Starting phenix.real_space_refine on Sun Sep 13 12:29:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd1_6634/09_2026/3jd1_6634.cif" } resolution = 3.3 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.36, per 1000 atoms: 0.18 Number of scatterers: 23814 At special positions: 0 Unit cell: (115.596, 129.116, 166.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 990.8 milliseconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 56.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.765A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 53 removed outlier: 3.607A pdb=" N LYS A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.855A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.745A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 212 through 228 removed outlier: 4.193A pdb=" N GLY A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.575A pdb=" N MET A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.519A pdb=" N HIS A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 496 removed outlier: 3.896A pdb=" N ASN A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 removed outlier: 3.766A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.606A pdb=" N LYS B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.854A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.744A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR B 190 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.192A pdb=" N GLY B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.575A pdb=" N MET B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.518A pdb=" N HIS B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 removed outlier: 3.895A pdb=" N ASN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.765A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 53 removed outlier: 3.606A pdb=" N LYS C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 140 through 154 removed outlier: 3.855A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.744A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 212 through 228 removed outlier: 4.192A pdb=" N GLY C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.574A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 244 Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.518A pdb=" N HIS C 450 " --> pdb=" O LYS C 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 496 removed outlier: 3.895A pdb=" N ASN C 484 " --> pdb=" O ALA C 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 32 removed outlier: 3.765A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 removed outlier: 3.607A pdb=" N LYS D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 140 through 154 removed outlier: 3.855A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.745A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 212 through 228 removed outlier: 4.193A pdb=" N GLY D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.575A pdb=" N MET D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 244 Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP D 293 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 425 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.519A pdb=" N HIS D 450 " --> pdb=" O LYS D 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 496 removed outlier: 3.896A pdb=" N ASN D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 32 removed outlier: 3.766A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 53 removed outlier: 3.606A pdb=" N LYS E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 140 through 154 removed outlier: 3.854A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.744A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 182 " --> pdb=" O TRP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR E 190 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 212 through 228 removed outlier: 4.192A pdb=" N GLY E 216 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.575A pdb=" N MET E 233 " --> pdb=" O GLU E 229 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'E' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP E 293 " --> pdb=" O LYS E 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 353 through 363 Processing helix chain 'E' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP E 404 " --> pdb=" O LYS E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.518A pdb=" N HIS E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 496 removed outlier: 3.895A pdb=" N ASN E 484 " --> pdb=" O ALA E 480 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 32 removed outlier: 3.765A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 53 removed outlier: 3.606A pdb=" N LYS F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.676A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 140 through 154 removed outlier: 3.855A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 185 removed outlier: 3.744A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR F 182 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 3.748A pdb=" N TYR F 190 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.144A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 212 through 228 removed outlier: 4.192A pdb=" N GLY F 216 " --> pdb=" O ILE F 212 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.574A pdb=" N MET F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 244 Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.606A pdb=" N LEU F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 298 removed outlier: 3.605A pdb=" N ASP F 293 " --> pdb=" O LYS F 289 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 353 through 363 Processing helix chain 'F' and resid 375 through 391 removed outlier: 3.659A pdb=" N THR F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.557A pdb=" N ASP F 404 " --> pdb=" O LYS F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.518A pdb=" N HIS F 450 " --> pdb=" O LYS F 446 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 496 removed outlier: 3.895A pdb=" N ASN F 484 " --> pdb=" O ALA F 480 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.720A pdb=" N GLU A 76 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU E 76 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.425A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 90 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 127 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 129 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU A 76 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU E 76 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS E 90 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA E 127 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY E 92 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL E 129 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER A 279 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL A 249 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 273 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 95 through 96 removed outlier: 4.719A pdb=" N GLU B 76 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU D 76 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.425A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS B 90 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA B 127 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY B 92 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL B 129 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU B 76 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU D 76 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS D 90 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA D 127 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY D 92 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL D 129 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER B 279 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL B 249 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 273 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.720A pdb=" N GLU C 76 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU F 76 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.425A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS C 90 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA C 127 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY C 92 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 129 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU C 76 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU F 76 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS F 90 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA F 127 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY F 92 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL F 129 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER C 279 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL C 249 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL C 273 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER D 279 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL D 249 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL D 273 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'E' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER E 279 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL E 249 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL E 273 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'F' and resid 308 through 310 removed outlier: 4.025A pdb=" N SER F 279 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL F 249 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL F 273 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3672 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: 5.41 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7792 1.34 - 1.45: 4474 1.45 - 1.57: 11854 1.57 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24360 Sorted by residual: bond pdb=" C4A NAI F 602 " pdb=" C5A NAI F 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAI C 602 " pdb=" C5A NAI C 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAI D 601 " pdb=" C5A NAI D 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C4A NAI A 601 " pdb=" C5A NAI A 601 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C4A NAI E 602 " pdb=" C5A NAI E 602 " ideal model delta sigma weight residual 1.386 1.470 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 32242 2.88 - 5.76: 686 5.76 - 8.64: 30 8.64 - 11.52: 30 11.52 - 14.40: 6 Bond angle restraints: 32994 Sorted by residual: angle pdb=" CA PRO A 7 " pdb=" N PRO A 7 " pdb=" CD PRO A 7 " ideal model delta sigma weight residual 112.00 106.02 5.98 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA PRO D 7 " pdb=" N PRO D 7 " pdb=" CD PRO D 7 " ideal model delta sigma weight residual 112.00 106.02 5.98 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA PRO E 7 " pdb=" N PRO E 7 " pdb=" CD PRO E 7 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CA PRO B 7 " pdb=" N PRO B 7 " pdb=" CD PRO B 7 " ideal model delta sigma weight residual 112.00 106.07 5.93 1.40e+00 5.10e-01 1.80e+01 angle pdb=" CA PRO C 7 " pdb=" N PRO C 7 " pdb=" CD PRO C 7 " ideal model delta sigma weight residual 112.00 106.08 5.92 1.40e+00 5.10e-01 1.79e+01 ... (remaining 32989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 14088 16.94 - 33.88: 216 33.88 - 50.83: 72 50.83 - 67.77: 0 67.77 - 84.71: 6 Dihedral angle restraints: 14382 sinusoidal: 5904 harmonic: 8478 Sorted by residual: dihedral pdb=" CA GLY C 497 " pdb=" C GLY C 497 " pdb=" N VAL C 498 " pdb=" CA VAL C 498 " ideal model delta harmonic sigma weight residual -180.00 -147.53 -32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA GLY B 497 " pdb=" C GLY B 497 " pdb=" N VAL B 498 " pdb=" CA VAL B 498 " ideal model delta harmonic sigma weight residual -180.00 -147.57 -32.43 0 5.00e+00 4.00e-02 4.21e+01 dihedral pdb=" CA GLY A 497 " pdb=" C GLY A 497 " pdb=" N VAL A 498 " pdb=" CA VAL A 498 " ideal model delta harmonic sigma weight residual -180.00 -147.57 -32.43 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 14379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2078 0.042 - 0.083: 978 0.083 - 0.125: 388 0.125 - 0.166: 100 0.166 - 0.208: 44 Chirality restraints: 3588 Sorted by residual: chirality pdb=" C1B NAI A 602 " pdb=" C2B NAI A 602 " pdb=" N9A NAI A 602 " pdb=" O4B NAI A 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NAI D 602 " pdb=" C2B NAI D 602 " pdb=" N9A NAI D 602 " pdb=" O4B NAI D 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1B NAI F 602 " pdb=" C2B NAI F 602 " pdb=" N9A NAI F 602 " pdb=" O4B NAI F 602 " both_signs ideal model delta sigma weight residual False 2.31 2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3585 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 166 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 167 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 166 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 166 " -0.048 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO B 167 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " -0.040 5.00e-02 4.00e+02 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 294 2.53 - 3.12: 20710 3.12 - 3.71: 35563 3.71 - 4.31: 54125 4.31 - 4.90: 88863 Nonbonded interactions: 199555 Sorted by model distance: nonbonded pdb=" OG1 THR D 272 " pdb=" O ILE D 280 " model vdw 1.935 3.040 nonbonded pdb=" OG1 THR A 272 " pdb=" O ILE A 280 " model vdw 1.935 3.040 nonbonded pdb=" OG1 THR F 272 " pdb=" O ILE F 280 " model vdw 1.935 3.040 nonbonded pdb=" OG1 THR C 272 " pdb=" O ILE C 280 " model vdw 1.935 3.040 nonbonded pdb=" OG1 THR E 272 " pdb=" O ILE E 280 " model vdw 1.935 3.040 ... (remaining 199550 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.019 0.789 24366 Z= 1.378 Angle : 1.013 14.400 32994 Z= 0.544 Chirality : 0.058 0.208 3588 Planarity : 0.006 0.072 4224 Dihedral : 8.097 84.712 8982 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.08 (0.12), residues: 2964 helix: -3.93 (0.08), residues: 1410 sheet: -2.39 (0.22), residues: 426 loop : -2.66 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.026 0.003 TYR B 372 PHE 0.025 0.003 PHE C 16 TRP 0.015 0.004 TRP E 385 HIS 0.014 0.002 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.01460 / 0.60 (24360) covalent geometry : angle 1.01348 / 0.54 (32994) hydrogen bonds : bond 0.27582 / 18.54 ( 1224) hydrogen bonds : angle 10.63852 / 7.54 ( 3672) Misc. bond : bond 0.78904 / 37.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7906 (tt0) cc_final: 0.7646 (tt0) REVERT: A 402 GLU cc_start: 0.7885 (tp30) cc_final: 0.7384 (tp30) REVERT: A 469 MET cc_start: 0.7160 (mmp) cc_final: 0.6814 (mmt) REVERT: B 25 GLU cc_start: 0.7987 (tt0) cc_final: 0.7660 (tt0) REVERT: B 228 ASN cc_start: 0.6833 (p0) cc_final: 0.6355 (t0) REVERT: B 402 GLU cc_start: 0.7882 (tp30) cc_final: 0.7393 (tp30) REVERT: B 469 MET cc_start: 0.7154 (mmp) cc_final: 0.6827 (mmt) REVERT: C 25 GLU cc_start: 0.7932 (tt0) cc_final: 0.7687 (tt0) REVERT: C 402 GLU cc_start: 0.7844 (tp30) cc_final: 0.7386 (tp30) REVERT: C 469 MET cc_start: 0.7211 (mmp) cc_final: 0.6857 (mmt) REVERT: D 25 GLU cc_start: 0.7906 (tt0) cc_final: 0.7652 (tt0) REVERT: D 402 GLU cc_start: 0.7885 (tp30) cc_final: 0.7384 (tp30) REVERT: D 469 MET cc_start: 0.7158 (mmp) cc_final: 0.6811 (mmt) REVERT: E 25 GLU cc_start: 0.7987 (tt0) cc_final: 0.7590 (tt0) REVERT: E 228 ASN cc_start: 0.6832 (p0) cc_final: 0.6352 (t0) REVERT: E 402 GLU cc_start: 0.7880 (tp30) cc_final: 0.7393 (tp30) REVERT: E 469 MET cc_start: 0.7147 (mmp) cc_final: 0.6820 (mmt) REVERT: F 25 GLU cc_start: 0.7935 (tt0) cc_final: 0.7688 (tt0) REVERT: F 402 GLU cc_start: 0.7838 (tp30) cc_final: 0.7380 (tp30) REVERT: F 469 MET cc_start: 0.7210 (mmp) cc_final: 0.6855 (mmt) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.2239 time to fit residues: 191.7234 Evaluate side-chains 243 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0070 chunk 111 optimal weight: 6.9990 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 388 ASN A 450 HIS A 494 ASN B 40 GLN B 209 HIS B 388 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN C 40 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 ASN D 40 GLN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 388 ASN D 450 HIS D 494 ASN E 40 GLN E 209 HIS E 258 HIS E 388 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 ASN F 40 GLN F 56 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 494 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.098975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072533 restraints weight = 56639.748| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.88 r_work: 0.2994 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24366 Z= 0.199 Angle : 0.692 7.311 32994 Z= 0.362 Chirality : 0.047 0.180 3588 Planarity : 0.007 0.088 4224 Dihedral : 6.637 76.792 3390 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.04 % Allowed : 5.85 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -2.39 (0.14), residues: 2964 helix: -1.21 (0.12), residues: 1452 sheet: -1.70 (0.23), residues: 420 loop : -1.81 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 66 TYR 0.016 0.002 TYR B 382 PHE 0.022 0.002 PHE A 9 TRP 0.010 0.002 TRP A 281 HIS 0.011 0.002 HIS C 408 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (24360) covalent geometry : angle 0.69228 / 0.36 (32994) hydrogen bonds : bond 0.05829 / 3.90 ( 1224) hydrogen bonds : angle 5.34707 / 3.80 ( 3672) Misc. bond : bond 0.00081 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 321 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.8756 (tpp) cc_final: 0.8536 (tpp) REVERT: A 224 GLU cc_start: 0.7588 (pt0) cc_final: 0.7302 (pt0) REVERT: A 233 MET cc_start: 0.7559 (mmm) cc_final: 0.7209 (mmt) REVERT: A 402 GLU cc_start: 0.8026 (tp30) cc_final: 0.7426 (tp30) REVERT: A 469 MET cc_start: 0.7845 (mmp) cc_final: 0.7520 (ttt) REVERT: A 476 ASP cc_start: 0.7941 (t0) cc_final: 0.7634 (t0) REVERT: B 224 GLU cc_start: 0.7530 (pt0) cc_final: 0.7324 (pt0) REVERT: B 401 TYR cc_start: 0.8165 (t80) cc_final: 0.7833 (t80) REVERT: B 402 GLU cc_start: 0.7952 (tp30) cc_final: 0.7297 (tp30) REVERT: B 476 ASP cc_start: 0.8091 (t0) cc_final: 0.7783 (t0) REVERT: B 495 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7114 (mt-10) REVERT: C 66 ARG cc_start: 0.8157 (ttt-90) cc_final: 0.7928 (ttt180) REVERT: C 238 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5950 (mpp) REVERT: C 402 GLU cc_start: 0.8055 (tp30) cc_final: 0.7490 (tp30) REVERT: C 403 ARG cc_start: 0.8671 (ttt180) cc_final: 0.8405 (ttm170) REVERT: C 462 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8169 (mtp-110) REVERT: C 469 MET cc_start: 0.7759 (mmp) cc_final: 0.7554 (ttp) REVERT: C 476 ASP cc_start: 0.7939 (t0) cc_final: 0.7597 (t0) REVERT: D 111 MET cc_start: 0.8770 (tpp) cc_final: 0.8547 (tpp) REVERT: D 224 GLU cc_start: 0.7589 (pt0) cc_final: 0.7304 (pt0) REVERT: D 233 MET cc_start: 0.7560 (mmm) cc_final: 0.7211 (mmt) REVERT: D 402 GLU cc_start: 0.8021 (tp30) cc_final: 0.7418 (tp30) REVERT: D 469 MET cc_start: 0.7833 (mmp) cc_final: 0.7515 (ttt) REVERT: D 476 ASP cc_start: 0.7941 (t0) cc_final: 0.7635 (t0) REVERT: E 224 GLU cc_start: 0.7525 (pt0) cc_final: 0.7320 (pt0) REVERT: E 238 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.6008 (mpp) REVERT: E 271 ILE cc_start: 0.8234 (pt) cc_final: 0.8034 (tt) REVERT: E 401 TYR cc_start: 0.8163 (t80) cc_final: 0.7829 (t80) REVERT: E 402 GLU cc_start: 0.7962 (tp30) cc_final: 0.7306 (tp30) REVERT: E 469 MET cc_start: 0.7852 (mmp) cc_final: 0.7649 (ttp) REVERT: E 476 ASP cc_start: 0.8094 (t0) cc_final: 0.7785 (t0) REVERT: E 495 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7112 (mt-10) REVERT: F 66 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7931 (ttt180) REVERT: F 238 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5957 (mpp) REVERT: F 402 GLU cc_start: 0.8043 (tp30) cc_final: 0.7478 (tp30) REVERT: F 403 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8417 (ttm170) REVERT: F 462 ARG cc_start: 0.8356 (tpp-160) cc_final: 0.8136 (tmt-80) REVERT: F 476 ASP cc_start: 0.7939 (t0) cc_final: 0.7576 (t0) outliers start: 51 outliers final: 24 residues processed: 363 average time/residue: 0.1959 time to fit residues: 104.4772 Evaluate side-chains 221 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 273 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN B 135 ASN B 205 GLN B 408 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN C 205 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN E 135 ASN E 205 GLN E 408 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 ASN F 205 GLN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.095515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069205 restraints weight = 57949.603| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.84 r_work: 0.2916 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24366 Z= 0.237 Angle : 0.699 7.874 32994 Z= 0.364 Chirality : 0.048 0.145 3588 Planarity : 0.006 0.052 4224 Dihedral : 6.632 84.690 3390 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.60 % Allowed : 8.17 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -1.02 (0.15), residues: 2964 helix: -0.01 (0.13), residues: 1452 sheet: -1.24 (0.25), residues: 390 loop : -1.19 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 86 TYR 0.021 0.002 TYR D 78 PHE 0.023 0.003 PHE F 9 TRP 0.016 0.002 TRP F 281 HIS 0.008 0.002 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (24360) covalent geometry : angle 0.69880 / 0.36 (32994) hydrogen bonds : bond 0.05762 / 3.85 ( 1224) hydrogen bonds : angle 4.79163 / 3.40 ( 3672) Misc. bond : bond 0.00209 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 254 time to evaluate : 0.914 Fit side-chains REVERT: A 103 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 224 GLU cc_start: 0.7512 (pt0) cc_final: 0.7272 (pt0) REVERT: A 297 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7629 (tt0) REVERT: A 314 ILE cc_start: 0.7160 (mm) cc_final: 0.6933 (mm) REVERT: A 402 GLU cc_start: 0.8278 (tp30) cc_final: 0.7652 (tp30) REVERT: A 469 MET cc_start: 0.7715 (mmp) cc_final: 0.7438 (ttp) REVERT: A 476 ASP cc_start: 0.8046 (t0) cc_final: 0.7675 (t0) REVERT: B 103 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8007 (tp30) REVERT: B 224 GLU cc_start: 0.7577 (pt0) cc_final: 0.7294 (pt0) REVERT: B 238 MET cc_start: 0.5905 (mtm) cc_final: 0.5505 (tpp) REVERT: B 294 PHE cc_start: 0.6486 (m-80) cc_final: 0.6165 (m-80) REVERT: B 297 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7542 (tt0) REVERT: B 402 GLU cc_start: 0.8203 (tp30) cc_final: 0.7659 (tp30) REVERT: B 476 ASP cc_start: 0.8082 (t0) cc_final: 0.7685 (t0) REVERT: B 495 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7061 (mt-10) REVERT: C 66 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7969 (ttt180) REVERT: C 103 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7816 (tp30) REVERT: C 176 MET cc_start: 0.9086 (mmp) cc_final: 0.8855 (mmp) REVERT: C 296 LEU cc_start: 0.7543 (mt) cc_final: 0.7103 (pp) REVERT: C 297 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7674 (tt0) REVERT: C 366 MET cc_start: 0.6779 (tpp) cc_final: 0.6101 (ttm) REVERT: C 402 GLU cc_start: 0.8268 (tp30) cc_final: 0.7672 (tp30) REVERT: C 403 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8583 (ttm170) REVERT: C 469 MET cc_start: 0.7652 (mmp) cc_final: 0.7436 (ttp) REVERT: C 476 ASP cc_start: 0.8043 (t0) cc_final: 0.7634 (t0) REVERT: D 224 GLU cc_start: 0.7505 (pt0) cc_final: 0.7267 (pt0) REVERT: D 297 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7633 (tt0) REVERT: D 314 ILE cc_start: 0.7165 (mm) cc_final: 0.6939 (mm) REVERT: D 402 GLU cc_start: 0.8275 (tp30) cc_final: 0.7646 (tp30) REVERT: D 469 MET cc_start: 0.7734 (mmp) cc_final: 0.7448 (ttp) REVERT: D 476 ASP cc_start: 0.8046 (t0) cc_final: 0.7676 (t0) REVERT: E 103 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8015 (tp30) REVERT: E 224 GLU cc_start: 0.7561 (pt0) cc_final: 0.7275 (pt0) REVERT: E 294 PHE cc_start: 0.6489 (m-80) cc_final: 0.6166 (m-80) REVERT: E 297 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7543 (tt0) REVERT: E 402 GLU cc_start: 0.8218 (tp30) cc_final: 0.7672 (tp30) REVERT: E 476 ASP cc_start: 0.8089 (t0) cc_final: 0.7696 (t0) REVERT: E 495 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7070 (mt-10) REVERT: F 66 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7970 (ttt180) REVERT: F 103 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7809 (tp30) REVERT: F 176 MET cc_start: 0.9087 (mmp) cc_final: 0.8849 (mmp) REVERT: F 297 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7804 (mp10) REVERT: F 366 MET cc_start: 0.6774 (tpp) cc_final: 0.6104 (ttm) REVERT: F 402 GLU cc_start: 0.8282 (tp30) cc_final: 0.7690 (tp30) REVERT: F 476 ASP cc_start: 0.8022 (t0) cc_final: 0.7610 (t0) outliers start: 65 outliers final: 39 residues processed: 306 average time/residue: 0.1550 time to fit residues: 75.4914 Evaluate side-chains 244 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 20.0000 chunk 269 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 135 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 135 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 ASN F 135 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.095550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069183 restraints weight = 57654.275| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.85 r_work: 0.2917 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24366 Z= 0.193 Angle : 0.619 6.787 32994 Z= 0.321 Chirality : 0.045 0.148 3588 Planarity : 0.005 0.039 4224 Dihedral : 6.315 82.214 3390 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.96 % Allowed : 9.50 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.33 (0.15), residues: 2964 helix: 0.54 (0.14), residues: 1452 sheet: -1.13 (0.25), residues: 420 loop : -0.70 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.013 0.002 TYR C 493 PHE 0.019 0.002 PHE F 9 TRP 0.013 0.002 TRP C 385 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (24360) covalent geometry : angle 0.61941 / 0.32 (32994) hydrogen bonds : bond 0.04951 / 3.31 ( 1224) hydrogen bonds : angle 4.39036 / 3.12 ( 3672) Misc. bond : bond 0.00157 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.862 Fit side-chains REVERT: A 224 GLU cc_start: 0.7504 (pt0) cc_final: 0.7206 (pt0) REVERT: A 238 MET cc_start: 0.6068 (mtm) cc_final: 0.5222 (tpt) REVERT: A 297 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7683 (tt0) REVERT: A 314 ILE cc_start: 0.7201 (mm) cc_final: 0.6955 (mm) REVERT: A 402 GLU cc_start: 0.8291 (tp30) cc_final: 0.7876 (tp30) REVERT: A 476 ASP cc_start: 0.8041 (t0) cc_final: 0.7653 (t0) REVERT: B 224 GLU cc_start: 0.7445 (pt0) cc_final: 0.7119 (pt0) REVERT: B 238 MET cc_start: 0.6136 (mtm) cc_final: 0.5582 (tpp) REVERT: B 294 PHE cc_start: 0.6524 (m-80) cc_final: 0.6233 (m-80) REVERT: B 297 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7653 (tt0) REVERT: B 402 GLU cc_start: 0.8219 (tp30) cc_final: 0.7658 (tp30) REVERT: B 465 MET cc_start: 0.8447 (mtm) cc_final: 0.8168 (mtm) REVERT: B 476 ASP cc_start: 0.8027 (t0) cc_final: 0.7591 (t70) REVERT: C 297 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7706 (tt0) REVERT: C 314 ILE cc_start: 0.7217 (mm) cc_final: 0.6989 (mm) REVERT: C 366 MET cc_start: 0.6789 (tpp) cc_final: 0.6182 (ttm) REVERT: C 402 GLU cc_start: 0.8254 (tp30) cc_final: 0.7642 (tp30) REVERT: C 403 ARG cc_start: 0.8775 (ttt180) cc_final: 0.8556 (ttm170) REVERT: C 476 ASP cc_start: 0.8012 (t0) cc_final: 0.7492 (t0) REVERT: D 224 GLU cc_start: 0.7510 (pt0) cc_final: 0.7212 (pt0) REVERT: D 238 MET cc_start: 0.5999 (mtm) cc_final: 0.5243 (tpt) REVERT: D 297 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7679 (tt0) REVERT: D 314 ILE cc_start: 0.7185 (mm) cc_final: 0.6937 (mm) REVERT: D 402 GLU cc_start: 0.8284 (tp30) cc_final: 0.7650 (tp30) REVERT: D 476 ASP cc_start: 0.8030 (t0) cc_final: 0.7648 (t0) REVERT: E 224 GLU cc_start: 0.7456 (pt0) cc_final: 0.7133 (pt0) REVERT: E 294 PHE cc_start: 0.6533 (m-80) cc_final: 0.6231 (m-80) REVERT: E 297 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7659 (tt0) REVERT: E 402 GLU cc_start: 0.8223 (tp30) cc_final: 0.7659 (tp30) REVERT: E 465 MET cc_start: 0.8414 (mtm) cc_final: 0.8111 (mtm) REVERT: E 476 ASP cc_start: 0.8028 (t0) cc_final: 0.7585 (t0) REVERT: F 297 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7703 (tt0) REVERT: F 314 ILE cc_start: 0.7282 (mm) cc_final: 0.7061 (mm) REVERT: F 366 MET cc_start: 0.6794 (tpp) cc_final: 0.6169 (ttm) REVERT: F 402 GLU cc_start: 0.8274 (tp30) cc_final: 0.7667 (tp30) REVERT: F 403 ARG cc_start: 0.8789 (ttt180) cc_final: 0.8572 (ttm170) REVERT: F 476 ASP cc_start: 0.8015 (t0) cc_final: 0.7480 (t0) outliers start: 49 outliers final: 33 residues processed: 255 average time/residue: 0.1583 time to fit residues: 63.9897 Evaluate side-chains 224 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 130 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 277 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 298 HIS B 56 ASN B 450 HIS C 56 ASN C 81 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 298 HIS E 56 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.094173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068171 restraints weight = 57793.081| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.81 r_work: 0.2893 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24366 Z= 0.237 Angle : 0.658 7.834 32994 Z= 0.342 Chirality : 0.047 0.144 3588 Planarity : 0.005 0.045 4224 Dihedral : 6.076 63.782 3390 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.12 % Allowed : 9.78 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: -0.24 (0.15), residues: 2964 helix: 0.53 (0.13), residues: 1458 sheet: -0.93 (0.25), residues: 420 loop : -0.60 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 86 TYR 0.014 0.002 TYR C 78 PHE 0.021 0.002 PHE D 148 TRP 0.019 0.002 TRP E 281 HIS 0.007 0.002 HIS F 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (24360) covalent geometry : angle 0.65819 / 0.34 (32994) hydrogen bonds : bond 0.05435 / 3.64 ( 1224) hydrogen bonds : angle 4.40767 / 3.13 ( 3672) Misc. bond : bond 0.00193 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.873 Fit side-chains REVERT: A 90 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8721 (mtpp) REVERT: A 94 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8290 (ttm170) REVERT: A 238 MET cc_start: 0.5914 (mtm) cc_final: 0.5439 (tpt) REVERT: A 297 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7740 (tt0) REVERT: A 402 GLU cc_start: 0.8370 (tp30) cc_final: 0.7778 (tp30) REVERT: B 111 MET cc_start: 0.8900 (tpp) cc_final: 0.8509 (tpp) REVERT: B 224 GLU cc_start: 0.7434 (pt0) cc_final: 0.7072 (pt0) REVERT: B 262 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: B 294 PHE cc_start: 0.6486 (m-80) cc_final: 0.6183 (m-80) REVERT: B 297 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7654 (tt0) REVERT: B 465 MET cc_start: 0.8438 (mtm) cc_final: 0.8173 (mtm) REVERT: B 476 ASP cc_start: 0.8093 (t0) cc_final: 0.7601 (t70) REVERT: C 94 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7968 (ttm-80) REVERT: C 238 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5944 (mtm) REVERT: C 297 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7750 (tt0) REVERT: C 366 MET cc_start: 0.6795 (tpp) cc_final: 0.6231 (ttm) REVERT: C 402 GLU cc_start: 0.8327 (tp30) cc_final: 0.7851 (tp30) REVERT: C 476 ASP cc_start: 0.8036 (t0) cc_final: 0.7505 (t0) REVERT: D 90 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8706 (mtpp) REVERT: D 94 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8289 (ttm170) REVERT: D 238 MET cc_start: 0.5963 (mtm) cc_final: 0.5480 (tpt) REVERT: D 297 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7739 (tt0) REVERT: D 402 GLU cc_start: 0.8375 (tp30) cc_final: 0.7787 (tp30) REVERT: E 111 MET cc_start: 0.8926 (tpp) cc_final: 0.8533 (tpp) REVERT: E 224 GLU cc_start: 0.7442 (pt0) cc_final: 0.7086 (pt0) REVERT: E 238 MET cc_start: 0.6303 (mtm) cc_final: 0.5468 (tpt) REVERT: E 294 PHE cc_start: 0.6493 (m-80) cc_final: 0.6186 (m-80) REVERT: E 297 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7663 (tt0) REVERT: E 308 LYS cc_start: 0.4741 (pttm) cc_final: 0.4246 (pttm) REVERT: E 465 MET cc_start: 0.8435 (mtm) cc_final: 0.8187 (mtm) REVERT: E 476 ASP cc_start: 0.8108 (t0) cc_final: 0.7622 (t70) REVERT: F 90 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: F 94 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.7961 (ttm-80) REVERT: F 238 MET cc_start: 0.6248 (OUTLIER) cc_final: 0.6037 (mtm) REVERT: F 297 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7778 (tt0) REVERT: F 314 ILE cc_start: 0.7270 (mm) cc_final: 0.7043 (mm) REVERT: F 366 MET cc_start: 0.6820 (tpp) cc_final: 0.6226 (ttm) REVERT: F 402 GLU cc_start: 0.8330 (tp30) cc_final: 0.7858 (tp30) REVERT: F 476 ASP cc_start: 0.8037 (t0) cc_final: 0.7480 (t0) outliers start: 78 outliers final: 52 residues processed: 258 average time/residue: 0.1689 time to fit residues: 68.0853 Evaluate side-chains 245 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 280 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS F 56 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068891 restraints weight = 58323.496| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.81 r_work: 0.2910 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24366 Z= 0.192 Angle : 0.603 8.457 32994 Z= 0.313 Chirality : 0.045 0.142 3588 Planarity : 0.005 0.038 4224 Dihedral : 5.633 50.924 3390 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.49 % Allowed : 10.46 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.15), residues: 2964 helix: 0.76 (0.13), residues: 1458 sheet: -0.85 (0.25), residues: 420 loop : -0.53 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.011 0.002 TYR F 493 PHE 0.018 0.002 PHE D 148 TRP 0.016 0.002 TRP C 281 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (24360) covalent geometry : angle 0.60303 / 0.31 (32994) hydrogen bonds : bond 0.04941 / 3.31 ( 1224) hydrogen bonds : angle 4.25864 / 3.03 ( 3672) Misc. bond : bond 0.00152 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 208 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8711 (mtpp) REVERT: A 238 MET cc_start: 0.6193 (mtm) cc_final: 0.5382 (tpt) REVERT: A 297 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7771 (tt0) REVERT: A 402 GLU cc_start: 0.8342 (tp30) cc_final: 0.7725 (tp30) REVERT: A 476 ASP cc_start: 0.8161 (t0) cc_final: 0.7692 (t0) REVERT: B 111 MET cc_start: 0.8890 (tpp) cc_final: 0.8505 (tpp) REVERT: B 224 GLU cc_start: 0.7416 (pt0) cc_final: 0.7061 (pt0) REVERT: B 238 MET cc_start: 0.6167 (mtm) cc_final: 0.5621 (tpp) REVERT: B 252 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6045 (t80) REVERT: B 262 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: B 294 PHE cc_start: 0.6428 (m-80) cc_final: 0.6143 (m-80) REVERT: B 297 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7721 (tt0) REVERT: B 462 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7398 (mmm-85) REVERT: B 465 MET cc_start: 0.8415 (mtm) cc_final: 0.8152 (mtm) REVERT: C 94 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8096 (ttm-80) REVERT: C 238 MET cc_start: 0.6234 (mtp) cc_final: 0.5580 (tpt) REVERT: C 297 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7755 (tt0) REVERT: C 308 LYS cc_start: 0.5085 (pttm) cc_final: 0.4522 (pttm) REVERT: C 338 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7751 (mtt180) REVERT: C 366 MET cc_start: 0.6781 (tpp) cc_final: 0.6186 (ttm) REVERT: C 402 GLU cc_start: 0.8284 (tp30) cc_final: 0.7696 (tp30) REVERT: C 403 ARG cc_start: 0.8806 (ttt180) cc_final: 0.8595 (ttm170) REVERT: C 476 ASP cc_start: 0.7980 (t0) cc_final: 0.7421 (t0) REVERT: D 90 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8714 (mtpp) REVERT: D 238 MET cc_start: 0.6174 (mtm) cc_final: 0.5374 (tpt) REVERT: D 297 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7749 (tt0) REVERT: D 402 GLU cc_start: 0.8338 (tp30) cc_final: 0.7732 (tp30) REVERT: D 476 ASP cc_start: 0.8156 (t0) cc_final: 0.7722 (t0) REVERT: E 111 MET cc_start: 0.8915 (tpp) cc_final: 0.8529 (tpp) REVERT: E 224 GLU cc_start: 0.7393 (pt0) cc_final: 0.7053 (pt0) REVERT: E 238 MET cc_start: 0.6302 (mtm) cc_final: 0.5430 (tpt) REVERT: E 262 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: E 294 PHE cc_start: 0.6460 (m-80) cc_final: 0.6144 (m-80) REVERT: E 297 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7698 (tt0) REVERT: E 465 MET cc_start: 0.8396 (mtm) cc_final: 0.8151 (mtm) REVERT: F 90 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8315 (mtpp) REVERT: F 94 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: F 238 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5618 (tpt) REVERT: F 297 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7778 (tt0) REVERT: F 308 LYS cc_start: 0.5066 (pttm) cc_final: 0.4497 (pttm) REVERT: F 338 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7726 (mtt180) REVERT: F 366 MET cc_start: 0.6786 (tpp) cc_final: 0.6202 (ttm) REVERT: F 402 GLU cc_start: 0.8276 (tp30) cc_final: 0.7689 (tp30) REVERT: F 403 ARG cc_start: 0.8800 (ttt180) cc_final: 0.8590 (ttm170) REVERT: F 476 ASP cc_start: 0.8004 (t0) cc_final: 0.7423 (t0) outliers start: 87 outliers final: 63 residues processed: 273 average time/residue: 0.1649 time to fit residues: 70.7136 Evaluate side-chains 272 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 197 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 93 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.094849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068967 restraints weight = 57623.203| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.79 r_work: 0.2912 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24366 Z= 0.185 Angle : 0.594 8.772 32994 Z= 0.309 Chirality : 0.045 0.142 3588 Planarity : 0.004 0.038 4224 Dihedral : 5.586 50.828 3390 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.85 % Allowed : 10.42 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 2964 helix: 0.91 (0.13), residues: 1458 sheet: -0.76 (0.25), residues: 420 loop : -0.45 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.010 0.002 TYR F 493 PHE 0.018 0.002 PHE C 63 TRP 0.016 0.002 TRP D 281 HIS 0.005 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (24360) covalent geometry : angle 0.59429 / 0.31 (32994) hydrogen bonds : bond 0.04866 / 3.26 ( 1224) hydrogen bonds : angle 4.21732 / 3.00 ( 3672) Misc. bond : bond 0.00151 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 196 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8721 (mtpp) REVERT: A 94 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8321 (ttm170) REVERT: A 297 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7785 (tt0) REVERT: A 402 GLU cc_start: 0.8318 (tp30) cc_final: 0.7713 (tp30) REVERT: A 476 ASP cc_start: 0.8140 (t0) cc_final: 0.7677 (t0) REVERT: B 94 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8508 (ttm-80) REVERT: B 111 MET cc_start: 0.8859 (tpp) cc_final: 0.8484 (tpp) REVERT: B 224 GLU cc_start: 0.7432 (pt0) cc_final: 0.7073 (pt0) REVERT: B 238 MET cc_start: 0.6228 (mtm) cc_final: 0.5718 (tpp) REVERT: B 260 MET cc_start: 0.8532 (ptm) cc_final: 0.8120 (ppp) REVERT: B 262 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: B 294 PHE cc_start: 0.6403 (m-80) cc_final: 0.6137 (m-80) REVERT: B 297 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7716 (tt0) REVERT: B 308 LYS cc_start: 0.4692 (pttm) cc_final: 0.4200 (pttm) REVERT: B 462 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7402 (mmm-85) REVERT: B 465 MET cc_start: 0.8421 (mtm) cc_final: 0.8070 (mtm) REVERT: C 94 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8087 (ttm-80) REVERT: C 297 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7767 (tt0) REVERT: C 338 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7808 (mtt180) REVERT: C 366 MET cc_start: 0.6734 (tpp) cc_final: 0.6209 (ttm) REVERT: C 402 GLU cc_start: 0.8307 (tp30) cc_final: 0.7719 (tp30) REVERT: C 403 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8588 (ttm170) REVERT: C 476 ASP cc_start: 0.7993 (t0) cc_final: 0.7415 (t0) REVERT: D 90 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8716 (mtpp) REVERT: D 94 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: D 297 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7783 (tt0) REVERT: D 402 GLU cc_start: 0.8322 (tp30) cc_final: 0.7720 (tp30) REVERT: D 476 ASP cc_start: 0.8124 (t0) cc_final: 0.7661 (t0) REVERT: E 94 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8510 (ttm-80) REVERT: E 111 MET cc_start: 0.8904 (tpp) cc_final: 0.8528 (tpp) REVERT: E 224 GLU cc_start: 0.7414 (pt0) cc_final: 0.7068 (pt0) REVERT: E 238 MET cc_start: 0.6288 (mtm) cc_final: 0.5716 (tpp) REVERT: E 294 PHE cc_start: 0.6398 (m-80) cc_final: 0.6117 (m-80) REVERT: E 297 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7726 (tt0) REVERT: E 308 LYS cc_start: 0.4680 (pttm) cc_final: 0.4223 (pttm) REVERT: E 465 MET cc_start: 0.8397 (mtm) cc_final: 0.8112 (mtm) REVERT: F 94 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8079 (ttm-80) REVERT: F 297 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7809 (tt0) REVERT: F 338 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7794 (mtt180) REVERT: F 366 MET cc_start: 0.6760 (tpp) cc_final: 0.6227 (ttm) REVERT: F 402 GLU cc_start: 0.8289 (tp30) cc_final: 0.7702 (tp30) REVERT: F 403 ARG cc_start: 0.8804 (ttt180) cc_final: 0.8593 (ttm170) REVERT: F 476 ASP cc_start: 0.8003 (t0) cc_final: 0.7405 (t0) outliers start: 96 outliers final: 73 residues processed: 275 average time/residue: 0.1715 time to fit residues: 73.2806 Evaluate side-chains 278 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 193 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 139 ASN Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.068969 restraints weight = 58296.118| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.83 r_work: 0.2910 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24366 Z= 0.163 Angle : 0.574 8.161 32994 Z= 0.297 Chirality : 0.044 0.138 3588 Planarity : 0.004 0.038 4224 Dihedral : 5.515 50.072 3390 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.81 % Allowed : 10.74 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2964 helix: 1.08 (0.13), residues: 1458 sheet: -0.79 (0.26), residues: 384 loop : -0.29 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 86 TYR 0.009 0.001 TYR C 493 PHE 0.020 0.002 PHE C 63 TRP 0.021 0.002 TRP D 281 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (24360) covalent geometry : angle 0.57355 / 0.30 (32994) hydrogen bonds : bond 0.04632 / 3.11 ( 1224) hydrogen bonds : angle 4.15919 / 2.96 ( 3672) Misc. bond : bond 0.00139 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 203 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8710 (mtpp) REVERT: A 94 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8314 (ttm170) REVERT: A 238 MET cc_start: 0.6095 (mtm) cc_final: 0.5360 (tpt) REVERT: A 476 ASP cc_start: 0.8093 (t0) cc_final: 0.7631 (t0) REVERT: B 94 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8476 (ttm-80) REVERT: B 111 MET cc_start: 0.8784 (tpp) cc_final: 0.8412 (tpp) REVERT: B 224 GLU cc_start: 0.7405 (pt0) cc_final: 0.7055 (pt0) REVERT: B 238 MET cc_start: 0.6151 (mtm) cc_final: 0.5686 (tpp) REVERT: B 260 MET cc_start: 0.8506 (ptm) cc_final: 0.8062 (ppp) REVERT: B 294 PHE cc_start: 0.6344 (m-80) cc_final: 0.6110 (m-80) REVERT: B 297 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7743 (tt0) REVERT: B 308 LYS cc_start: 0.4778 (pttm) cc_final: 0.4340 (pttm) REVERT: B 462 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7396 (mmm-85) REVERT: C 94 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8078 (ttm-80) REVERT: C 176 MET cc_start: 0.9045 (mmp) cc_final: 0.8818 (mmp) REVERT: C 297 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7736 (tt0) REVERT: C 308 LYS cc_start: 0.5047 (pttm) cc_final: 0.4414 (pttm) REVERT: C 338 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7885 (mtt180) REVERT: C 366 MET cc_start: 0.6762 (tpp) cc_final: 0.6211 (ttm) REVERT: C 402 GLU cc_start: 0.8277 (tp30) cc_final: 0.7663 (tp30) REVERT: C 403 ARG cc_start: 0.8795 (ttt180) cc_final: 0.8586 (ttm170) REVERT: C 476 ASP cc_start: 0.7996 (t0) cc_final: 0.7400 (t0) REVERT: D 90 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8716 (mtpp) REVERT: D 94 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: D 238 MET cc_start: 0.6010 (mtm) cc_final: 0.5333 (tpt) REVERT: D 476 ASP cc_start: 0.8090 (t0) cc_final: 0.7631 (t0) REVERT: E 94 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8471 (ttm-80) REVERT: E 111 MET cc_start: 0.8813 (tpp) cc_final: 0.8443 (tpp) REVERT: E 224 GLU cc_start: 0.7390 (pt0) cc_final: 0.7043 (pt0) REVERT: E 238 MET cc_start: 0.6199 (mtm) cc_final: 0.5658 (tpp) REVERT: E 294 PHE cc_start: 0.6364 (m-80) cc_final: 0.6127 (m-80) REVERT: E 297 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7788 (tt0) REVERT: E 308 LYS cc_start: 0.4677 (pttm) cc_final: 0.4230 (pttm) REVERT: E 465 MET cc_start: 0.8399 (mtm) cc_final: 0.8072 (mtm) REVERT: F 94 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8072 (ttm-80) REVERT: F 297 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7807 (tt0) REVERT: F 308 LYS cc_start: 0.4943 (pttm) cc_final: 0.4320 (pttm) REVERT: F 338 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7861 (mtt180) REVERT: F 366 MET cc_start: 0.6763 (tpp) cc_final: 0.6241 (ttm) REVERT: F 402 GLU cc_start: 0.8271 (tp30) cc_final: 0.7660 (tp30) REVERT: F 403 ARG cc_start: 0.8802 (ttt180) cc_final: 0.8592 (ttm170) REVERT: F 476 ASP cc_start: 0.7982 (t0) cc_final: 0.7346 (t0) outliers start: 95 outliers final: 70 residues processed: 281 average time/residue: 0.1658 time to fit residues: 73.0202 Evaluate side-chains 274 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 193 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 10 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 224 optimal weight: 0.1980 chunk 95 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.095320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069487 restraints weight = 58527.587| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.84 r_work: 0.2917 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24366 Z= 0.141 Angle : 0.551 7.723 32994 Z= 0.285 Chirality : 0.043 0.139 3588 Planarity : 0.004 0.038 4224 Dihedral : 5.402 49.601 3390 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.25 % Allowed : 11.86 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: 0.56 (0.16), residues: 2964 helix: 1.25 (0.14), residues: 1476 sheet: -0.70 (0.27), residues: 384 loop : -0.30 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 86 TYR 0.008 0.001 TYR F 493 PHE 0.018 0.002 PHE F 63 TRP 0.016 0.001 TRP A 281 HIS 0.004 0.001 HIS D 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (24360) covalent geometry : angle 0.55107 / 0.29 (32994) hydrogen bonds : bond 0.04332 / 2.91 ( 1224) hydrogen bonds : angle 4.06762 / 2.89 ( 3672) Misc. bond : bond 0.00119 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 207 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8335 (ttm170) REVERT: A 238 MET cc_start: 0.6069 (mtm) cc_final: 0.5326 (tpt) REVERT: A 476 ASP cc_start: 0.8056 (t0) cc_final: 0.7585 (t0) REVERT: B 111 MET cc_start: 0.8767 (tpp) cc_final: 0.8406 (tpp) REVERT: B 224 GLU cc_start: 0.7431 (pt0) cc_final: 0.7084 (pt0) REVERT: B 238 MET cc_start: 0.6139 (mtm) cc_final: 0.5727 (tpp) REVERT: B 260 MET cc_start: 0.8518 (ptm) cc_final: 0.8150 (ppp) REVERT: B 262 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: B 294 PHE cc_start: 0.6319 (m-80) cc_final: 0.6083 (m-80) REVERT: B 297 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7765 (tt0) REVERT: B 308 LYS cc_start: 0.4830 (pttm) cc_final: 0.4373 (pttm) REVERT: B 462 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7521 (mtp-110) REVERT: B 465 MET cc_start: 0.8424 (mtm) cc_final: 0.8014 (mtm) REVERT: C 94 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8101 (ttm-80) REVERT: C 176 MET cc_start: 0.9036 (mmp) cc_final: 0.8821 (mmp) REVERT: C 238 MET cc_start: 0.6175 (mtm) cc_final: 0.5190 (tpp) REVERT: C 308 LYS cc_start: 0.5009 (pttm) cc_final: 0.4345 (pttm) REVERT: C 338 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7901 (mtt180) REVERT: C 366 MET cc_start: 0.6744 (tpp) cc_final: 0.6157 (ttm) REVERT: C 402 GLU cc_start: 0.8291 (tp30) cc_final: 0.7685 (tp30) REVERT: C 403 ARG cc_start: 0.8796 (ttt180) cc_final: 0.8593 (ttm170) REVERT: C 476 ASP cc_start: 0.7945 (t0) cc_final: 0.7340 (t0) REVERT: D 94 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8313 (ttm170) REVERT: D 238 MET cc_start: 0.6059 (mtm) cc_final: 0.5316 (tpt) REVERT: D 401 TYR cc_start: 0.8242 (t80) cc_final: 0.7972 (t80) REVERT: D 476 ASP cc_start: 0.8054 (t0) cc_final: 0.7586 (t0) REVERT: E 111 MET cc_start: 0.8790 (tpp) cc_final: 0.8428 (tpp) REVERT: E 224 GLU cc_start: 0.7397 (pt0) cc_final: 0.7057 (pt0) REVERT: E 238 MET cc_start: 0.6173 (mtm) cc_final: 0.5731 (tpp) REVERT: E 294 PHE cc_start: 0.6319 (m-80) cc_final: 0.6090 (m-80) REVERT: E 297 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7795 (tt0) REVERT: E 308 LYS cc_start: 0.4652 (pttm) cc_final: 0.4259 (pttm) REVERT: E 465 MET cc_start: 0.8388 (mtm) cc_final: 0.8026 (mtm) REVERT: F 94 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8095 (ttm-80) REVERT: F 176 MET cc_start: 0.9056 (mmp) cc_final: 0.8817 (mmp) REVERT: F 238 MET cc_start: 0.6263 (mtm) cc_final: 0.5216 (tpp) REVERT: F 308 LYS cc_start: 0.4923 (pttm) cc_final: 0.4271 (pttm) REVERT: F 338 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7890 (mtt180) REVERT: F 366 MET cc_start: 0.6733 (tpp) cc_final: 0.6152 (ttm) REVERT: F 402 GLU cc_start: 0.8290 (tp30) cc_final: 0.7687 (tp30) REVERT: F 403 ARG cc_start: 0.8809 (ttt180) cc_final: 0.8600 (ttm170) REVERT: F 476 ASP cc_start: 0.7942 (t0) cc_final: 0.7314 (t0) outliers start: 81 outliers final: 64 residues processed: 272 average time/residue: 0.1617 time to fit residues: 69.0596 Evaluate side-chains 271 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 469 MET Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 249 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.094804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068932 restraints weight = 58546.556| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.83 r_work: 0.2908 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24366 Z= 0.160 Angle : 0.576 9.748 32994 Z= 0.298 Chirality : 0.044 0.139 3588 Planarity : 0.004 0.036 4224 Dihedral : 5.497 50.320 3390 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.08 % Allowed : 12.30 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: 0.53 (0.16), residues: 2964 helix: 1.24 (0.13), residues: 1476 sheet: -0.71 (0.27), residues: 384 loop : -0.35 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 86 TYR 0.009 0.001 TYR C 493 PHE 0.018 0.002 PHE F 63 TRP 0.016 0.002 TRP D 281 HIS 0.005 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (24360) covalent geometry : angle 0.57635 / 0.30 (32994) hydrogen bonds : bond 0.04516 / 3.03 ( 1224) hydrogen bonds : angle 4.11036 / 2.93 ( 3672) Misc. bond : bond 0.00132 / 0.06 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 200 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8336 (ttm170) REVERT: A 476 ASP cc_start: 0.8055 (t0) cc_final: 0.7573 (t0) REVERT: B 94 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8489 (ttm-80) REVERT: B 111 MET cc_start: 0.8769 (tpp) cc_final: 0.8410 (tpp) REVERT: B 224 GLU cc_start: 0.7404 (pt0) cc_final: 0.7065 (pt0) REVERT: B 238 MET cc_start: 0.6092 (mtm) cc_final: 0.5708 (tpp) REVERT: B 260 MET cc_start: 0.8522 (ptm) cc_final: 0.8121 (ppp) REVERT: B 262 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: B 294 PHE cc_start: 0.6328 (m-80) cc_final: 0.6076 (m-80) REVERT: B 297 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7780 (tt0) REVERT: B 462 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7451 (mmm-85) REVERT: B 465 MET cc_start: 0.8431 (mtm) cc_final: 0.8016 (mtm) REVERT: C 94 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8099 (ttm-80) REVERT: C 176 MET cc_start: 0.9044 (mmp) cc_final: 0.8831 (mmp) REVERT: C 238 MET cc_start: 0.5987 (mtm) cc_final: 0.5293 (tpt) REVERT: C 308 LYS cc_start: 0.5037 (pttm) cc_final: 0.4364 (pttm) REVERT: C 338 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7922 (mtt180) REVERT: C 402 GLU cc_start: 0.8290 (tp30) cc_final: 0.7679 (tp30) REVERT: C 403 ARG cc_start: 0.8816 (ttt180) cc_final: 0.8601 (ttm170) REVERT: C 476 ASP cc_start: 0.7948 (t0) cc_final: 0.7345 (t0) REVERT: D 94 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8328 (ttm170) REVERT: D 476 ASP cc_start: 0.8037 (t0) cc_final: 0.7567 (t0) REVERT: E 94 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8481 (ttm-80) REVERT: E 111 MET cc_start: 0.8801 (tpp) cc_final: 0.8441 (tpp) REVERT: E 224 GLU cc_start: 0.7370 (pt0) cc_final: 0.7032 (pt0) REVERT: E 238 MET cc_start: 0.6125 (mtm) cc_final: 0.5745 (tpp) REVERT: E 294 PHE cc_start: 0.6322 (m-80) cc_final: 0.6076 (m-80) REVERT: E 297 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7797 (tt0) REVERT: E 308 LYS cc_start: 0.4676 (pttm) cc_final: 0.4282 (pttm) REVERT: E 465 MET cc_start: 0.8399 (mtm) cc_final: 0.8047 (mtm) REVERT: F 94 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8087 (ttm-80) REVERT: F 176 MET cc_start: 0.9054 (mmp) cc_final: 0.8816 (mmp) REVERT: F 238 MET cc_start: 0.6015 (mtm) cc_final: 0.5343 (tpt) REVERT: F 308 LYS cc_start: 0.4907 (pttm) cc_final: 0.4255 (pttm) REVERT: F 338 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: F 366 MET cc_start: 0.6743 (tpp) cc_final: 0.6166 (ttm) REVERT: F 402 GLU cc_start: 0.8295 (tp30) cc_final: 0.7685 (tp30) REVERT: F 403 ARG cc_start: 0.8815 (ttt180) cc_final: 0.8602 (ttm170) REVERT: F 476 ASP cc_start: 0.7955 (t0) cc_final: 0.7329 (t0) outliers start: 77 outliers final: 65 residues processed: 260 average time/residue: 0.1670 time to fit residues: 67.6443 Evaluate side-chains 269 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 194 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 94 ARG Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 372 TYR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 181 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 275 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069971 restraints weight = 58312.836| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.85 r_work: 0.2928 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24366 Z= 0.131 Angle : 0.549 9.807 32994 Z= 0.282 Chirality : 0.043 0.144 3588 Planarity : 0.004 0.036 4224 Dihedral : 5.368 49.405 3390 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.96 % Allowed : 12.54 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % 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: 0.71 (0.16), residues: 2964 helix: 1.44 (0.14), residues: 1470 sheet: -0.69 (0.27), residues: 384 loop : -0.29 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 86 TYR 0.008 0.001 TYR F 493 PHE 0.018 0.002 PHE F 63 TRP 0.014 0.001 TRP D 281 HIS 0.004 0.001 HIS A 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (24360) covalent geometry : angle 0.54904 / 0.28 (32994) hydrogen bonds : bond 0.04154 / 2.79 ( 1224) hydrogen bonds : angle 4.02284 / 2.86 ( 3672) Misc. bond : bond 0.00105 / 0.05 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5119.04 seconds wall clock time: 89 minutes 7.30 seconds (5347.30 seconds total)