Starting phenix.real_space_refine on Thu Nov 20 12:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683.map" model { file = "/net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t4o_25683/11_2025/7t4o_25683_trim.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17751 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 5 5.60 5 P 12 5.49 5 S 87 5.16 5 C 12684 2.51 5 N 3054 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19142 Number of models: 1 Model: "" Number of chains: 9 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: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'P1O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 110 Unusual residues: {'D10': 3, 'P1O': 1, 'PLC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: E, I, F, J, G, K Time building chain proxies: 4.46, per 1000 atoms: 0.23 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: 1.62 Conformation dependent library (CDL) restraints added in 847.0 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: 0.69 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: 3.20 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3086 1.32 - 1.45: 5668 1.45 - 1.57: 10746 1.57 - 1.69: 39 1.69 - 1.81: 168 Bond restraints: 19707 Sorted by residual: bond pdb=" C19 P1O G 302 " pdb=" O7 P1O G 302 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C19 P1O K 302 " pdb=" O7 P1O K 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C19 P1O C 302 " pdb=" O7 P1O C 302 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C9 P1O K 301 " pdb=" O5 P1O K 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C9 P1O C 301 " pdb=" O5 P1O C 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 19702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 25724 2.16 - 4.32: 862 4.32 - 6.48: 123 6.48 - 8.63: 27 8.63 - 10.79: 21 Bond angle restraints: 26757 Sorted by residual: angle pdb=" CA PRO K 200 " pdb=" C PRO K 200 " pdb=" O PRO K 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO C 200 " pdb=" C PRO C 200 " pdb=" O PRO C 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CA PRO G 200 " pdb=" C PRO G 200 " pdb=" O PRO G 200 " ideal model delta sigma weight residual 122.15 116.97 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" C GLU I 287 " pdb=" N ASP I 288 " pdb=" CA ASP I 288 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C GLU A 287 " pdb=" N ASP A 288 " pdb=" CA ASP A 288 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 ... (remaining 26752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 10810 30.46 - 60.91: 536 60.91 - 91.37: 24 91.37 - 121.83: 6 121.83 - 152.28: 12 Dihedral angle restraints: 11388 sinusoidal: 4740 harmonic: 6648 Sorted by residual: dihedral pdb=" C1 P1O G 302 " pdb=" O3 P1O G 302 " pdb=" P1 P1O G 302 " pdb=" O4 P1O G 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.47 152.28 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O C 302 " pdb=" O3 P1O C 302 " pdb=" P1 P1O C 302 " pdb=" O4 P1O C 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.51 152.24 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C1 P1O K 302 " pdb=" O3 P1O K 302 " pdb=" P1 P1O K 302 " pdb=" O4 P1O K 302 " ideal model delta sinusoidal sigma weight residual 168.75 16.53 152.22 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 11385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1976 0.042 - 0.084: 558 0.084 - 0.126: 280 0.126 - 0.167: 21 0.167 - 0.209: 18 Chirality restraints: 2853 Sorted by residual: chirality pdb=" CA ILE G 193 " pdb=" N ILE G 193 " pdb=" C ILE G 193 " pdb=" CB ILE G 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE K 193 " pdb=" N ILE K 193 " pdb=" C ILE K 193 " pdb=" CB ILE K 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 193 " pdb=" N ILE C 193 " pdb=" C ILE C 193 " pdb=" CB ILE C 193 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2850 not shown) Planarity restraints: 3261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 95 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.03e+00 pdb=" N PRO I 96 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO I 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 96 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 95 " -0.046 5.00e-02 4.00e+02 7.05e-02 7.96e+00 pdb=" N PRO E 96 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 95 " 0.046 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO A 96 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.038 5.00e-02 4.00e+02 ... (remaining 3258 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 62 2.40 - 3.03: 11348 3.03 - 3.65: 29766 3.65 - 4.28: 45145 4.28 - 4.90: 75650 Nonbonded interactions: 161971 Sorted by model distance: nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS I 33 " pdb="CU CU I 501 " model vdw 1.776 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.777 2.320 nonbonded pdb=" NE2 HIS I 139 " pdb="CU CU I 501 " model vdw 1.783 2.320 nonbonded pdb=" NE2 HIS E 139 " pdb="CU CU E 501 " model vdw 1.783 2.320 ... (remaining 161966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 501) selection = (chain 'E' and resid 33 through 501) selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'F' and (resid 7 through 247 or resid 303 through 304)) selection = (chain 'J' and (resid 7 through 247 or resid 303 through 304)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.160 Find NCS groups from input model: 0.390 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 19707 Z= 0.366 Angle : 0.877 10.792 26757 Z= 0.474 Chirality : 0.049 0.209 2853 Planarity : 0.005 0.071 3261 Dihedral : 16.839 152.282 7134 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.37 % Rotamer: Outliers : 1.85 % Allowed : 0.97 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2274 helix: 0.63 (0.16), residues: 951 sheet: 0.51 (0.29), residues: 348 loop : -0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 45 TYR 0.029 0.002 TYR F 37 PHE 0.026 0.001 PHE G 251 TRP 0.037 0.002 TRP J 54 HIS 0.023 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00663 (19707) covalent geometry : angle 0.87674 (26757) hydrogen bonds : bond 0.16992 ( 954) hydrogen bonds : angle 7.02098 ( 2835) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 427 time to evaluate : 0.663 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: 0.7129 (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: 0.1749 time to fit residues: 113.4360 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 : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 251 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.159367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.137979 restraints weight = 21431.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.137207 restraints weight = 27945.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.139289 restraints weight = 18850.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.139357 restraints weight = 14210.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.139772 restraints weight = 14095.990| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19707 Z= 0.203 Angle : 0.669 7.056 26757 Z= 0.347 Chirality : 0.048 0.259 2853 Planarity : 0.006 0.054 3261 Dihedral : 15.425 145.970 3009 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.75 % Favored : 94.99 % Rotamer: Outliers : 2.10 % Allowed : 9.03 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2274 helix: 0.68 (0.16), residues: 1005 sheet: 0.39 (0.30), residues: 339 loop : -0.60 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 400 TYR 0.031 0.002 TYR C 184 PHE 0.031 0.002 PHE K 251 TRP 0.035 0.002 TRP B 54 HIS 0.008 0.002 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00484 (19707) covalent geometry : angle 0.66922 (26757) hydrogen bonds : bond 0.05165 ( 954) hydrogen bonds : angle 5.46642 ( 2835) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4548 Ramachandran restraints generated. 2274 Oldfield, 0 Emsley, 2274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 291 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 218 MET cc_start: 0.5507 (mmp) cc_final: 0.4973 (mmp) REVERT: A 237 MET cc_start: 0.6637 (mtt) cc_final: 0.6390 (mtt) REVERT: A 269 MET cc_start: 0.7717 (mtp) cc_final: 0.7455 (mtp) REVERT: C 49 LYS cc_start: 0.6461 (OUTLIER) cc_final: 0.4923 (ptmt) REVERT: B 22 ASP cc_start: 0.8245 (m-30) cc_final: 0.7943 (m-30) REVERT: B 236 ARG cc_start: 0.6611 (tpp80) cc_final: 0.6006 (mtp85) REVERT: G 49 LYS cc_start: 0.6395 (OUTLIER) cc_final: 0.4817 (ptmt) REVERT: K 210 TYR cc_start: 0.7855 (t80) cc_final: 0.7623 (t80) REVERT: F 236 ARG cc_start: 0.6610 (tpp80) cc_final: 0.6001 (mtp85) REVERT: J 22 ASP cc_start: 0.8247 (m-30) cc_final: 0.7818 (m-30) REVERT: J 236 ARG cc_start: 0.6616 (tpp80) cc_final: 0.5984 (mtp85) REVERT: E 163 MET cc_start: 0.8224 (ttt) cc_final: 0.7947 (ttm) REVERT: E 218 MET cc_start: 0.5343 (mmp) cc_final: 0.5058 (mmp) REVERT: I 68 LYS cc_start: 0.7902 (mtmm) cc_final: 0.7644 (mttp) REVERT: I 151 ILE cc_start: 0.8353 (mm) cc_final: 0.8088 (mm) outliers start: 41 outliers final: 23 residues processed: 312 average time/residue: 0.1640 time to fit residues: 75.6021 Evaluate side-chains 278 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 321 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 97 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 GLN E 38 GLN I 38 GLN I 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.156444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.136867 restraints weight = 21365.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.136135 restraints weight = 23849.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.136732 restraints weight = 23814.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.137415 restraints weight = 19825.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.137588 restraints weight = 17555.814| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2975 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= 0.171 Angle : 0.613 6.623 26757 Z= 0.319 Chirality : 0.046 0.170 2853 Planarity : 0.005 0.042 3261 Dihedral : 14.669 143.324 2999 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.44 % Favored : 95.29 % Rotamer: Outliers : 2.82 % Allowed : 11.64 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2274 helix: 0.77 (0.16), residues: 990 sheet: 0.12 (0.28), residues: 351 loop : -0.57 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 100 TYR 0.030 0.002 TYR K 184 PHE 0.030 0.002 PHE G 251 TRP 0.024 0.002 TRP G 253 HIS 0.007 0.001 HIS J 11 Details of bonding type rmsd covalent geometry : bond 0.00398 (19707) covalent geometry : angle 0.61296 (26757) hydrogen bonds : bond 0.04577 ( 954) hydrogen bonds : angle 5.20640 ( 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 350 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.721 Fit side-chains REVERT: A 218 MET cc_start: 0.5727 (mmp) cc_final: 0.5519 (mmp) REVERT: C 49 LYS cc_start: 0.6463 (OUTLIER) cc_final: 0.4581 (mttt) REVERT: B 22 ASP cc_start: 0.8566 (m-30) cc_final: 0.8274 (m-30) REVERT: B 236 ARG cc_start: 0.6959 (tpp80) cc_final: 0.6315 (mtp85) REVERT: G 49 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.4595 (ptmt) REVERT: F 22 ASP cc_start: 0.8443 (m-30) cc_final: 0.8082 (m-30) REVERT: F 236 ARG cc_start: 0.6979 (tpp80) cc_final: 0.6304 (mtp85) REVERT: J 236 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6231 (mtp85) REVERT: E 82 ASP cc_start: 0.5866 (m-30) cc_final: 0.5638 (m-30) REVERT: I 56 LYS cc_start: 0.7093 (mttt) cc_final: 0.6596 (mmmm) REVERT: I 151 ILE cc_start: 0.8450 (mm) cc_final: 0.8246 (mm) outliers start: 55 outliers final: 31 residues processed: 329 average time/residue: 0.1474 time to fit residues: 73.7292 Evaluate side-chains 298 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 167 ARG Chi-restraints excluded: chain A residue 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 F residue 91 VAL Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 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 321 SER Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 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: 1.9990 chunk 226 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 189 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 38 optimal weight: 30.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.153594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.136017 restraints weight = 21575.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.134567 restraints weight = 28905.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.135822 restraints weight = 27468.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.135902 restraints weight = 21689.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.136119 restraints weight = 20076.758| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19707 Z= 0.167 Angle : 0.612 6.991 26757 Z= 0.318 Chirality : 0.046 0.213 2853 Planarity : 0.005 0.041 3261 Dihedral : 14.058 145.065 2999 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.75 % Favored : 94.99 % Rotamer: Outliers : 3.54 % Allowed : 13.64 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2274 helix: 0.77 (0.16), residues: 996 sheet: 0.33 (0.29), residues: 321 loop : -0.66 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 400 TYR 0.028 0.002 TYR C 184 PHE 0.024 0.002 PHE C 251 TRP 0.023 0.002 TRP G 253 HIS 0.007 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00393 (19707) covalent geometry : angle 0.61191 (26757) hydrogen bonds : bond 0.04341 ( 954) hydrogen bonds : angle 5.05992 ( 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 356 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 287 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.6819 (mtt) cc_final: 0.6565 (mtt) REVERT: A 310 SER cc_start: 0.7951 (t) cc_final: 0.7702 (m) REVERT: C 49 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.4331 (mttt) REVERT: C 114 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6007 (t) REVERT: B 223 MET cc_start: 0.7735 (tpp) cc_final: 0.7150 (tpp) REVERT: B 236 ARG cc_start: 0.7198 (tpp80) cc_final: 0.6297 (mtp85) REVERT: G 49 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.4487 (ptmt) REVERT: F 22 ASP cc_start: 0.8560 (m-30) cc_final: 0.8263 (m-30) REVERT: F 49 ASP cc_start: 0.7618 (t70) cc_final: 0.7378 (t70) REVERT: F 136 MET cc_start: 0.7502 (tmm) cc_final: 0.7146 (ttt) REVERT: J 236 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6318 (mtp85) REVERT: E 218 MET cc_start: 0.5650 (mmp) cc_final: 0.5309 (tpt) REVERT: I 56 LYS cc_start: 0.7185 (mttt) cc_final: 0.6686 (mmmm) REVERT: I 151 ILE cc_start: 0.8476 (mm) cc_final: 0.8226 (mm) REVERT: I 310 SER cc_start: 0.7908 (t) cc_final: 0.7616 (m) outliers start: 69 outliers final: 44 residues processed: 330 average time/residue: 0.1576 time to fit residues: 77.6242 Evaluate side-chains 308 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 313 ARG Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 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 K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 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 339 ASP Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 354 LEU 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: 0.6980 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 221 optimal weight: 0.6980 overall best weight: 1.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 62 ASN B 245 GLN F 38 HIS F 245 GLN J 245 GLN E 33 HIS I 62 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.154833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.134783 restraints weight = 21422.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.134861 restraints weight = 26336.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.136570 restraints weight = 20990.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.136878 restraints weight = 16087.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.137033 restraints weight = 15366.908| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3721 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= 0.131 Angle : 0.570 6.134 26757 Z= 0.297 Chirality : 0.045 0.164 2853 Planarity : 0.005 0.042 3261 Dihedral : 13.713 144.669 2999 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 2.77 % Allowed : 15.33 % Favored : 81.90 % 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: 0.39 (0.17), residues: 2274 helix: 1.10 (0.16), residues: 975 sheet: 0.33 (0.28), residues: 321 loop : -0.56 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 236 TYR 0.024 0.001 TYR K 184 PHE 0.021 0.001 PHE K 251 TRP 0.026 0.001 TRP C 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00297 (19707) covalent geometry : angle 0.56956 (26757) hydrogen bonds : bond 0.04042 ( 954) hydrogen bonds : angle 4.97870 ( 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 328 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 SER cc_start: 0.7972 (t) cc_final: 0.7755 (m) REVERT: C 49 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.4063 (mttt) REVERT: B 223 MET cc_start: 0.7690 (tpp) cc_final: 0.7099 (tpp) REVERT: B 236 ARG cc_start: 0.7240 (tpp80) cc_final: 0.6367 (mtp85) REVERT: G 49 LYS cc_start: 0.5665 (OUTLIER) cc_final: 0.4178 (ptmt) REVERT: F 136 MET cc_start: 0.7535 (tmm) cc_final: 0.7126 (ttt) REVERT: F 229 PHE cc_start: 0.7451 (t80) cc_final: 0.7006 (t80) REVERT: J 223 MET cc_start: 0.7636 (tpp) cc_final: 0.7011 (tpp) REVERT: J 236 ARG cc_start: 0.7148 (tpp80) cc_final: 0.6336 (mtp85) REVERT: E 218 MET cc_start: 0.5568 (mmp) cc_final: 0.5271 (mmp) REVERT: I 151 ILE cc_start: 0.8462 (mm) cc_final: 0.8225 (mm) REVERT: I 310 SER cc_start: 0.7896 (t) cc_final: 0.7637 (m) outliers start: 54 outliers final: 33 residues processed: 305 average time/residue: 0.1605 time to fit residues: 72.8923 Evaluate side-chains 286 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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 K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER 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 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 348 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 5 optimal weight: 0.6980 chunk 128 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 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 = 0.3521 r_free = 0.3521 target = 0.148907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.129747 restraints weight = 21771.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.127606 restraints weight = 29629.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.129429 restraints weight = 27802.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.129114 restraints weight = 21532.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.129216 restraints weight = 18606.497| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19707 Z= 0.230 Angle : 0.667 7.123 26757 Z= 0.346 Chirality : 0.048 0.164 2853 Planarity : 0.005 0.042 3261 Dihedral : 13.969 148.143 2990 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 3.95 % Allowed : 15.44 % Favored : 80.62 % 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: -0.07 (0.17), residues: 2274 helix: 0.64 (0.15), residues: 999 sheet: -0.11 (0.26), residues: 357 loop : -0.66 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 323 TYR 0.029 0.002 TYR C 184 PHE 0.020 0.002 PHE C 202 TRP 0.019 0.002 TRP C 253 HIS 0.009 0.002 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00553 (19707) covalent geometry : angle 0.66723 (26757) hydrogen bonds : bond 0.04762 ( 954) hydrogen bonds : angle 5.14779 ( 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 339 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7395 (mtpp) REVERT: A 142 MET cc_start: 0.8315 (tpt) cc_final: 0.8031 (tpt) REVERT: A 310 SER cc_start: 0.7981 (t) cc_final: 0.7745 (m) REVERT: A 387 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8548 (p90) REVERT: C 49 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.3814 (mttt) REVERT: C 114 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6155 (t) REVERT: B 49 ASP cc_start: 0.7673 (t0) cc_final: 0.7343 (t70) REVERT: B 223 MET cc_start: 0.7817 (tpp) cc_final: 0.7194 (tpp) REVERT: B 236 ARG cc_start: 0.7470 (tpp80) cc_final: 0.6516 (mtp85) REVERT: G 49 LYS cc_start: 0.5460 (OUTLIER) cc_final: 0.3991 (ptmt) REVERT: F 22 ASP cc_start: 0.8597 (m-30) cc_final: 0.8281 (m-30) REVERT: F 229 PHE cc_start: 0.7547 (t80) cc_final: 0.7035 (t80) REVERT: J 23 TRP cc_start: 0.7990 (m100) cc_final: 0.7497 (m100) REVERT: J 236 ARG cc_start: 0.7404 (tpp80) cc_final: 0.6481 (mtp85) REVERT: E 142 MET cc_start: 0.8318 (tpt) cc_final: 0.8056 (tpt) REVERT: I 56 LYS cc_start: 0.7212 (mttt) cc_final: 0.6686 (mmmm) REVERT: I 60 LYS cc_start: 0.7529 (pttp) cc_final: 0.7079 (ptmt) REVERT: I 151 ILE cc_start: 0.8716 (mm) cc_final: 0.8292 (mm) REVERT: I 310 SER cc_start: 0.7900 (t) cc_final: 0.7640 (m) outliers start: 77 outliers final: 58 residues processed: 314 average time/residue: 0.1573 time to fit residues: 74.1897 Evaluate side-chains 309 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 247 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain 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 134 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 134 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 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: 6.9990 chunk 116 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS B 245 GLN F 245 GLN J 245 GLN E 62 ASN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.149320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.127302 restraints weight = 21892.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.127033 restraints weight = 23513.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.128066 restraints weight = 21570.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.129015 restraints weight = 17984.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.129245 restraints weight = 15411.623| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19707 Z= 0.197 Angle : 0.632 6.957 26757 Z= 0.330 Chirality : 0.047 0.158 2853 Planarity : 0.005 0.043 3261 Dihedral : 14.063 155.085 2990 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 3.95 % Allowed : 16.00 % Favored : 80.05 % 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: -0.15 (0.17), residues: 2274 helix: 0.62 (0.15), residues: 999 sheet: -0.36 (0.26), residues: 354 loop : -0.67 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 215 TYR 0.027 0.002 TYR C 184 PHE 0.019 0.002 PHE C 202 TRP 0.027 0.002 TRP K 253 HIS 0.008 0.002 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00473 (19707) covalent geometry : angle 0.63160 (26757) hydrogen bonds : bond 0.04549 ( 954) hydrogen bonds : angle 5.11051 ( 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 338 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 0.746 Fit side-chains REVERT: A 142 MET cc_start: 0.8301 (tpt) cc_final: 0.8045 (tpt) REVERT: A 163 MET cc_start: 0.8304 (ttt) cc_final: 0.8045 (ttm) REVERT: A 310 SER cc_start: 0.8027 (t) cc_final: 0.7794 (m) REVERT: A 387 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8528 (p90) REVERT: C 49 LYS cc_start: 0.5165 (OUTLIER) cc_final: 0.3377 (mttt) REVERT: C 114 THR cc_start: 0.6689 (OUTLIER) cc_final: 0.6203 (t) REVERT: B 49 ASP cc_start: 0.7671 (t0) cc_final: 0.7365 (t70) REVERT: B 223 MET cc_start: 0.7800 (tpp) cc_final: 0.7205 (tpp) REVERT: B 229 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: G 49 LYS cc_start: 0.4993 (OUTLIER) cc_final: 0.3590 (ptmt) REVERT: F 22 ASP cc_start: 0.8554 (m-30) cc_final: 0.8255 (m-30) REVERT: F 223 MET cc_start: 0.7719 (tpp) cc_final: 0.7162 (tpp) REVERT: F 229 PHE cc_start: 0.7574 (t80) cc_final: 0.7014 (t80) REVERT: E 142 MET cc_start: 0.8301 (tpt) cc_final: 0.8057 (tpt) REVERT: I 56 LYS cc_start: 0.7234 (mttt) cc_final: 0.6666 (mmmm) REVERT: I 60 LYS cc_start: 0.7551 (pttp) cc_final: 0.7095 (ptmt) REVERT: I 310 SER cc_start: 0.7898 (t) cc_final: 0.7665 (m) outliers start: 77 outliers final: 64 residues processed: 309 average time/residue: 0.1474 time to fit residues: 69.4281 Evaluate side-chains 317 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 248 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 PHE 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 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 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 204 THR Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 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 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 362 VAL Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 138 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 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 = 0.3527 r_free = 0.3527 target = 0.149347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130394 restraints weight = 21706.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.128171 restraints weight = 34466.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.129126 restraints weight = 33688.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.129552 restraints weight = 24481.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.130042 restraints weight = 21428.888| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19707 Z= 0.169 Angle : 0.605 6.729 26757 Z= 0.316 Chirality : 0.045 0.162 2853 Planarity : 0.005 0.044 3261 Dihedral : 13.843 161.644 2990 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Rotamer: Outliers : 3.59 % Allowed : 16.72 % Favored : 79.69 % 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: -0.05 (0.17), residues: 2274 helix: 0.73 (0.15), residues: 1002 sheet: -0.38 (0.27), residues: 354 loop : -0.63 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 132 TYR 0.024 0.002 TYR K 184 PHE 0.015 0.001 PHE C 202 TRP 0.020 0.001 TRP K 253 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00401 (19707) covalent geometry : angle 0.60457 (26757) hydrogen bonds : bond 0.04336 ( 954) hydrogen bonds : angle 5.04727 ( 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 333 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 263 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8280 (tpt) cc_final: 0.8032 (tpt) REVERT: A 163 MET cc_start: 0.8309 (ttt) cc_final: 0.8055 (ttm) REVERT: A 310 SER cc_start: 0.7949 (t) cc_final: 0.7727 (m) REVERT: C 49 LYS cc_start: 0.5306 (OUTLIER) cc_final: 0.3559 (mttt) REVERT: C 114 THR cc_start: 0.6738 (OUTLIER) cc_final: 0.6286 (t) REVERT: B 49 ASP cc_start: 0.7668 (t0) cc_final: 0.7375 (t70) REVERT: B 229 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: G 49 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.3786 (ptmt) REVERT: F 22 ASP cc_start: 0.8555 (m-30) cc_final: 0.8308 (m-30) REVERT: F 223 MET cc_start: 0.7669 (tpp) cc_final: 0.7119 (tpp) REVERT: E 142 MET cc_start: 0.8289 (tpt) cc_final: 0.8053 (tpt) REVERT: I 56 LYS cc_start: 0.7246 (mttt) cc_final: 0.6694 (mmmm) REVERT: I 60 LYS cc_start: 0.7526 (pttp) cc_final: 0.7111 (ptmt) REVERT: I 151 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8342 (mm) REVERT: I 310 SER cc_start: 0.7831 (t) cc_final: 0.7608 (m) outliers start: 70 outliers final: 55 residues processed: 306 average time/residue: 0.1475 time to fit residues: 68.5281 Evaluate side-chains 310 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 229 PHE Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 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 204 THR 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 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 35 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 196 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN B 245 GLN F 245 GLN J 245 GLN E 143 ASN I 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.152022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.132397 restraints weight = 21503.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132294 restraints weight = 20800.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132294 restraints weight = 18723.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132294 restraints weight = 18723.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132294 restraints weight = 18723.460| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4515 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= 0.123 Angle : 0.562 7.302 26757 Z= 0.295 Chirality : 0.044 0.170 2853 Planarity : 0.005 0.045 3261 Dihedral : 13.384 164.283 2990 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.66 % Favored : 95.21 % Rotamer: Outliers : 2.67 % Allowed : 18.10 % Favored : 79.23 % 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: 0.22 (0.17), residues: 2274 helix: 0.99 (0.16), residues: 1002 sheet: -0.19 (0.27), residues: 360 loop : -0.55 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 132 TYR 0.021 0.001 TYR C 184 PHE 0.013 0.001 PHE C 251 TRP 0.020 0.001 TRP K 253 HIS 0.004 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00275 (19707) covalent geometry : angle 0.56227 (26757) hydrogen bonds : bond 0.03932 ( 954) hydrogen bonds : angle 4.91654 ( 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: 52 poor density : 261 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8241 (tpt) cc_final: 0.7989 (tpt) REVERT: A 163 MET cc_start: 0.8238 (ttt) cc_final: 0.7968 (ttm) REVERT: C 49 LYS cc_start: 0.4799 (OUTLIER) cc_final: 0.3156 (mttt) REVERT: C 114 THR cc_start: 0.6617 (OUTLIER) cc_final: 0.6142 (t) REVERT: B 22 ASP cc_start: 0.8314 (m-30) cc_final: 0.7961 (m-30) REVERT: B 49 ASP cc_start: 0.7667 (t0) cc_final: 0.7382 (t70) REVERT: B 229 PHE cc_start: 0.7835 (t80) cc_final: 0.7450 (m-80) REVERT: G 49 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.3318 (ptmt) REVERT: G 114 THR cc_start: 0.6335 (OUTLIER) cc_final: 0.6065 (t) REVERT: K 114 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6289 (t) REVERT: F 223 MET cc_start: 0.7496 (tpp) cc_final: 0.6783 (tpp) REVERT: J 100 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7930 (mm-30) REVERT: E 142 MET cc_start: 0.8202 (tpt) cc_final: 0.7973 (tpt) REVERT: I 56 LYS cc_start: 0.7217 (mttt) cc_final: 0.6669 (mmmm) REVERT: I 60 LYS cc_start: 0.7439 (pttp) cc_final: 0.7053 (ptmt) REVERT: I 151 ILE cc_start: 0.8594 (mm) cc_final: 0.8221 (mm) outliers start: 52 outliers final: 39 residues processed: 289 average time/residue: 0.1436 time to fit residues: 62.9892 Evaluate side-chains 298 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 136 MET Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 114 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 204 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 313 ARG 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 298 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.150409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.141827 restraints weight = 21651.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 90)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.128153 restraints weight = 31500.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.129405 restraints weight = 27324.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.130630 restraints weight = 22042.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.131383 restraints weight = 19095.904| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19707 Z= 0.164 Angle : 0.599 9.571 26757 Z= 0.313 Chirality : 0.045 0.172 2853 Planarity : 0.005 0.045 3261 Dihedral : 13.410 171.796 2990 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 2.97 % Allowed : 17.74 % Favored : 79.28 % 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: 0.15 (0.17), residues: 2274 helix: 0.92 (0.16), residues: 1002 sheet: -0.23 (0.27), residues: 360 loop : -0.57 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 57 TYR 0.024 0.002 TYR C 184 PHE 0.017 0.001 PHE C 251 TRP 0.022 0.001 TRP C 253 HIS 0.006 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00391 (19707) covalent geometry : angle 0.59918 (26757) hydrogen bonds : bond 0.04245 ( 954) hydrogen bonds : angle 4.96040 ( 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 320 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.8302 (tpt) cc_final: 0.8051 (tpt) REVERT: A 163 MET cc_start: 0.8242 (ttt) cc_final: 0.7955 (ttm) REVERT: C 49 LYS cc_start: 0.4865 (OUTLIER) cc_final: 0.3202 (mttt) REVERT: C 114 THR cc_start: 0.6791 (OUTLIER) cc_final: 0.6334 (t) REVERT: B 22 ASP cc_start: 0.8320 (m-30) cc_final: 0.7962 (m-30) REVERT: B 49 ASP cc_start: 0.7714 (t0) cc_final: 0.7428 (t70) REVERT: B 229 PHE cc_start: 0.7877 (t80) cc_final: 0.7445 (m-80) REVERT: G 49 LYS cc_start: 0.4695 (OUTLIER) cc_final: 0.3406 (ptmt) REVERT: G 122 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.3911 (mp) REVERT: F 22 ASP cc_start: 0.8435 (m-30) cc_final: 0.8200 (m-30) REVERT: J 100 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 142 MET cc_start: 0.8304 (tpt) cc_final: 0.8076 (tpt) REVERT: I 56 LYS cc_start: 0.7288 (mttt) cc_final: 0.6707 (mmmm) REVERT: I 60 LYS cc_start: 0.7528 (pttp) cc_final: 0.7071 (ptmt) REVERT: I 151 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8301 (mm) outliers start: 58 outliers final: 47 residues processed: 295 average time/residue: 0.1533 time to fit residues: 68.8403 Evaluate side-chains 305 residues out of total 1950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 136 MET 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 122 LEU Chi-restraints excluded: chain G residue 261 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 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 204 THR Chi-restraints excluded: chain J residue 45 MET Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 251 MET Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 382 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 151 ILE Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 382 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 205 optimal weight: 9.9990 chunk 206 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 224 optimal weight: 0.1980 chunk 156 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 GLN F 245 GLN J 245 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.150488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130841 restraints weight = 21682.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130841 restraints weight = 20292.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130841 restraints weight = 20292.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130841 restraints weight = 20292.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.130841 restraints weight = 20292.245| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19707 Z= 0.149 Angle : 0.581 9.003 26757 Z= 0.304 Chirality : 0.045 0.165 2853 Planarity : 0.005 0.045 3261 Dihedral : 13.314 178.721 2990 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.16 % Rotamer: Outliers : 2.92 % Allowed : 17.85 % Favored : 79.23 % 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: 0.98 (0.16), residues: 999 sheet: -0.06 (0.28), residues: 330 loop : -0.58 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 132 TYR 0.023 0.001 TYR G 184 PHE 0.012 0.001 PHE A 71 TRP 0.022 0.001 TRP C 253 HIS 0.005 0.001 HIS B 11 Details of bonding type rmsd covalent geometry : bond 0.00349 (19707) covalent geometry : angle 0.58064 (26757) hydrogen bonds : bond 0.04120 ( 954) hydrogen bonds : angle 4.93069 ( 2835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.77 seconds wall clock time: 51 minutes 24.17 seconds (3084.17 seconds total)