residues processed: 299 average time/residue: 0.1506 time to fit residues: 69.1540 Evaluate side-chains 300 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 257 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 167 ARG 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 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 145 ILE Chi-restraints excluded: chain C residue 199 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 K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU 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 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 189 VAL Chi-restraints excluded: chain E residue 65 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 313 ARG Chi-restraints excluded: chain E residue 382 ASP 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 382 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 GLN F 245 GLN J 245 GLN E 33 HIS I 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.150700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.132426 restraints weight = 20985.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.131017 restraints weight = 28445.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.132016 restraints weight = 27541.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.132105 restraints weight = 22744.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.132337 restraints weight = 21690.046| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19707 Z= 0.208 Angle : 0.667 5.924 26757 Z= 0.346 Chirality : 0.048 0.220 2853 Planarity : 0.005 0.042 3261 Dihedral : 14.067 151.576 2996 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 3.44 % Allowed : 15.64 % Favored : 80.92 % 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: 0.00 (0.17), residues: 2274 helix: 0.65 (0.15), residues: 999 sheet: -0.02 (0.27), residues: 357 loop : -0.59 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 198 TYR 0.031 0.002 TYR C 184 PHE 0.027 0.002 PHE K 251 TRP 0.045 0.002 TRP C 253 HIS 0.010 0.002 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (19707) covalent geometry : angle 0.66690 / 0.35 (26757) hydrogen bonds : bond 0.04726 / 3.07 ( 954) hydrogen bonds : angle 5.17215 / 3.63 ( 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 340 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 273 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 SER cc_start: 0.7919 (t) cc_final: 0.7702 (m) REVERT: C 49 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.4021 (mttt) REVERT: C 114 THR cc_start: 0.6547 (OUTLIER) cc_final: 0.6097 (t) REVERT: B 22 ASP cc_start: 0.8532 (m-30) cc_final: 0.8237 (m-30) REVERT: B 49 ASP cc_start: 0.7665 (t0) cc_final: 0.7333 (t70) REVERT: B 223 MET cc_start: 0.7821 (tpp) cc_final: 0.7210 (tpp) REVERT: B 236 ARG cc_start: 0.7434 (tpp80) cc_final: 0.6525 (mtp85) REVERT: G 49 LYS cc_start: 0.5630 (OUTLIER) cc_final: 0.4180 (ptmt) REVERT: F 22 ASP cc_start: 0.8591 (m-30) cc_final: 0.8315 (m-30) REVERT: F 229 PHE cc_start: 0.7499 (t80) cc_final: 0.6989 (t80) REVERT: I 56 LYS cc_start: 0.7224 (mttt) cc_final: 0.6656 (mmmm) REVERT: I 310 SER cc_start: 0.7888 (t) cc_final: 0.7638 (m) outliers start: 67 outliers final: 48 residues processed: 317 average time/residue: 0.1540 time to fit residues: 73.9501 Evaluate side-chains 302 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 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 145 ILE 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 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 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 189 VAL Chi-restraints excluded: chain J residue 204 THR 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 298 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 387 PHE 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 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: 20.0000 chunk 108 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 209 optimal weight: 0.0050 chunk 168 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 163 optimal weight: 5.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3572 r_free = 0.3572 target = 0.153439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.130937 restraints weight = 21198.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.131317 restraints weight = 23759.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.131513 restraints weight = 21124.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132162 restraints weight = 18722.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.132327 restraints weight = 16931.880| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19707 Z= 0.133 Angle : 0.574 6.087 26757 Z= 0.300 Chirality : 0.044 0.172 2853 Planarity : 0.005 0.043 3261 Dihedral : 13.688 154.385 2996 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.18 % Allowed : 16.56 % Favored : 80.26 % 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: 0.27 (0.17), residues: 2274 helix: 0.93 (0.16), residues: 999 sheet: 0.25 (0.28), residues: 321 loop : -0.56 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 400 TYR 0.024 0.001 TYR K 184 PHE 0.018 0.001 PHE K 251 TRP 0.034 0.001 TRP K 253 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (19707) covalent geometry : angle 0.57367 / 0.30 (26757) hydrogen bonds : bond 0.04067 / 2.67 ( 954) hydrogen bonds : angle 4.98714 / 3.49 ( 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 323 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 SER cc_start: 0.8011 (t) cc_final: 0.7789 (m) REVERT: C 49 LYS cc_start: 0.5181 (OUTLIER) cc_final: 0.3446 (mttt) REVERT: C 114 THR cc_start: 0.6478 (OUTLIER) cc_final: 0.6007 (t) REVERT: B 22 ASP cc_start: 0.8434 (m-30) cc_final: 0.8170 (m-30) REVERT: B 49 ASP cc_start: 0.7644 (t0) cc_final: 0.7334 (t70) REVERT: B 229 PHE cc_start: 0.7893 (t80) cc_final: 0.7455 (m-80) REVERT: B 236 ARG cc_start: 0.7432 (tpp80) cc_final: 0.6514 (mtp85) REVERT: G 49 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.3596 (ptmt) REVERT: G 110 TYR cc_start: 0.5581 (t80) cc_final: 0.4982 (t80) REVERT: K 114 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6212 (t) REVERT: F 223 MET cc_start: 0.7593 (tpp) cc_final: 0.7092 (tpp) REVERT: F 229 PHE cc_start: 0.7507 (t80) cc_final: 0.7038 (t80) REVERT: J 24 MET cc_start: 0.7143 (mtp) cc_final: 0.6932 (mtm) REVERT: I 56 LYS cc_start: 0.7271 (mttt) cc_final: 0.6677 (mmmm) REVERT: I 310 SER cc_start: 0.7939 (t) cc_final: 0.7722 (m) outliers start: 62 outliers final: 45 residues processed: 301 average time/residue: 0.1518 time to fit residues: 68.7718 Evaluate side-chains 298 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 249 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 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 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 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 189 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 82 ASP 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 65 VAL Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR 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: 9.9990 chunk 198 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.152804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.144412 restraints weight = 21129.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 91)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.129658 restraints weight = 30280.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132790 restraints weight = 25776.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.132253 restraints weight = 20254.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.132949 restraints weight = 20392.976| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19707 Z= 0.159 Angle : 0.596 7.411 26757 Z= 0.310 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.043 3261 Dihedral : 13.524 157.368 2990 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 3.18 % Allowed : 16.72 % 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: 0.23 (0.17), residues: 2274 helix: 0.92 (0.16), residues: 1002 sheet: -0.07 (0.26), residues: 360 loop : -0.50 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 400 TYR 0.025 0.002 TYR K 184 PHE 0.016 0.001 PHE K 251 TRP 0.033 0.001 TRP K 253 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (19707) covalent geometry : angle 0.59582 / 0.31 (26757) hydrogen bonds : bond 0.04201 / 2.75 ( 954) hydrogen bonds : angle 4.98644 / 3.49 ( 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 327 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 SER cc_start: 0.8034 (t) cc_final: 0.7800 (m) REVERT: C 49 LYS cc_start: 0.5024 (OUTLIER) cc_final: 0.3310 (mttt) REVERT: C 114 THR cc_start: 0.6536 (OUTLIER) cc_final: 0.6066 (t) REVERT: B 22 ASP cc_start: 0.8423 (m-30) cc_final: 0.8159 (m-30) REVERT: B 49 ASP cc_start: 0.7670 (t0) cc_final: 0.7368 (t70) REVERT: B 229 PHE cc_start: 0.7889 (t80) cc_final: 0.7457 (m-80) REVERT: B 236 ARG cc_start: 0.7489 (tpp80) cc_final: 0.6552 (mtp85) REVERT: G 49 LYS cc_start: 0.4878 (OUTLIER) cc_final: 0.3456 (ptmt) REVERT: G 110 TYR cc_start: 0.5641 (t80) cc_final: 0.5074 (t80) REVERT: G 114 THR cc_start: 0.6312 (OUTLIER) cc_final: 0.6095 (t) REVERT: F 223 MET cc_start: 0.7591 (tpp) cc_final: 0.7090 (tpp) REVERT: F 226 LEU cc_start: 0.8702 (mt) cc_final: 0.8423 (mt) REVERT: F 229 PHE cc_start: 0.7512 (t80) cc_final: 0.7023 (t80) REVERT: J 24 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6962 (mtm) REVERT: I 56 LYS cc_start: 0.7261 (mttt) cc_final: 0.6671 (mmmm) REVERT: I 310 SER cc_start: 0.7923 (t) cc_final: 0.7695 (m) outliers start: 62 outliers final: 53 residues processed: 302 average time/residue: 0.1444 time to fit residues: 66.1618 Evaluate side-chains 311 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 253 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 145 ILE Chi-restraints excluded: chain C residue 249 VAL 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 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 199 LEU Chi-restraints excluded: chain K residue 249 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 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 24 MET 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 189 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 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 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 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 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: 4.9990 chunk 181 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 196 optimal weight: 0.0870 chunk 13 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.153667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.134862 restraints weight = 20917.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.132563 restraints weight = 34724.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.133305 restraints weight = 34425.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.134096 restraints weight = 26113.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.134294 restraints weight = 22838.456| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19707 Z= 0.134 Angle : 0.571 8.075 26757 Z= 0.297 Chirality : 0.044 0.166 2853 Planarity : 0.004 0.043 3261 Dihedral : 13.292 161.176 2990 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 3.08 % Allowed : 17.33 % 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: 0.36 (0.17), residues: 2274 helix: 1.04 (0.16), residues: 1002 sheet: 0.14 (0.28), residues: 330 loop : -0.50 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 132 TYR 0.023 0.001 TYR K 184 PHE 0.016 0.001 PHE C 251 TRP 0.033 0.001 TRP C 253 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (19707) covalent geometry : angle 0.57102 / 0.30 (26757) hydrogen bonds : bond 0.04000 / 2.63 ( 954) hydrogen bonds : angle 4.92345 / 3.45 ( 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 313 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 LYS cc_start: 0.5435 (OUTLIER) cc_final: 0.3729 (mttt) REVERT: C 114 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6195 (t) REVERT: B 22 ASP cc_start: 0.8453 (m-30) cc_final: 0.8205 (m-30) REVERT: B 49 ASP cc_start: 0.7664 (t0) cc_final: 0.7359 (t70) REVERT: B 229 PHE cc_start: 0.7841 (t80) cc_final: 0.7427 (m-80) REVERT: B 236 ARG cc_start: 0.7465 (tpp80) cc_final: 0.6593 (mtp85) REVERT: G 49 LYS cc_start: 0.5229 (OUTLIER) cc_final: 0.3905 (ptmt) REVERT: G 110 TYR cc_start: 0.5562 (t80) cc_final: 0.5111 (t80) REVERT: K 114 THR cc_start: 0.6792 (OUTLIER) cc_final: 0.6423 (t) REVERT: F 223 MET cc_start: 0.7544 (tpp) cc_final: 0.6821 (tpp) REVERT: F 226 LEU cc_start: 0.8659 (mt) cc_final: 0.8374 (mt) REVERT: F 229 PHE cc_start: 0.7492 (t80) cc_final: 0.7010 (t80) REVERT: I 56 LYS cc_start: 0.7256 (mttt) cc_final: 0.6664 (mmmm) outliers start: 60 outliers final: 48 residues processed: 290 average time/residue: 0.1503 time to fit residues: 66.1707 Evaluate side-chains 302 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 250 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 145 ILE 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 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 199 LEU Chi-restraints excluded: chain K residue 249 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 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 189 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 313 ARG 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 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 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL 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: 1.9990 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 148 optimal weight: 0.0870 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.152392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.143609 restraints weight = 21115.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.128961 restraints weight = 32503.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.130168 restraints weight = 29378.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.130829 restraints weight = 24614.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.132791 restraints weight = 21448.131| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19707 Z= 0.165 Angle : 0.599 7.999 26757 Z= 0.312 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.042 3261 Dihedral : 13.333 164.912 2990 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.25 % Rotamer: Outliers : 2.77 % Allowed : 17.79 % Favored : 79.44 % 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: 0.26 (0.17), residues: 2274 helix: 0.94 (0.16), residues: 1002 sheet: 0.05 (0.28), residues: 330 loop : -0.52 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 115 TYR 0.034 0.002 TYR A 330 PHE 0.015 0.001 PHE A 394 TRP 0.036 0.001 TRP K 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (19707) covalent geometry : angle 0.59941 / 0.31 (26757) hydrogen bonds : bond 0.04214 / 2.76 ( 954) hydrogen bonds : angle 4.96666 / 3.49 ( 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 308 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: C 49 LYS cc_start: 0.4788 (OUTLIER) cc_final: 0.3151 (mttt) REVERT: C 114 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6224 (t) REVERT: B 22 ASP cc_start: 0.8383 (m-30) cc_final: 0.8127 (m-30) REVERT: B 49 ASP cc_start: 0.7695 (t0) cc_final: 0.7405 (t70) REVERT: B 229 PHE cc_start: 0.7884 (t80) cc_final: 0.7489 (m-80) REVERT: B 236 ARG cc_start: 0.7519 (tpp80) cc_final: 0.6579 (mtp85) REVERT: G 49 LYS cc_start: 0.4631 (OUTLIER) cc_final: 0.3300 (ptmt) REVERT: F 223 MET cc_start: 0.7564 (tpp) cc_final: 0.6828 (tpp) REVERT: F 226 LEU cc_start: 0.8665 (mt) cc_final: 0.8388 (mt) REVERT: F 229 PHE cc_start: 0.7561 (t80) cc_final: 0.7024 (t80) REVERT: I 56 LYS cc_start: 0.7309 (mttt) cc_final: 0.6723 (mmmm) REVERT: I 60 LYS cc_start: 0.7418 (pttp) cc_final: 0.7041 (ptmt) outliers start: 54 outliers final: 50 residues processed: 290 average time/residue: 0.1546 time to fit residues: 67.4659 Evaluate side-chains 303 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 145 ILE 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 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 199 LEU Chi-restraints excluded: chain K residue 249 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 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 189 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 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 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 362 VAL 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: 9.9990 chunk 206 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 224 optimal weight: 0.0980 chunk 156 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 174 ASN B 245 GLN F 174 ASN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.153950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.145510 restraints weight = 21097.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.133101 restraints weight = 30436.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.133390 restraints weight = 24682.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.134401 restraints weight = 20664.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.134997 restraints weight = 18258.725| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19707 Z= 0.130 Angle : 0.567 7.479 26757 Z= 0.296 Chirality : 0.044 0.166 2853 Planarity : 0.004 0.042 3261 Dihedral : 13.118 168.800 2990 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 2.82 % Allowed : 17.85 % 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: 0.42 (0.17), residues: 2274 helix: 1.09 (0.16), residues: 999 sheet: 0.09 (0.28), residues: 330 loop : -0.43 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 296 TYR 0.026 0.001 TYR A 330 PHE 0.015 0.001 PHE K 251 TRP 0.036 0.001 TRP K 253 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (19707) covalent geometry : angle 0.56661 / 0.30 (26757) hydrogen bonds : bond 0.03971 / 2.62 ( 954) hydrogen bonds : angle 4.90962 / 3.45 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.12 seconds wall clock time: 52 minutes 59.56 seconds (3179.56 seconds total)