Starting phenix.real_space_refine on Fri Jun 20 05:36:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_6634.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_6634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_6634.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_6634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd1_6634/06_2025/3jd1_6634.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 9.89, per 1000 atoms: 0.42 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: 6.76 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.97 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: 9.58 Time building geometry restraints manager: 7.85 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: 14196 16.94 - 33.88: 462 33.88 - 50.83: 294 50.83 - 67.77: 18 67.77 - 84.71: 12 Dihedral angle restraints: 14982 sinusoidal: 6504 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 14979 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: 0.19 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 51.320 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 : 11.303 84.712 9582 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.004 TRP E 385 HIS 0.014 0.002 HIS D 450 PHE 0.025 0.003 PHE C 16 TYR 0.026 0.003 TYR B 372 ARG 0.005 0.001 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.27582 ( 1224) hydrogen bonds : angle 10.63852 ( 3672) covalent geometry : bond 0.01460 (24360) covalent geometry : angle 1.01348 (32994) Misc. bond : bond 0.78904 ( 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 : 2.510 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: 0.7383 (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: 0.6858 (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: 0.4929 time to fit residues: 416.8349 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 : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN 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 56 ASN ** 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 209 HIS D 388 ASN D 450 HIS D 494 ASN E 40 GLN ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3686 r_free = 0.3686 target = 0.098429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072089 restraints weight = 56324.192| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.87 r_work: 0.2984 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24366 Z= 0.208 Angle : 0.687 6.941 32994 Z= 0.363 Chirality : 0.047 0.163 3588 Planarity : 0.006 0.072 4224 Dihedral : 10.170 89.422 3990 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.96 % Allowed : 6.49 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 2964 helix: -1.22 (0.12), residues: 1452 sheet: -1.76 (0.23), residues: 420 loop : -1.81 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 281 HIS 0.011 0.002 HIS A 221 PHE 0.023 0.003 PHE A 9 TYR 0.018 0.002 TYR B 382 ARG 0.010 0.001 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.05882 ( 1224) hydrogen bonds : angle 5.34203 ( 3672) covalent geometry : bond 0.00468 (24360) covalent geometry : angle 0.68705 (32994) Misc. bond : bond 0.00735 ( 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 369 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 2.575 Fit side-chains REVERT: A 111 MET cc_start: 0.8767 (tpp) cc_final: 0.8547 (tpp) REVERT: A 233 MET cc_start: 0.7552 (mmm) cc_final: 0.7201 (mmt) REVERT: A 402 GLU cc_start: 0.8007 (tp30) cc_final: 0.7414 (tp30) REVERT: A 469 MET cc_start: 0.7838 (mmp) cc_final: 0.7519 (ttt) REVERT: A 476 ASP cc_start: 0.7969 (t0) cc_final: 0.7666 (t0) REVERT: B 224 GLU cc_start: 0.7564 (pt0) cc_final: 0.7307 (pt0) REVERT: B 401 TYR cc_start: 0.8161 (t80) cc_final: 0.7810 (t80) REVERT: B 402 GLU cc_start: 0.7974 (tp30) cc_final: 0.7321 (tp30) REVERT: B 469 MET cc_start: 0.7843 (mmp) cc_final: 0.7636 (ttp) REVERT: B 476 ASP cc_start: 0.8091 (t0) cc_final: 0.7769 (t0) REVERT: B 495 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7113 (mt-10) REVERT: C 66 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7912 (ttt180) REVERT: C 238 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5969 (mpp) REVERT: C 402 GLU cc_start: 0.8070 (tp30) cc_final: 0.7530 (tp30) REVERT: C 403 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8425 (ttm170) REVERT: C 462 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.8152 (tmt-80) REVERT: C 469 MET cc_start: 0.7744 (mmp) cc_final: 0.7528 (ttp) REVERT: C 476 ASP cc_start: 0.7926 (t0) cc_final: 0.7589 (t0) REVERT: D 111 MET cc_start: 0.8777 (tpp) cc_final: 0.8557 (tpp) REVERT: D 233 MET cc_start: 0.7551 (mmm) cc_final: 0.7203 (mmt) REVERT: D 402 GLU cc_start: 0.8006 (tp30) cc_final: 0.7410 (tp30) REVERT: D 469 MET cc_start: 0.7828 (mmp) cc_final: 0.7504 (ttt) REVERT: D 476 ASP cc_start: 0.7951 (t0) cc_final: 0.7651 (t0) REVERT: E 224 GLU cc_start: 0.7556 (pt0) cc_final: 0.7297 (pt0) REVERT: E 238 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.6063 (mpp) REVERT: E 401 TYR cc_start: 0.8162 (t80) cc_final: 0.7811 (t80) REVERT: E 402 GLU cc_start: 0.7993 (tp30) cc_final: 0.7342 (tp30) REVERT: E 469 MET cc_start: 0.7876 (mmp) cc_final: 0.7649 (ttp) REVERT: E 476 ASP cc_start: 0.8091 (t0) cc_final: 0.7769 (t0) REVERT: E 495 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7107 (mt-10) REVERT: F 66 ARG cc_start: 0.8167 (ttt-90) cc_final: 0.7903 (ttt180) REVERT: F 238 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5969 (mpp) REVERT: F 402 GLU cc_start: 0.8057 (tp30) cc_final: 0.7518 (tp30) REVERT: F 403 ARG cc_start: 0.8692 (ttt180) cc_final: 0.8440 (ttm170) REVERT: F 462 ARG cc_start: 0.8400 (tpp-160) cc_final: 0.8147 (tmt-80) REVERT: F 469 MET cc_start: 0.7725 (mmp) cc_final: 0.7520 (ttp) REVERT: F 476 ASP cc_start: 0.7939 (t0) cc_final: 0.7602 (t0) outliers start: 49 outliers final: 24 residues processed: 360 average time/residue: 0.4416 time to fit residues: 232.0037 Evaluate side-chains 223 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 2.897 ------------------------------------------------------------------------------- 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 219 optimal weight: 0.2980 chunk 191 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 215 optimal weight: 0.0070 chunk 154 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 HIS E 472 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072935 restraints weight = 56547.942| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.85 r_work: 0.3000 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24366 Z= 0.132 Angle : 0.560 7.031 32994 Z= 0.296 Chirality : 0.043 0.148 3588 Planarity : 0.005 0.040 4224 Dihedral : 9.183 78.237 3990 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.08 % Allowed : 7.97 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 2964 helix: 0.46 (0.13), residues: 1452 sheet: -0.92 (0.25), residues: 420 loop : -1.26 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 385 HIS 0.005 0.001 HIS D 408 PHE 0.019 0.002 PHE A 9 TYR 0.010 0.001 TYR F 78 ARG 0.005 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 1224) hydrogen bonds : angle 4.48316 ( 3672) covalent geometry : bond 0.00286 (24360) covalent geometry : angle 0.56050 (32994) Misc. bond : bond 0.00065 ( 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 329 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 2.721 Fit side-chains REVERT: A 111 MET cc_start: 0.8772 (tpp) cc_final: 0.8553 (tpp) REVERT: A 294 PHE cc_start: 0.6601 (m-80) cc_final: 0.6321 (t80) REVERT: A 402 GLU cc_start: 0.8077 (tp30) cc_final: 0.7499 (tp30) REVERT: A 469 MET cc_start: 0.7744 (mmp) cc_final: 0.7415 (ttp) REVERT: A 476 ASP cc_start: 0.7959 (t0) cc_final: 0.7690 (t0) REVERT: B 224 GLU cc_start: 0.7508 (pt0) cc_final: 0.7250 (pt0) REVERT: B 238 MET cc_start: 0.6091 (mtm) cc_final: 0.5428 (tpp) REVERT: B 297 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7542 (tt0) REVERT: B 402 GLU cc_start: 0.8038 (tp30) cc_final: 0.7449 (tp30) REVERT: B 476 ASP cc_start: 0.7931 (t0) cc_final: 0.7573 (t70) REVERT: C 111 MET cc_start: 0.8798 (tpp) cc_final: 0.8562 (tpp) REVERT: C 296 LEU cc_start: 0.7456 (mt) cc_final: 0.7170 (pp) REVERT: C 297 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7593 (tt0) REVERT: C 366 MET cc_start: 0.6669 (tpp) cc_final: 0.5999 (ttm) REVERT: C 402 GLU cc_start: 0.8083 (tp30) cc_final: 0.7457 (tp30) REVERT: C 403 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8448 (ttm170) REVERT: C 476 ASP cc_start: 0.7889 (t0) cc_final: 0.7489 (t0) REVERT: D 111 MET cc_start: 0.8782 (tpp) cc_final: 0.8562 (tpp) REVERT: D 294 PHE cc_start: 0.6624 (m-80) cc_final: 0.6379 (t80) REVERT: D 402 GLU cc_start: 0.8072 (tp30) cc_final: 0.7483 (tp30) REVERT: D 469 MET cc_start: 0.7749 (mmp) cc_final: 0.7415 (ttp) REVERT: D 476 ASP cc_start: 0.7955 (t0) cc_final: 0.7686 (t0) REVERT: E 224 GLU cc_start: 0.7502 (pt0) cc_final: 0.7245 (pt0) REVERT: E 260 MET cc_start: 0.8432 (ttm) cc_final: 0.8159 (ttt) REVERT: E 297 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7545 (tt0) REVERT: E 402 GLU cc_start: 0.8038 (tp30) cc_final: 0.7445 (tp30) REVERT: E 476 ASP cc_start: 0.7941 (t0) cc_final: 0.7583 (t70) REVERT: F 111 MET cc_start: 0.8825 (tpp) cc_final: 0.8589 (tpp) REVERT: F 296 LEU cc_start: 0.7415 (mt) cc_final: 0.7116 (pp) REVERT: F 297 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7608 (tt0) REVERT: F 366 MET cc_start: 0.6678 (tpp) cc_final: 0.5991 (ttm) REVERT: F 402 GLU cc_start: 0.8066 (tp30) cc_final: 0.7442 (tp30) REVERT: F 403 ARG cc_start: 0.8670 (ttt180) cc_final: 0.8458 (ttm170) REVERT: F 476 ASP cc_start: 0.7905 (t0) cc_final: 0.7502 (t0) outliers start: 52 outliers final: 21 residues processed: 315 average time/residue: 0.3886 time to fit residues: 185.8354 Evaluate side-chains 218 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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 417 LEU Chi-restraints excluded: chain B residue 24 VAL 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 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 252 PHE Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL 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 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 57 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 153 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 268 optimal weight: 40.0000 chunk 116 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN E 408 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.094830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.068587 restraints weight = 58148.793| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.84 r_work: 0.2902 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24366 Z= 0.223 Angle : 0.652 6.727 32994 Z= 0.339 Chirality : 0.047 0.140 3588 Planarity : 0.005 0.040 4224 Dihedral : 9.698 80.029 3990 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.24 % Allowed : 9.33 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 2964 helix: 0.58 (0.14), residues: 1452 sheet: -1.00 (0.24), residues: 450 loop : -0.86 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 385 HIS 0.008 0.002 HIS C 298 PHE 0.021 0.002 PHE D 148 TYR 0.016 0.002 TYR E 78 ARG 0.007 0.001 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.05408 ( 1224) hydrogen bonds : angle 4.41338 ( 3672) covalent geometry : bond 0.00512 (24360) covalent geometry : angle 0.65236 (32994) Misc. bond : bond 0.00128 ( 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 287 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 2.755 Fit side-chains REVERT: A 103 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7872 (tp30) REVERT: A 238 MET cc_start: 0.6213 (mtm) cc_final: 0.5205 (tpp) REVERT: A 297 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7592 (tt0) REVERT: A 314 ILE cc_start: 0.7215 (mm) cc_final: 0.7008 (mm) REVERT: A 402 GLU cc_start: 0.8209 (tp30) cc_final: 0.7731 (tp30) REVERT: A 476 ASP cc_start: 0.7966 (t0) cc_final: 0.7487 (t0) REVERT: B 103 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8056 (tp30) REVERT: B 224 GLU cc_start: 0.7518 (pt0) cc_final: 0.7190 (pt0) REVERT: B 233 MET cc_start: 0.7400 (mmt) cc_final: 0.7189 (mmt) REVERT: B 238 MET cc_start: 0.6070 (mtm) cc_final: 0.5450 (tpp) REVERT: B 252 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5654 (t80) REVERT: B 260 MET cc_start: 0.8439 (ttm) cc_final: 0.8157 (ttt) REVERT: B 297 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7658 (tt0) REVERT: B 314 ILE cc_start: 0.7189 (mm) cc_final: 0.6896 (mm) REVERT: B 402 GLU cc_start: 0.8202 (tp30) cc_final: 0.7736 (tp30) REVERT: B 465 MET cc_start: 0.8447 (mtm) cc_final: 0.8065 (mtm) REVERT: B 476 ASP cc_start: 0.8033 (t0) cc_final: 0.7573 (t0) REVERT: C 12 MET cc_start: 0.8135 (ptm) cc_final: 0.7833 (ptm) REVERT: C 103 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8059 (tp30) REVERT: C 176 MET cc_start: 0.9047 (mmp) cc_final: 0.8804 (mmp) REVERT: C 238 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.5537 (mmt) REVERT: C 296 LEU cc_start: 0.7650 (mt) cc_final: 0.7186 (pp) REVERT: C 297 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7737 (tt0) REVERT: C 314 ILE cc_start: 0.7220 (mm) cc_final: 0.7009 (mm) REVERT: C 366 MET cc_start: 0.6818 (tpp) cc_final: 0.6134 (ttm) REVERT: C 402 GLU cc_start: 0.8255 (tp30) cc_final: 0.7617 (tp30) REVERT: C 403 ARG cc_start: 0.8789 (ttt180) cc_final: 0.8549 (ttm170) REVERT: C 476 ASP cc_start: 0.8058 (t0) cc_final: 0.7556 (t0) REVERT: D 103 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7898 (tp30) REVERT: D 238 MET cc_start: 0.6219 (mtm) cc_final: 0.5210 (tpp) REVERT: D 297 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7588 (tt0) REVERT: D 314 ILE cc_start: 0.7223 (mm) cc_final: 0.7011 (mm) REVERT: D 402 GLU cc_start: 0.8205 (tp30) cc_final: 0.7718 (tp30) REVERT: D 476 ASP cc_start: 0.7967 (t0) cc_final: 0.7492 (t0) REVERT: E 103 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8068 (tp30) REVERT: E 224 GLU cc_start: 0.7502 (pt0) cc_final: 0.7181 (pt0) REVERT: E 252 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.5650 (t80) REVERT: E 260 MET cc_start: 0.8413 (ttm) cc_final: 0.8114 (ttt) REVERT: E 297 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7823 (mp10) REVERT: E 314 ILE cc_start: 0.7214 (mm) cc_final: 0.6927 (mm) REVERT: E 402 GLU cc_start: 0.8213 (tp30) cc_final: 0.7743 (tp30) REVERT: E 465 MET cc_start: 0.8426 (mtm) cc_final: 0.8029 (mtm) REVERT: E 476 ASP cc_start: 0.8045 (t0) cc_final: 0.7587 (t0) REVERT: F 12 MET cc_start: 0.8135 (ptm) cc_final: 0.7832 (ptm) REVERT: F 103 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8071 (tp30) REVERT: F 238 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5544 (mmt) REVERT: F 296 LEU cc_start: 0.7637 (mt) cc_final: 0.7174 (pp) REVERT: F 297 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7724 (tt0) REVERT: F 314 ILE cc_start: 0.7276 (mm) cc_final: 0.7060 (mm) REVERT: F 366 MET cc_start: 0.6830 (tpp) cc_final: 0.6144 (ttm) REVERT: F 402 GLU cc_start: 0.8250 (tp30) cc_final: 0.7614 (tp30) REVERT: F 403 ARG cc_start: 0.8799 (ttt180) cc_final: 0.8556 (ttm170) REVERT: F 476 ASP cc_start: 0.8054 (t0) cc_final: 0.7554 (t0) outliers start: 56 outliers final: 31 residues processed: 274 average time/residue: 0.4555 time to fit residues: 198.1876 Evaluate side-chains 240 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 205 time to evaluate : 6.523 ------------------------------------------------------------------------------- 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 252 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 24 VAL 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 139 ASN Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 293 ASP 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 252 PHE Chi-restraints excluded: chain D residue 322 LEU 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 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 139 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 76 optimal weight: 0.0470 chunk 152 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 274 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 210 optimal weight: 0.9980 overall best weight: 1.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 135 ASN B 135 ASN C 135 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN D 135 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 = 0.3678 r_free = 0.3678 target = 0.098098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071951 restraints weight = 57588.960| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.86 r_work: 0.2974 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24366 Z= 0.106 Angle : 0.519 8.437 32994 Z= 0.268 Chirality : 0.042 0.136 3588 Planarity : 0.004 0.036 4224 Dihedral : 9.194 82.591 3990 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.76 % Allowed : 10.18 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2964 helix: 1.28 (0.14), residues: 1446 sheet: -0.55 (0.25), residues: 420 loop : -0.71 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 385 HIS 0.004 0.001 HIS E 258 PHE 0.014 0.001 PHE C 63 TYR 0.010 0.001 TYR D 401 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1224) hydrogen bonds : angle 4.00134 ( 3672) covalent geometry : bond 0.00228 (24360) covalent geometry : angle 0.51896 (32994) Misc. bond : bond 0.00045 ( 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 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 2.713 Fit side-chains REVERT: A 238 MET cc_start: 0.6084 (mtm) cc_final: 0.5328 (tpt) REVERT: A 250 GLN cc_start: 0.7870 (tp-100) cc_final: 0.7451 (tt0) REVERT: A 294 PHE cc_start: 0.6806 (m-80) cc_final: 0.6602 (t80) REVERT: A 297 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7717 (tt0) REVERT: A 330 GLN cc_start: 0.7956 (mt0) cc_final: 0.7419 (mt0) REVERT: A 476 ASP cc_start: 0.7919 (t0) cc_final: 0.7394 (t0) REVERT: B 224 GLU cc_start: 0.7450 (pt0) cc_final: 0.7125 (pt0) REVERT: B 238 MET cc_start: 0.6165 (mtm) cc_final: 0.5467 (tpp) REVERT: B 297 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7678 (tt0) REVERT: B 402 GLU cc_start: 0.8147 (tp30) cc_final: 0.7581 (tp30) REVERT: B 465 MET cc_start: 0.8352 (mtm) cc_final: 0.8001 (mtm) REVERT: B 476 ASP cc_start: 0.7936 (t0) cc_final: 0.7450 (t0) REVERT: C 12 MET cc_start: 0.8077 (ptm) cc_final: 0.7835 (ptm) REVERT: C 90 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: C 176 MET cc_start: 0.9059 (mmp) cc_final: 0.8784 (mmp) REVERT: C 238 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5657 (tpt) REVERT: C 296 LEU cc_start: 0.7710 (mt) cc_final: 0.7274 (pp) REVERT: C 297 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7789 (tt0) REVERT: C 314 ILE cc_start: 0.7358 (mm) cc_final: 0.7058 (mm) REVERT: C 366 MET cc_start: 0.6703 (tpp) cc_final: 0.6038 (ttm) REVERT: C 402 GLU cc_start: 0.8140 (tp30) cc_final: 0.7652 (tp30) REVERT: C 403 ARG cc_start: 0.8706 (ttt180) cc_final: 0.8488 (ttm170) REVERT: C 476 ASP cc_start: 0.7933 (t0) cc_final: 0.7477 (t0) REVERT: D 238 MET cc_start: 0.6075 (mtm) cc_final: 0.5319 (tpt) REVERT: D 250 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7456 (tt0) REVERT: D 297 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7725 (tt0) REVERT: D 330 GLN cc_start: 0.7947 (mt0) cc_final: 0.7388 (mt0) REVERT: D 476 ASP cc_start: 0.7916 (t0) cc_final: 0.7390 (t0) REVERT: E 224 GLU cc_start: 0.7445 (pt0) cc_final: 0.7139 (pt0) REVERT: E 238 MET cc_start: 0.6099 (mtm) cc_final: 0.5354 (tpt) REVERT: E 260 MET cc_start: 0.8415 (ttm) cc_final: 0.8208 (ttt) REVERT: E 297 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7676 (tt0) REVERT: E 402 GLU cc_start: 0.8163 (tp30) cc_final: 0.7592 (tp30) REVERT: E 465 MET cc_start: 0.8304 (mtm) cc_final: 0.7956 (mtm) REVERT: E 476 ASP cc_start: 0.7944 (t0) cc_final: 0.7463 (t0) REVERT: F 12 MET cc_start: 0.8088 (ptm) cc_final: 0.7844 (ptm) REVERT: F 233 MET cc_start: 0.7502 (mmt) cc_final: 0.7298 (mmt) REVERT: F 238 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.5649 (tpt) REVERT: F 296 LEU cc_start: 0.7694 (mt) cc_final: 0.7262 (pp) REVERT: F 297 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7768 (tt0) REVERT: F 314 ILE cc_start: 0.7360 (mm) cc_final: 0.7094 (mm) REVERT: F 366 MET cc_start: 0.6714 (tpp) cc_final: 0.6038 (ttm) REVERT: F 402 GLU cc_start: 0.8147 (tp30) cc_final: 0.7663 (tp30) REVERT: F 403 ARG cc_start: 0.8701 (ttt180) cc_final: 0.8482 (ttm170) REVERT: F 476 ASP cc_start: 0.7938 (t0) cc_final: 0.7481 (t0) outliers start: 44 outliers final: 31 residues processed: 255 average time/residue: 0.3559 time to fit residues: 142.5242 Evaluate side-chains 239 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 260 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG 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 257 LEU 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 C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG 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 257 LEU Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain F residue 24 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 338 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 268 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 179 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 224 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.0050 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.097426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071082 restraints weight = 57054.429| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.85 r_work: 0.2959 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24366 Z= 0.118 Angle : 0.526 7.732 32994 Z= 0.270 Chirality : 0.043 0.146 3588 Planarity : 0.004 0.034 4224 Dihedral : 9.092 82.841 3990 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.24 % Allowed : 10.46 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2964 helix: 1.44 (0.14), residues: 1452 sheet: -0.46 (0.25), residues: 420 loop : -0.37 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 281 HIS 0.004 0.001 HIS D 391 PHE 0.015 0.002 PHE F 63 TYR 0.012 0.001 TYR A 401 ARG 0.003 0.000 ARG F 86 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 1224) hydrogen bonds : angle 3.89348 ( 3672) covalent geometry : bond 0.00264 (24360) covalent geometry : angle 0.52632 (32994) Misc. bond : bond 0.00050 ( 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 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 3.066 Fit side-chains REVERT: A 238 MET cc_start: 0.5987 (mtm) cc_final: 0.5376 (tpt) REVERT: A 250 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7381 (tt0) REVERT: A 297 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7739 (tt0) REVERT: A 330 GLN cc_start: 0.7944 (mt0) cc_final: 0.7387 (mt0) REVERT: A 476 ASP cc_start: 0.7941 (t0) cc_final: 0.7368 (t0) REVERT: B 224 GLU cc_start: 0.7446 (pt0) cc_final: 0.7097 (pt0) REVERT: B 238 MET cc_start: 0.6255 (mtm) cc_final: 0.5213 (tpt) REVERT: B 297 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7670 (tt0) REVERT: B 402 GLU cc_start: 0.8161 (tp30) cc_final: 0.7637 (tp30) REVERT: B 465 MET cc_start: 0.8362 (mtm) cc_final: 0.8045 (mtm) REVERT: B 476 ASP cc_start: 0.7939 (t0) cc_final: 0.7424 (t0) REVERT: C 12 MET cc_start: 0.8061 (ptm) cc_final: 0.7825 (ptm) REVERT: C 90 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: C 94 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8108 (ttm-80) REVERT: C 176 MET cc_start: 0.9069 (mmp) cc_final: 0.8793 (mmp) REVERT: C 296 LEU cc_start: 0.7717 (mt) cc_final: 0.7266 (pp) REVERT: C 297 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7798 (tt0) REVERT: C 308 LYS cc_start: 0.5087 (pttm) cc_final: 0.4662 (pttm) REVERT: C 314 ILE cc_start: 0.7392 (mm) cc_final: 0.7182 (mm) REVERT: C 402 GLU cc_start: 0.8171 (tp30) cc_final: 0.7692 (tp30) REVERT: C 403 ARG cc_start: 0.8733 (ttt180) cc_final: 0.8503 (ttm170) REVERT: C 476 ASP cc_start: 0.7919 (t0) cc_final: 0.7441 (t0) REVERT: D 238 MET cc_start: 0.5978 (mtm) cc_final: 0.5372 (tpt) REVERT: D 250 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7206 (tt0) REVERT: D 297 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7728 (tt0) REVERT: D 476 ASP cc_start: 0.7939 (t0) cc_final: 0.7370 (t0) REVERT: E 224 GLU cc_start: 0.7449 (pt0) cc_final: 0.7132 (pt0) REVERT: E 238 MET cc_start: 0.5925 (mtm) cc_final: 0.5199 (tpt) REVERT: E 297 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7672 (tt0) REVERT: E 308 LYS cc_start: 0.5126 (pttm) cc_final: 0.4801 (pttm) REVERT: E 402 GLU cc_start: 0.8175 (tp30) cc_final: 0.7650 (tp30) REVERT: E 465 MET cc_start: 0.8298 (mtm) cc_final: 0.7972 (mtm) REVERT: E 476 ASP cc_start: 0.7946 (t0) cc_final: 0.7434 (t0) REVERT: F 12 MET cc_start: 0.8071 (ptm) cc_final: 0.7831 (ptm) REVERT: F 90 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8279 (mtpp) REVERT: F 94 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8122 (ttm-80) REVERT: F 296 LEU cc_start: 0.7713 (mt) cc_final: 0.7283 (pp) REVERT: F 297 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7787 (tt0) REVERT: F 308 LYS cc_start: 0.5083 (pttm) cc_final: 0.4659 (pttm) REVERT: F 402 GLU cc_start: 0.8184 (tp30) cc_final: 0.7710 (tp30) REVERT: F 403 ARG cc_start: 0.8741 (ttt180) cc_final: 0.8510 (ttm170) REVERT: F 476 ASP cc_start: 0.7905 (t0) cc_final: 0.7427 (t0) outliers start: 56 outliers final: 37 residues processed: 253 average time/residue: 0.3868 time to fit residues: 151.3279 Evaluate side-chains 249 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 2.556 ------------------------------------------------------------------------------- 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 260 MET Chi-restraints excluded: chain A residue 296 LEU 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 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 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 90 LYS Chi-restraints excluded: chain C residue 94 ARG 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 252 PHE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 296 LEU 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 427 THR 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 15 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 255 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.095811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069546 restraints weight = 58100.324| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.83 r_work: 0.2924 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24366 Z= 0.171 Angle : 0.579 9.069 32994 Z= 0.297 Chirality : 0.044 0.136 3588 Planarity : 0.004 0.033 4224 Dihedral : 9.311 84.426 3990 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.56 % Allowed : 10.86 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2964 helix: 1.30 (0.14), residues: 1458 sheet: -0.48 (0.25), residues: 420 loop : -0.34 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 281 HIS 0.006 0.001 HIS A 258 PHE 0.017 0.002 PHE F 63 TYR 0.013 0.002 TYR A 401 ARG 0.004 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 1224) hydrogen bonds : angle 3.99382 ( 3672) covalent geometry : bond 0.00391 (24360) covalent geometry : angle 0.57911 (32994) Misc. bond : bond 0.00072 ( 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 273 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 2.625 Fit side-chains REVERT: A 238 MET cc_start: 0.6107 (mtm) cc_final: 0.5481 (tpt) REVERT: A 250 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7168 (tt0) REVERT: A 297 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7733 (tt0) REVERT: A 330 GLN cc_start: 0.7991 (mt0) cc_final: 0.7386 (mt0) REVERT: A 476 ASP cc_start: 0.8013 (t0) cc_final: 0.7452 (t0) REVERT: B 103 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7817 (tp30) REVERT: B 224 GLU cc_start: 0.7466 (pt0) cc_final: 0.7090 (pt0) REVERT: B 238 MET cc_start: 0.6257 (mtm) cc_final: 0.5170 (tpt) REVERT: B 297 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7726 (tt0) REVERT: B 402 GLU cc_start: 0.8196 (tp30) cc_final: 0.7627 (tp30) REVERT: B 465 MET cc_start: 0.8402 (mtm) cc_final: 0.8157 (mtm) REVERT: B 476 ASP cc_start: 0.7988 (t0) cc_final: 0.7412 (t0) REVERT: C 12 MET cc_start: 0.8077 (ptm) cc_final: 0.7846 (ptm) REVERT: C 90 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8171 (mtpp) REVERT: C 94 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8110 (ttm-80) REVERT: C 238 MET cc_start: 0.6219 (mtp) cc_final: 0.5700 (tpt) REVERT: C 296 LEU cc_start: 0.7752 (mt) cc_final: 0.7286 (pp) REVERT: C 297 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7818 (tt0) REVERT: C 308 LYS cc_start: 0.5042 (pttm) cc_final: 0.4631 (pttm) REVERT: C 338 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7733 (mtt180) REVERT: C 402 GLU cc_start: 0.8280 (tp30) cc_final: 0.7847 (tp30) REVERT: C 403 ARG cc_start: 0.8794 (ttt180) cc_final: 0.8562 (ttm170) REVERT: C 476 ASP cc_start: 0.7943 (t0) cc_final: 0.7394 (t0) REVERT: D 238 MET cc_start: 0.6088 (mtm) cc_final: 0.5474 (tpt) REVERT: D 250 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7161 (tt0) REVERT: D 297 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7744 (tt0) REVERT: D 330 GLN cc_start: 0.7936 (mt0) cc_final: 0.7324 (mt0) REVERT: E 103 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7825 (tp30) REVERT: E 224 GLU cc_start: 0.7450 (pt0) cc_final: 0.7093 (pt0) REVERT: E 238 MET cc_start: 0.5980 (mtm) cc_final: 0.5389 (tpt) REVERT: E 297 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7730 (tt0) REVERT: E 308 LYS cc_start: 0.5022 (pttm) cc_final: 0.4527 (pttm) REVERT: E 402 GLU cc_start: 0.8227 (tp30) cc_final: 0.7656 (tp30) REVERT: E 465 MET cc_start: 0.8367 (mtm) cc_final: 0.8128 (mtm) REVERT: E 476 ASP cc_start: 0.8046 (t0) cc_final: 0.7465 (t0) REVERT: F 12 MET cc_start: 0.8083 (ptm) cc_final: 0.7848 (ptm) REVERT: F 90 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: F 94 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8109 (ttm-80) REVERT: F 233 MET cc_start: 0.7561 (mmt) cc_final: 0.7300 (mmt) REVERT: F 238 MET cc_start: 0.6288 (mtp) cc_final: 0.5818 (tpp) REVERT: F 296 LEU cc_start: 0.7779 (mt) cc_final: 0.7329 (pp) REVERT: F 297 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7795 (tt0) REVERT: F 308 LYS cc_start: 0.5053 (pttm) cc_final: 0.4636 (pttm) REVERT: F 338 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7729 (mtt180) REVERT: F 402 GLU cc_start: 0.8276 (tp30) cc_final: 0.7844 (tp30) REVERT: F 403 ARG cc_start: 0.8794 (ttt180) cc_final: 0.8560 (ttm170) REVERT: F 476 ASP cc_start: 0.7942 (t0) cc_final: 0.7391 (t0) outliers start: 64 outliers final: 49 residues processed: 259 average time/residue: 0.3657 time to fit residues: 147.6586 Evaluate side-chains 255 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 200 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 252 PHE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 LEU 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 300 THR Chi-restraints excluded: chain B residue 322 LEU 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 C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 293 ASP 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 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 LEU 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 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 252 PHE 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 90 LYS Chi-restraints excluded: chain F residue 94 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.095301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069144 restraints weight = 57787.673| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.81 r_work: 0.2914 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24366 Z= 0.184 Angle : 0.599 8.100 32994 Z= 0.307 Chirality : 0.045 0.146 3588 Planarity : 0.004 0.034 4224 Dihedral : 9.594 89.733 3990 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.76 % Allowed : 11.30 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2964 helix: 1.25 (0.14), residues: 1464 sheet: -0.50 (0.25), residues: 420 loop : -0.27 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 281 HIS 0.006 0.001 HIS A 258 PHE 0.019 0.002 PHE F 63 TYR 0.013 0.002 TYR D 401 ARG 0.004 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 1224) hydrogen bonds : angle 4.07390 ( 3672) covalent geometry : bond 0.00422 (24360) covalent geometry : angle 0.59881 (32994) Misc. bond : bond 0.00101 ( 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 276 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 2.773 Fit side-chains revert: symmetry clash REVERT: A 238 MET cc_start: 0.6088 (mtm) cc_final: 0.5536 (tpt) REVERT: A 297 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7785 (tt0) REVERT: A 476 ASP cc_start: 0.8014 (t0) cc_final: 0.7441 (t0) REVERT: B 111 MET cc_start: 0.8848 (tpp) cc_final: 0.8464 (tpp) REVERT: B 224 GLU cc_start: 0.7473 (pt0) cc_final: 0.7089 (pt0) REVERT: B 238 MET cc_start: 0.6250 (mtm) cc_final: 0.5173 (tpt) REVERT: B 297 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7751 (tt0) REVERT: B 402 GLU cc_start: 0.8229 (tp30) cc_final: 0.7680 (tp30) REVERT: B 465 MET cc_start: 0.8413 (mtm) cc_final: 0.8145 (mtm) REVERT: B 476 ASP cc_start: 0.8067 (t0) cc_final: 0.7452 (t0) REVERT: C 90 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8217 (mtpp) REVERT: C 94 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8112 (ttm-80) REVERT: C 238 MET cc_start: 0.6252 (mtp) cc_final: 0.5726 (tpt) REVERT: C 296 LEU cc_start: 0.7845 (mt) cc_final: 0.7382 (pp) REVERT: C 297 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7809 (tt0) REVERT: C 308 LYS cc_start: 0.4940 (pttm) cc_final: 0.4631 (pttm) REVERT: C 338 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7750 (mtt180) REVERT: C 402 GLU cc_start: 0.8308 (tp30) cc_final: 0.7894 (tp30) REVERT: C 403 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8579 (ttm170) REVERT: C 476 ASP cc_start: 0.7955 (t0) cc_final: 0.7383 (t0) REVERT: D 238 MET cc_start: 0.6058 (mtm) cc_final: 0.5532 (tpt) REVERT: D 297 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7822 (tt0) REVERT: E 111 MET cc_start: 0.8890 (tpp) cc_final: 0.8503 (tpp) REVERT: E 224 GLU cc_start: 0.7427 (pt0) cc_final: 0.7068 (pt0) REVERT: E 238 MET cc_start: 0.5860 (mtm) cc_final: 0.5580 (tpp) REVERT: E 297 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7752 (tt0) REVERT: E 308 LYS cc_start: 0.4842 (pttm) cc_final: 0.4320 (pttm) REVERT: E 402 GLU cc_start: 0.8238 (tp30) cc_final: 0.7686 (tp30) REVERT: E 465 MET cc_start: 0.8376 (mtm) cc_final: 0.8125 (mtm) REVERT: F 90 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8283 (mtpp) REVERT: F 94 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8100 (ttm-80) REVERT: F 238 MET cc_start: 0.6268 (mtp) cc_final: 0.5867 (tpp) REVERT: F 297 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7772 (tt0) REVERT: F 308 LYS cc_start: 0.4953 (pttm) cc_final: 0.4644 (pttm) REVERT: F 338 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7777 (mtt180) REVERT: F 402 GLU cc_start: 0.8295 (tp30) cc_final: 0.7880 (tp30) REVERT: F 403 ARG cc_start: 0.8797 (ttt180) cc_final: 0.8574 (ttm170) REVERT: F 476 ASP cc_start: 0.7948 (t0) cc_final: 0.7371 (t0) outliers start: 69 outliers final: 59 residues processed: 261 average time/residue: 0.3752 time to fit residues: 152.9309 Evaluate side-chains 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 291 LEU 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 219 VAL Chi-restraints excluded: chain B residue 252 PHE 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 C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 293 ASP 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 139 ASN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 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 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 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 90 LYS Chi-restraints excluded: chain F residue 94 ARG 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 498 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 48 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.070082 restraints weight = 57440.612| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.82 r_work: 0.2931 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24366 Z= 0.141 Angle : 0.557 9.665 32994 Z= 0.284 Chirality : 0.043 0.139 3588 Planarity : 0.004 0.034 4224 Dihedral : 9.489 89.583 3990 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.60 % Allowed : 11.70 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2964 helix: 1.39 (0.14), residues: 1476 sheet: -0.37 (0.26), residues: 420 loop : -0.28 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.005 0.001 HIS A 391 PHE 0.018 0.002 PHE F 63 TYR 0.012 0.001 TYR D 401 ARG 0.003 0.000 ARG F 86 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 1224) hydrogen bonds : angle 3.95760 ( 3672) covalent geometry : bond 0.00320 (24360) covalent geometry : angle 0.55655 (32994) Misc. bond : bond 0.00079 ( 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 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6081 (mtm) cc_final: 0.5564 (tpt) REVERT: A 297 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7758 (tt0) REVERT: A 476 ASP cc_start: 0.8028 (t0) cc_final: 0.7419 (t0) REVERT: B 111 MET cc_start: 0.8859 (tpp) cc_final: 0.8482 (tpp) REVERT: B 224 GLU cc_start: 0.7473 (pt0) cc_final: 0.7075 (pt0) REVERT: B 238 MET cc_start: 0.6257 (mtm) cc_final: 0.5174 (tpt) REVERT: B 297 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7764 (tt0) REVERT: B 402 GLU cc_start: 0.8194 (tp30) cc_final: 0.7619 (tp30) REVERT: B 465 MET cc_start: 0.8403 (mtm) cc_final: 0.8058 (mtm) REVERT: C 90 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8203 (mtpp) REVERT: C 94 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8097 (ttm-80) REVERT: C 238 MET cc_start: 0.6200 (mtp) cc_final: 0.5725 (tpt) REVERT: C 242 PHE cc_start: 0.7112 (m-10) cc_final: 0.6862 (m-10) REVERT: C 296 LEU cc_start: 0.7846 (mt) cc_final: 0.7386 (pp) REVERT: C 297 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7784 (tt0) REVERT: C 308 LYS cc_start: 0.4942 (pttm) cc_final: 0.4644 (pttm) REVERT: C 338 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7792 (mtt180) REVERT: C 402 GLU cc_start: 0.8271 (tp30) cc_final: 0.7841 (tp30) REVERT: C 403 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8542 (ttm170) REVERT: C 476 ASP cc_start: 0.7920 (t0) cc_final: 0.7350 (t0) REVERT: D 238 MET cc_start: 0.6061 (mtm) cc_final: 0.5556 (tpt) REVERT: D 297 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7822 (tt0) REVERT: E 111 MET cc_start: 0.8859 (tpp) cc_final: 0.8479 (tpp) REVERT: E 224 GLU cc_start: 0.7427 (pt0) cc_final: 0.7079 (pt0) REVERT: E 238 MET cc_start: 0.5996 (mtm) cc_final: 0.5562 (tpp) REVERT: E 252 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5096 (t80) REVERT: E 297 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7781 (tt0) REVERT: E 308 LYS cc_start: 0.4843 (pttm) cc_final: 0.4313 (pttm) REVERT: E 330 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7424 (mt0) REVERT: E 402 GLU cc_start: 0.8214 (tp30) cc_final: 0.7633 (tp30) REVERT: E 465 MET cc_start: 0.8349 (mtm) cc_final: 0.8013 (mtm) REVERT: F 90 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8256 (mtpp) REVERT: F 94 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8089 (ttm-80) REVERT: F 229 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6782 (tp30) REVERT: F 238 MET cc_start: 0.6220 (mtp) cc_final: 0.5700 (tpt) REVERT: F 242 PHE cc_start: 0.7058 (m-10) cc_final: 0.6805 (m-10) REVERT: F 297 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7775 (tt0) REVERT: F 308 LYS cc_start: 0.4980 (pttm) cc_final: 0.4381 (pttm) REVERT: F 338 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7798 (mtt180) REVERT: F 402 GLU cc_start: 0.8279 (tp30) cc_final: 0.7844 (tp30) REVERT: F 403 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8543 (ttm170) REVERT: F 476 ASP cc_start: 0.7921 (t0) cc_final: 0.7347 (t0) outliers start: 65 outliers final: 52 residues processed: 254 average time/residue: 0.3724 time to fit residues: 146.7808 Evaluate side-chains 257 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 198 time to evaluate : 2.536 ------------------------------------------------------------------------------- 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 219 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 260 MET 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 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 300 THR Chi-restraints excluded: chain B residue 322 LEU 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 C residue 24 VAL Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 293 ASP 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 139 ASN Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 MET 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 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 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 90 LYS Chi-restraints excluded: chain F residue 94 ARG 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 498 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 140 optimal weight: 0.0170 chunk 148 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 216 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 247 optimal weight: 10.0000 chunk 213 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** 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 = 0.3669 r_free = 0.3669 target = 0.097804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071722 restraints weight = 58434.883| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.86 r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24366 Z= 0.102 Angle : 0.514 9.319 32994 Z= 0.261 Chirality : 0.042 0.147 3588 Planarity : 0.004 0.039 4224 Dihedral : 9.097 85.990 3990 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.96 % Allowed : 12.38 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.16), residues: 2964 helix: 1.68 (0.14), residues: 1470 sheet: -0.29 (0.28), residues: 348 loop : -0.22 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 281 HIS 0.004 0.001 HIS E 258 PHE 0.016 0.001 PHE B 16 TYR 0.012 0.001 TYR A 401 ARG 0.002 0.000 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 1224) hydrogen bonds : angle 3.83483 ( 3672) covalent geometry : bond 0.00222 (24360) covalent geometry : angle 0.51399 (32994) Misc. bond : bond 0.00054 ( 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 267 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6056 (mtm) cc_final: 0.5462 (tpt) REVERT: A 242 PHE cc_start: 0.6837 (m-10) cc_final: 0.6469 (m-80) REVERT: A 293 ASP cc_start: 0.8258 (m-30) cc_final: 0.6709 (t0) REVERT: A 296 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7321 (pp) REVERT: A 308 LYS cc_start: 0.4766 (pttm) cc_final: 0.4221 (pttm) REVERT: A 316 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 338 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7505 (ptp-170) REVERT: A 476 ASP cc_start: 0.7972 (t0) cc_final: 0.7317 (t0) REVERT: B 111 MET cc_start: 0.8811 (tpp) cc_final: 0.8445 (tpp) REVERT: B 224 GLU cc_start: 0.7454 (pt0) cc_final: 0.7071 (pt0) REVERT: B 233 MET cc_start: 0.7403 (mmm) cc_final: 0.7195 (mmm) REVERT: B 238 MET cc_start: 0.6333 (mtm) cc_final: 0.5190 (tpt) REVERT: B 252 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5087 (t80) REVERT: B 297 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7786 (tt0) REVERT: B 402 GLU cc_start: 0.8105 (tp30) cc_final: 0.7526 (tp30) REVERT: B 465 MET cc_start: 0.8373 (mtm) cc_final: 0.7925 (mtm) REVERT: C 94 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8074 (ttm-80) REVERT: C 176 MET cc_start: 0.9071 (mmp) cc_final: 0.8804 (mmp) REVERT: C 229 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6809 (tp30) REVERT: C 238 MET cc_start: 0.6218 (mtp) cc_final: 0.5915 (tpp) REVERT: C 250 GLN cc_start: 0.8029 (tp40) cc_final: 0.7545 (tp40) REVERT: C 296 LEU cc_start: 0.7810 (mt) cc_final: 0.7330 (pp) REVERT: C 308 LYS cc_start: 0.4976 (pttm) cc_final: 0.4366 (pttm) REVERT: C 402 GLU cc_start: 0.8183 (tp30) cc_final: 0.7713 (tp30) REVERT: C 403 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8464 (ttm170) REVERT: C 476 ASP cc_start: 0.7878 (t0) cc_final: 0.7323 (t0) REVERT: D 238 MET cc_start: 0.6048 (mtm) cc_final: 0.5453 (tpt) REVERT: D 242 PHE cc_start: 0.6818 (m-10) cc_final: 0.6449 (m-10) REVERT: D 308 LYS cc_start: 0.4821 (pttm) cc_final: 0.4264 (pttm) REVERT: D 476 ASP cc_start: 0.7965 (t0) cc_final: 0.7316 (t0) REVERT: E 111 MET cc_start: 0.8812 (tpp) cc_final: 0.8444 (tpp) REVERT: E 224 GLU cc_start: 0.7365 (pt0) cc_final: 0.7045 (pt0) REVERT: E 238 MET cc_start: 0.6076 (mtm) cc_final: 0.5524 (tpp) REVERT: E 252 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5360 (t80) REVERT: E 297 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7795 (tt0) REVERT: E 308 LYS cc_start: 0.4973 (pttm) cc_final: 0.4463 (pttm) REVERT: E 402 GLU cc_start: 0.8148 (tp30) cc_final: 0.7547 (tp30) REVERT: E 465 MET cc_start: 0.8351 (mtm) cc_final: 0.7908 (mtm) REVERT: F 90 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: F 94 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8077 (ttm-80) REVERT: F 229 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6803 (tp30) REVERT: F 238 MET cc_start: 0.6180 (mtp) cc_final: 0.5910 (tpp) REVERT: F 242 PHE cc_start: 0.7001 (m-10) cc_final: 0.6701 (m-10) REVERT: F 296 LEU cc_start: 0.8013 (mp) cc_final: 0.7542 (pp) REVERT: F 297 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7802 (tt0) REVERT: F 308 LYS cc_start: 0.5001 (pttm) cc_final: 0.4362 (pttm) REVERT: F 338 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7825 (mtt180) REVERT: F 402 GLU cc_start: 0.8175 (tp30) cc_final: 0.7707 (tp30) REVERT: F 403 ARG cc_start: 0.8715 (ttt180) cc_final: 0.8469 (ttm170) REVERT: F 476 ASP cc_start: 0.7855 (t0) cc_final: 0.7304 (t0) outliers start: 49 outliers final: 36 residues processed: 251 average time/residue: 0.3842 time to fit residues: 150.5589 Evaluate side-chains 245 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 260 MET Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 296 LEU 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 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 322 LEU Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 291 LEU 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 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 252 PHE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 372 TYR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 162 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068851 restraints weight = 57786.266| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.82 r_work: 0.2905 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24366 Z= 0.198 Angle : 0.618 9.506 32994 Z= 0.316 Chirality : 0.045 0.148 3588 Planarity : 0.004 0.035 4224 Dihedral : 9.538 86.806 3990 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.52 % Allowed : 11.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2964 helix: 1.38 (0.14), residues: 1476 sheet: -0.39 (0.25), residues: 420 loop : -0.26 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.008 0.002 HIS F 408 PHE 0.018 0.002 PHE D 148 TYR 0.015 0.002 TYR A 401 ARG 0.005 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 1224) hydrogen bonds : angle 4.05569 ( 3672) covalent geometry : bond 0.00453 (24360) covalent geometry : angle 0.61802 (32994) Misc. bond : bond 0.00105 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11571.48 seconds wall clock time: 202 minutes 23.15 seconds (12143.15 seconds total)