Starting phenix.real_space_refine on Sun Sep 29 20:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_6634.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_6634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_6634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_6634.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd1_6634/09_2024/3jd1_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-5461/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: 9.48, per 1000 atoms: 0.40 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: 5.79 Conformation dependent library (CDL) restraints added in 2.8 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: 2.63 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: 7.61 Time building geometry restraints manager: 6.70 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.010 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.860 Find NCS groups from input model: 0.840 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: 0.010 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: 50.850 ------------------------------------------------------------------------------- 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 : 0.015 0.124 24360 Z= 0.951 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 2.597 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: 0.4780 time to fit residues: 403.1550 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 24360 Z= 0.306 Angle : 0.687 6.941 32994 Z= 0.363 Chirality : 0.047 0.163 3588 Planarity : 0.006 0.072 4224 Dihedral : 10.170 89.425 3990 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.08 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 *********************** 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 fitting. rotamer outliers: 49 poor density : 320 time to evaluate : 2.674 Fit side-chains REVERT: A 233 MET cc_start: 0.7545 (mmm) cc_final: 0.7342 (mmt) REVERT: A 292 GLU cc_start: 0.7162 (pp20) cc_final: 0.6890 (pp20) REVERT: A 402 GLU cc_start: 0.7758 (tp30) cc_final: 0.7370 (tp30) REVERT: B 401 TYR cc_start: 0.8167 (t80) cc_final: 0.7907 (t80) REVERT: B 402 GLU cc_start: 0.7723 (tp30) cc_final: 0.7297 (tp30) REVERT: C 402 GLU cc_start: 0.7782 (tp30) cc_final: 0.7430 (tp30) REVERT: D 233 MET cc_start: 0.7546 (mmm) cc_final: 0.7342 (mmt) REVERT: D 292 GLU cc_start: 0.7163 (pp20) cc_final: 0.6894 (pp20) REVERT: D 402 GLU cc_start: 0.7763 (tp30) cc_final: 0.7372 (tp30) REVERT: E 401 TYR cc_start: 0.8166 (t80) cc_final: 0.7904 (t80) REVERT: E 402 GLU cc_start: 0.7727 (tp30) cc_final: 0.7299 (tp30) REVERT: F 402 GLU cc_start: 0.7782 (tp30) cc_final: 0.7432 (tp30) outliers start: 49 outliers final: 24 residues processed: 360 average time/residue: 0.4283 time to fit residues: 224.5336 Evaluate side-chains 218 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 2.606 ------------------------------------------------------------------------------- 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 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 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 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 148 optimal weight: 9.9990 chunk 82 optimal weight: 30.0000 chunk 222 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 288 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 214 optimal weight: 10.0000 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 135 ASN B 205 GLN 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 205 GLN ** E 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24360 Z= 0.344 Angle : 0.682 7.763 32994 Z= 0.357 Chirality : 0.047 0.139 3588 Planarity : 0.005 0.041 4224 Dihedral : 9.886 87.376 3990 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.64 % Allowed : 8.13 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.09 (0.15), residues: 2964 helix: -0.00 (0.13), residues: 1452 sheet: -1.32 (0.23), residues: 450 loop : -1.28 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 281 HIS 0.007 0.002 HIS C 258 PHE 0.022 0.003 PHE D 148 TYR 0.020 0.002 TYR D 78 ARG 0.007 0.001 ARG F 217 *********************** 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 307 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 241 time to evaluate : 2.609 Fit side-chains REVERT: A 402 GLU cc_start: 0.7977 (tp30) cc_final: 0.7651 (tp30) REVERT: B 103 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7486 (tp30) REVERT: B 402 GLU cc_start: 0.7950 (tp30) cc_final: 0.7560 (tp30) REVERT: C 103 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7302 (tp30) REVERT: C 238 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5941 (tpt) REVERT: C 296 LEU cc_start: 0.7610 (mt) cc_final: 0.7262 (pp) REVERT: C 366 MET cc_start: 0.6614 (tpp) cc_final: 0.6076 (ttm) REVERT: C 402 GLU cc_start: 0.7990 (tp30) cc_final: 0.7534 (tp30) REVERT: D 402 GLU cc_start: 0.7977 (tp30) cc_final: 0.7648 (tp30) REVERT: E 103 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7485 (tp30) REVERT: E 402 GLU cc_start: 0.7948 (tp30) cc_final: 0.7560 (tp30) REVERT: F 103 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7305 (tp30) REVERT: F 238 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5948 (tpt) REVERT: F 296 LEU cc_start: 0.7637 (mt) cc_final: 0.7269 (pp) REVERT: F 366 MET cc_start: 0.6606 (tpp) cc_final: 0.6066 (ttm) REVERT: F 402 GLU cc_start: 0.7989 (tp30) cc_final: 0.7535 (tp30) outliers start: 66 outliers final: 34 residues processed: 291 average time/residue: 0.3377 time to fit residues: 156.7631 Evaluate side-chains 235 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 2.438 ------------------------------------------------------------------------------- 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 362 GLU 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 338 ARG Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain F residue 238 MET 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 264 optimal weight: 6.9990 chunk 201 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 254 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 298 HIS B 298 HIS C 135 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 298 HIS E 298 HIS 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24360 Z= 0.174 Angle : 0.542 7.083 32994 Z= 0.282 Chirality : 0.043 0.147 3588 Planarity : 0.004 0.038 4224 Dihedral : 9.474 85.049 3990 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.72 % Allowed : 10.22 % 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: -0.11 (0.15), residues: 2964 helix: 0.84 (0.14), residues: 1446 sheet: -0.64 (0.26), residues: 384 loop : -0.96 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 385 HIS 0.004 0.001 HIS A 391 PHE 0.016 0.002 PHE B 9 TYR 0.009 0.001 TYR F 78 ARG 0.004 0.001 ARG C 217 *********************** 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 262 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 2.776 Fit side-chains REVERT: A 238 MET cc_start: 0.6075 (mtm) cc_final: 0.5463 (tpt) REVERT: A 402 GLU cc_start: 0.7879 (tp30) cc_final: 0.7516 (tp30) REVERT: A 435 GLU cc_start: 0.7448 (pm20) cc_final: 0.7210 (pm20) REVERT: B 252 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6100 (t80) REVERT: B 314 ILE cc_start: 0.7016 (mm) cc_final: 0.6802 (mm) REVERT: B 402 GLU cc_start: 0.7872 (tp30) cc_final: 0.7498 (tp30) REVERT: B 435 GLU cc_start: 0.7343 (pm20) cc_final: 0.7122 (pm20) REVERT: C 238 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5810 (tpt) REVERT: C 296 LEU cc_start: 0.7656 (mt) cc_final: 0.7381 (pp) REVERT: C 314 ILE cc_start: 0.7089 (mm) cc_final: 0.6858 (mm) REVERT: C 366 MET cc_start: 0.6607 (tpp) cc_final: 0.6038 (ttm) REVERT: C 402 GLU cc_start: 0.7895 (tp30) cc_final: 0.7590 (tp30) REVERT: D 238 MET cc_start: 0.6076 (mtm) cc_final: 0.5463 (tpt) REVERT: D 402 GLU cc_start: 0.7873 (tp30) cc_final: 0.7504 (tp30) REVERT: D 435 GLU cc_start: 0.7445 (pm20) cc_final: 0.7202 (pm20) REVERT: E 238 MET cc_start: 0.6489 (mtm) cc_final: 0.6261 (tpp) REVERT: E 252 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6208 (t80) REVERT: E 314 ILE cc_start: 0.7007 (mm) cc_final: 0.6803 (mm) REVERT: E 402 GLU cc_start: 0.7879 (tp30) cc_final: 0.7503 (tp30) REVERT: E 435 GLU cc_start: 0.7350 (pm20) cc_final: 0.7128 (pm20) REVERT: F 176 MET cc_start: 0.8850 (mmp) cc_final: 0.8640 (mmp) REVERT: F 238 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5793 (tpt) REVERT: F 296 LEU cc_start: 0.7729 (mt) cc_final: 0.7406 (pp) REVERT: F 366 MET cc_start: 0.6609 (tpp) cc_final: 0.6038 (ttm) REVERT: F 402 GLU cc_start: 0.7892 (tp30) cc_final: 0.7591 (tp30) outliers start: 43 outliers final: 21 residues processed: 254 average time/residue: 0.3551 time to fit residues: 143.0083 Evaluate side-chains 211 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 252 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 ARG Chi-restraints excluded: chain B residue 372 TYR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 238 MET 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 E residue 24 VAL Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 338 ARG Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 238 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 196 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** B 56 ASN B 450 HIS ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 450 HIS F 56 ASN ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24360 Z= 0.242 Angle : 0.582 8.600 32994 Z= 0.301 Chirality : 0.044 0.142 3588 Planarity : 0.004 0.036 4224 Dihedral : 9.569 87.457 3990 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.40 % Allowed : 10.70 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.16), residues: 2964 helix: 0.99 (0.14), residues: 1446 sheet: -0.73 (0.24), residues: 450 loop : -0.64 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 385 HIS 0.007 0.001 HIS B 298 PHE 0.017 0.002 PHE D 148 TYR 0.011 0.001 TYR C 493 ARG 0.004 0.001 ARG A 217 *********************** 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 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7528 (tpp) cc_final: 0.7275 (mmt) REVERT: A 238 MET cc_start: 0.5918 (mtm) cc_final: 0.5372 (tpt) REVERT: A 402 GLU cc_start: 0.7934 (tp30) cc_final: 0.7567 (tp30) REVERT: A 435 GLU cc_start: 0.7482 (pm20) cc_final: 0.7264 (pm20) REVERT: B 252 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6358 (t80) REVERT: B 402 GLU cc_start: 0.7967 (tp30) cc_final: 0.7612 (tp30) REVERT: C 90 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8191 (mtpp) REVERT: C 94 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: C 103 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7209 (tp30) REVERT: C 238 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5406 (mmt) REVERT: C 296 LEU cc_start: 0.7711 (mt) cc_final: 0.7411 (pp) REVERT: C 402 GLU cc_start: 0.8005 (tp30) cc_final: 0.7725 (tp30) REVERT: D 233 MET cc_start: 0.7530 (tpp) cc_final: 0.7284 (mmt) REVERT: D 238 MET cc_start: 0.5914 (mtm) cc_final: 0.5377 (tpt) REVERT: D 435 GLU cc_start: 0.7484 (pm20) cc_final: 0.7265 (pm20) REVERT: E 252 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6387 (t80) REVERT: E 296 LEU cc_start: 0.7931 (mp) cc_final: 0.7606 (pp) REVERT: E 402 GLU cc_start: 0.7971 (tp30) cc_final: 0.7617 (tp30) REVERT: F 90 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8158 (mtpp) REVERT: F 94 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7907 (ttm-80) REVERT: F 103 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7212 (tp30) REVERT: F 238 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5427 (mmt) REVERT: F 296 LEU cc_start: 0.7663 (mt) cc_final: 0.7394 (pp) REVERT: F 402 GLU cc_start: 0.8008 (tp30) cc_final: 0.7727 (tp30) outliers start: 60 outliers final: 41 residues processed: 248 average time/residue: 0.3643 time to fit residues: 140.1906 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 2.592 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 338 ARG 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 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU 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 139 ASN Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 300 THR 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 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 260 MET 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 417 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 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 56 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24360 Z= 0.261 Angle : 0.583 6.789 32994 Z= 0.302 Chirality : 0.044 0.136 3588 Planarity : 0.004 0.035 4224 Dihedral : 9.647 89.407 3990 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.96 % Allowed : 11.02 % Favored : 86.02 % 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: 0.33 (0.16), residues: 2964 helix: 1.08 (0.14), residues: 1446 sheet: -0.55 (0.26), residues: 408 loop : -0.50 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 281 HIS 0.005 0.001 HIS C 258 PHE 0.017 0.002 PHE D 148 TYR 0.011 0.002 TYR F 493 ARG 0.004 0.001 ARG A 86 *********************** 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 270 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 196 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7511 (tpp) cc_final: 0.7219 (tpp) REVERT: A 238 MET cc_start: 0.5970 (mtm) cc_final: 0.5484 (tpt) REVERT: A 435 GLU cc_start: 0.7450 (pm20) cc_final: 0.7223 (pm20) REVERT: B 111 MET cc_start: 0.8618 (tpp) cc_final: 0.8284 (tpp) REVERT: B 308 LYS cc_start: 0.5146 (pttm) cc_final: 0.4544 (pttm) REVERT: C 66 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7404 (mtt180) REVERT: C 90 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8195 (mtpp) REVERT: C 94 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7877 (ttm-80) REVERT: C 238 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5943 (tpt) REVERT: C 296 LEU cc_start: 0.7798 (mt) cc_final: 0.7495 (pp) REVERT: C 402 GLU cc_start: 0.8045 (tp30) cc_final: 0.7778 (tp30) REVERT: D 233 MET cc_start: 0.7514 (tpp) cc_final: 0.7219 (tpp) REVERT: D 238 MET cc_start: 0.5968 (mtm) cc_final: 0.5486 (tpt) REVERT: D 435 GLU cc_start: 0.7453 (pm20) cc_final: 0.7220 (pm20) REVERT: E 111 MET cc_start: 0.8611 (tpp) cc_final: 0.8278 (tpp) REVERT: E 252 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6478 (t80) REVERT: E 296 LEU cc_start: 0.7964 (mp) cc_final: 0.7663 (pp) REVERT: F 66 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7402 (mtt180) REVERT: F 90 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: F 94 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7889 (ttm-80) REVERT: F 103 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7238 (tp30) REVERT: F 238 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5901 (tpt) REVERT: F 296 LEU cc_start: 0.7735 (mt) cc_final: 0.7477 (pp) REVERT: F 402 GLU cc_start: 0.8043 (tp30) cc_final: 0.7770 (tp30) outliers start: 74 outliers final: 53 residues processed: 252 average time/residue: 0.3658 time to fit residues: 143.9430 Evaluate side-chains 243 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 181 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE 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 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 66 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 338 ARG 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 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE 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 252 PHE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 238 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 293 ASP Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 338 ARG Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 498 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 30.0000 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 283 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24360 Z= 0.146 Angle : 0.513 8.923 32994 Z= 0.262 Chirality : 0.042 0.150 3588 Planarity : 0.004 0.035 4224 Dihedral : 9.222 86.524 3990 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.56 % Allowed : 11.78 % 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: 0.76 (0.16), residues: 2964 helix: 1.50 (0.14), residues: 1458 sheet: -0.48 (0.25), residues: 420 loop : -0.35 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 281 HIS 0.004 0.001 HIS E 258 PHE 0.015 0.001 PHE C 63 TYR 0.007 0.001 TYR F 493 ARG 0.002 0.000 ARG F 211 *********************** 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 265 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 2.620 Fit side-chains REVERT: A 238 MET cc_start: 0.5834 (mtm) cc_final: 0.5358 (tpt) REVERT: A 435 GLU cc_start: 0.7314 (pm20) cc_final: 0.7041 (pm20) REVERT: B 252 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5574 (t80) REVERT: B 308 LYS cc_start: 0.5242 (pttm) cc_final: 0.4624 (pttm) REVERT: C 66 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: C 90 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8164 (mtpp) REVERT: C 94 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7838 (ttm-80) REVERT: C 238 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5807 (tpt) REVERT: C 296 LEU cc_start: 0.7785 (mt) cc_final: 0.7506 (pp) REVERT: C 308 LYS cc_start: 0.5179 (pttm) cc_final: 0.4581 (pttm) REVERT: C 402 GLU cc_start: 0.7970 (tp30) cc_final: 0.7657 (tp30) REVERT: D 238 MET cc_start: 0.5834 (mtm) cc_final: 0.5357 (tpt) REVERT: D 250 GLN cc_start: 0.7646 (tp-100) cc_final: 0.7189 (tt0) REVERT: D 435 GLU cc_start: 0.7317 (pm20) cc_final: 0.7039 (pm20) REVERT: E 252 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.6410 (t80) REVERT: E 296 LEU cc_start: 0.8009 (mp) cc_final: 0.7699 (pp) REVERT: E 308 LYS cc_start: 0.5182 (pttm) cc_final: 0.4586 (pttm) REVERT: F 66 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7294 (mtt180) REVERT: F 90 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8145 (mtpp) REVERT: F 94 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7833 (ttm-80) REVERT: F 296 LEU cc_start: 0.7786 (mt) cc_final: 0.7523 (pp) REVERT: F 308 LYS cc_start: 0.5224 (pttm) cc_final: 0.4680 (pttm) REVERT: F 402 GLU cc_start: 0.7949 (tp30) cc_final: 0.7638 (tp30) outliers start: 64 outliers final: 41 residues processed: 247 average time/residue: 0.3723 time to fit residues: 142.6590 Evaluate side-chains 236 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 2.677 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE 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 252 PHE Chi-restraints excluded: chain B residue 257 LEU 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 C residue 66 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain 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 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 90 LYS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 372 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 0.3980 chunk 26 optimal weight: 40.0000 chunk 222 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- 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 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24360 Z= 0.184 Angle : 0.544 8.316 32994 Z= 0.279 Chirality : 0.043 0.156 3588 Planarity : 0.004 0.034 4224 Dihedral : 9.208 86.153 3990 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.32 % Allowed : 12.38 % Favored : 85.30 % 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: 0.82 (0.16), residues: 2964 helix: 1.55 (0.14), residues: 1458 sheet: -0.42 (0.25), residues: 420 loop : -0.33 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 281 HIS 0.004 0.001 HIS D 391 PHE 0.017 0.002 PHE F 63 TYR 0.008 0.001 TYR F 493 ARG 0.004 0.000 ARG B 462 *********************** 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 247 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.5918 (mtm) cc_final: 0.5548 (tpt) REVERT: A 435 GLU cc_start: 0.7345 (pm20) cc_final: 0.7070 (pm20) REVERT: B 111 MET cc_start: 0.8550 (tpp) cc_final: 0.8227 (tpp) REVERT: B 252 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.5663 (t80) REVERT: B 308 LYS cc_start: 0.5094 (pttm) cc_final: 0.4390 (pttm) REVERT: C 66 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: C 90 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: C 94 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7812 (ttm-80) REVERT: C 238 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5739 (tpt) REVERT: C 296 LEU cc_start: 0.7878 (mt) cc_final: 0.7565 (pp) REVERT: C 308 LYS cc_start: 0.5226 (pttm) cc_final: 0.4641 (pttm) REVERT: C 402 GLU cc_start: 0.7995 (tp30) cc_final: 0.7686 (tp30) REVERT: D 238 MET cc_start: 0.5923 (mtm) cc_final: 0.5551 (tpt) REVERT: D 435 GLU cc_start: 0.7341 (pm20) cc_final: 0.7063 (pm20) REVERT: E 111 MET cc_start: 0.8549 (tpp) cc_final: 0.8224 (tpp) REVERT: E 252 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6463 (t80) REVERT: E 296 LEU cc_start: 0.8009 (mp) cc_final: 0.7708 (pp) REVERT: E 308 LYS cc_start: 0.5010 (pttm) cc_final: 0.4428 (pttm) REVERT: F 66 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7347 (mtt180) REVERT: F 90 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8160 (mtpp) REVERT: F 94 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7826 (ttm-80) REVERT: F 296 LEU cc_start: 0.7902 (mt) cc_final: 0.7637 (pp) REVERT: F 308 LYS cc_start: 0.5226 (pttm) cc_final: 0.4668 (pttm) REVERT: F 402 GLU cc_start: 0.7982 (tp30) cc_final: 0.7681 (tp30) outliers start: 58 outliers final: 45 residues processed: 230 average time/residue: 0.3734 time to fit residues: 133.4873 Evaluate side-chains 241 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 187 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP 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 66 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 372 TYR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain 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 339 VAL Chi-restraints excluded: chain E residue 372 TYR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 66 ARG 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 260 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 294 PHE Chi-restraints excluded: chain F residue 372 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 238 optimal weight: 30.0000 chunk 249 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24360 Z= 0.201 Angle : 0.557 7.944 32994 Z= 0.285 Chirality : 0.043 0.160 3588 Planarity : 0.004 0.033 4224 Dihedral : 9.207 84.405 3990 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.72 % Allowed : 11.98 % Favored : 85.30 % 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: 0.89 (0.16), residues: 2964 helix: 1.56 (0.14), residues: 1464 sheet: -0.37 (0.26), residues: 420 loop : -0.24 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 281 HIS 0.004 0.001 HIS A 391 PHE 0.017 0.002 PHE C 63 TYR 0.009 0.001 TYR C 493 ARG 0.003 0.000 ARG A 86 *********************** 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 255 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 187 time to evaluate : 2.923 Fit side-chains REVERT: A 238 MET cc_start: 0.5795 (mtm) cc_final: 0.5493 (tpt) REVERT: B 111 MET cc_start: 0.8564 (tpp) cc_final: 0.8234 (tpp) REVERT: B 252 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5861 (t80) REVERT: B 308 LYS cc_start: 0.5133 (pttm) cc_final: 0.4430 (pttm) REVERT: C 66 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7370 (mtt180) REVERT: C 90 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8161 (mtpp) REVERT: C 94 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7821 (ttm-80) REVERT: C 238 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5743 (tpt) REVERT: C 296 LEU cc_start: 0.7857 (mt) cc_final: 0.7533 (pp) REVERT: C 308 LYS cc_start: 0.5217 (pttm) cc_final: 0.4630 (pttm) REVERT: C 402 GLU cc_start: 0.8022 (tp30) cc_final: 0.7737 (tp30) REVERT: C 465 MET cc_start: 0.8309 (mtm) cc_final: 0.7956 (mtt) REVERT: D 238 MET cc_start: 0.5801 (mtm) cc_final: 0.5498 (tpt) REVERT: E 111 MET cc_start: 0.8564 (tpp) cc_final: 0.8232 (tpp) REVERT: E 252 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.6486 (t80) REVERT: E 296 LEU cc_start: 0.7961 (mp) cc_final: 0.7686 (pp) REVERT: E 308 LYS cc_start: 0.4970 (pttm) cc_final: 0.4383 (pttm) REVERT: F 66 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7364 (mtt180) REVERT: F 90 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8156 (mtpp) REVERT: F 94 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7823 (ttm-80) REVERT: F 296 LEU cc_start: 0.7918 (mt) cc_final: 0.7607 (pp) REVERT: F 308 LYS cc_start: 0.5223 (pttm) cc_final: 0.4667 (pttm) REVERT: F 338 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6683 (ptp-170) REVERT: F 402 GLU cc_start: 0.8012 (tp30) cc_final: 0.7727 (tp30) REVERT: F 465 MET cc_start: 0.8298 (mtm) cc_final: 0.7952 (mtt) outliers start: 68 outliers final: 53 residues processed: 240 average time/residue: 0.3695 time to fit residues: 137.8104 Evaluate side-chains 246 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 184 time to evaluate : 2.639 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 ARG 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 66 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 372 TYR 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 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ILE 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 66 ARG 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 260 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 294 PHE 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 173 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24360 Z= 0.251 Angle : 0.592 9.677 32994 Z= 0.302 Chirality : 0.044 0.167 3588 Planarity : 0.004 0.035 4224 Dihedral : 9.417 81.694 3990 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.88 % Allowed : 12.06 % Favored : 85.06 % 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: 0.80 (0.16), residues: 2964 helix: 1.48 (0.14), residues: 1464 sheet: -0.45 (0.26), residues: 420 loop : -0.26 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 281 HIS 0.005 0.001 HIS D 258 PHE 0.017 0.002 PHE C 63 TYR 0.011 0.001 TYR C 493 ARG 0.004 0.000 ARG A 86 ********************** 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 261 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 2.484 Fit side-chains REVERT: A 238 MET cc_start: 0.5788 (mtm) cc_final: 0.5569 (tpt) REVERT: B 111 MET cc_start: 0.8562 (tpp) cc_final: 0.8242 (tpp) REVERT: B 228 ASN cc_start: 0.7054 (p0) cc_final: 0.6297 (t0) REVERT: B 252 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.5918 (t80) REVERT: B 308 LYS cc_start: 0.5073 (pttm) cc_final: 0.4356 (pttm) REVERT: C 66 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7427 (mtt180) REVERT: C 90 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8182 (mtpp) REVERT: C 94 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7841 (ttm-80) REVERT: C 238 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5594 (mmt) REVERT: C 296 LEU cc_start: 0.7920 (mt) cc_final: 0.7605 (pp) REVERT: C 308 LYS cc_start: 0.5178 (pttm) cc_final: 0.4592 (pttm) REVERT: C 338 ARG cc_start: 0.7260 (mtp180) cc_final: 0.7054 (mtp180) REVERT: C 402 GLU cc_start: 0.8046 (tp30) cc_final: 0.7777 (tp30) REVERT: C 465 MET cc_start: 0.8331 (mtm) cc_final: 0.7992 (mtt) REVERT: D 238 MET cc_start: 0.5802 (mtm) cc_final: 0.5583 (tpt) REVERT: E 111 MET cc_start: 0.8559 (tpp) cc_final: 0.8240 (tpp) REVERT: E 228 ASN cc_start: 0.7128 (p0) cc_final: 0.6525 (t0) REVERT: E 252 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6434 (t80) REVERT: E 296 LEU cc_start: 0.7908 (mp) cc_final: 0.7673 (pp) REVERT: E 308 LYS cc_start: 0.4971 (pttm) cc_final: 0.4381 (pttm) REVERT: F 66 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7415 (mtt180) REVERT: F 90 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: F 94 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7859 (ttm-80) REVERT: F 296 LEU cc_start: 0.7963 (mt) cc_final: 0.7656 (pp) REVERT: F 308 LYS cc_start: 0.5196 (pttm) cc_final: 0.4465 (pttm) REVERT: F 402 GLU cc_start: 0.8038 (tp30) cc_final: 0.7770 (tp30) REVERT: F 465 MET cc_start: 0.8309 (mtm) cc_final: 0.7971 (mtt) outliers start: 72 outliers final: 58 residues processed: 245 average time/residue: 0.3641 time to fit residues: 139.1798 Evaluate side-chains 256 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 189 time to evaluate : 2.444 ------------------------------------------------------------------------------- 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 291 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 372 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 63 PHE Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 338 ARG 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 66 ARG Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 94 ARG Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 372 TYR 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 252 PHE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 372 TYR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 63 PHE Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 252 PHE Chi-restraints excluded: chain E residue 293 ASP 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 66 ARG 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 260 MET Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 294 PHE 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 185 optimal weight: 4.9990 chunk 248 optimal weight: 0.0270 chunk 71 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 ASN ** C 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 = 0.3642 r_free = 0.3642 target = 0.096351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070668 restraints weight = 57839.608| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.77 r_work: 0.2958 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24360 Z= 0.156 Angle : 0.530 9.544 32994 Z= 0.269 Chirality : 0.042 0.172 3588 Planarity : 0.004 0.043 4224 Dihedral : 9.076 77.772 3990 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 12.86 % Favored : 84.74 % 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: 1.10 (0.16), residues: 2964 helix: 1.72 (0.14), residues: 1464 sheet: -0.49 (0.27), residues: 384 loop : -0.06 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.004 0.001 HIS E 258 PHE 0.018 0.001 PHE F 63 TYR 0.007 0.001 TYR F 493 ARG 0.002 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4882.05 seconds wall clock time: 88 minutes 32.29 seconds (5312.29 seconds total)