Starting phenix.real_space_refine on Tue Dec 31 05:12:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnm_27574/12_2024/8dnm_27574.cif" } resolution = 2.76 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= 0.000 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9368 2.51 5 N 2556 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14880 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "B" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "C" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Chain: "D" Number of atoms: 3720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3720 Classifications: {'peptide': 483} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 460} Time building chain proxies: 9.04, per 1000 atoms: 0.61 Number of scatterers: 14880 At special positions: 0 Unit cell: (129.47, 90.95, 99.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2884 8.00 N 2556 7.00 C 9368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 2.1 seconds 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 16 sheets defined 43.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 Processing helix chain 'A' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN A 149 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS A 289 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.615A pdb=" N PHE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 376 through 385 Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 131 Processing helix chain 'B' and resid 145 through 159 removed outlier: 4.085A pdb=" N GLN B 149 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 Processing helix chain 'B' and resid 279 through 285 Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS B 289 " --> pdb=" O ASP B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 3.615A pdb=" N PHE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 392 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 131 Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN C 149 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 219 through 227 removed outlier: 4.031A pdb=" N HIS C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 247 removed outlier: 4.263A pdb=" N GLU C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS C 289 " --> pdb=" O ASP C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 301 removed outlier: 3.616A pdb=" N PHE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 360 through 370 Processing helix chain 'C' and resid 376 through 385 Processing helix chain 'C' and resid 385 through 392 Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.619A pdb=" N LYS C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ARG C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.556A pdb=" N THR D 93 " --> pdb=" O PHE D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 145 through 159 removed outlier: 4.083A pdb=" N GLN D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU D 150 " --> pdb=" O LYS D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 219 through 227 removed outlier: 4.030A pdb=" N HIS D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 247 removed outlier: 4.262A pdb=" N GLU D 232 " --> pdb=" O PRO D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 270 Processing helix chain 'D' and resid 279 through 285 Processing helix chain 'D' and resid 286 through 292 removed outlier: 4.152A pdb=" N HIS D 289 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 301 removed outlier: 3.616A pdb=" N PHE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 385 through 392 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.618A pdb=" N LYS D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE D 482 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR A 36 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 45 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 34 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR A 36 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 45 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 34 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N PHE A 31 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 23 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 33 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 65 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 23 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL A 25 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 64 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 409 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL A 446 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 411 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP A 415 " --> pdb=" O ARG A 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG A 440 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 417 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU A 438 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU A 444 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 455 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 446 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.841A pdb=" N GLY A 69 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE A 104 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP A 71 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP A 106 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N HIS A 73 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL A 108 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 102 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER A 136 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 104 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS A 138 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP A 106 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP A 140 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 108 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER A 163 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR A 167 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE A 164 " --> pdb=" O GLN A 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS A 198 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 166 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 195 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 253 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 197 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 255 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 275 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N THR A 253 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A 277 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR B 36 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 45 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 34 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR B 36 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 45 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 34 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE B 31 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS B 23 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 33 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL B 65 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS B 23 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N VAL B 25 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET B 64 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 409 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL B 446 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 411 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP B 415 " --> pdb=" O ARG B 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG B 440 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL B 417 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU B 438 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N LEU B 444 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 455 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 446 " --> pdb=" O VAL B 453 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.841A pdb=" N GLY B 69 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE B 104 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 71 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP B 106 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS B 73 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL B 108 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR B 102 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N SER B 136 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE B 104 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS B 138 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 106 " --> pdb=" O HIS B 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP B 140 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 108 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER B 163 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR B 167 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE B 164 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS B 198 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL B 166 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA B 195 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR B 253 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 197 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL B 255 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 275 " --> pdb=" O TYR B 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR B 253 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B 277 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR C 36 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 45 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 34 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 46 removed outlier: 6.671A pdb=" N TYR C 36 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 45 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 34 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE C 31 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS C 23 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 33 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY C 21 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL C 65 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS C 23 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL C 25 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 64 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 409 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 446 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 411 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP C 415 " --> pdb=" O ARG C 440 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ARG C 440 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 417 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N GLU C 438 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU C 444 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU C 455 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 446 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 74 removed outlier: 6.842A pdb=" N GLY C 69 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 104 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP C 71 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP C 106 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS C 73 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N VAL C 108 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR C 102 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER C 136 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 104 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS C 138 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP C 106 " --> pdb=" O HIS C 138 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASP C 140 " --> pdb=" O ASP C 106 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 108 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER C 163 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR C 167 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE C 164 " --> pdb=" O GLN C 196 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N HIS C 198 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL C 166 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 195 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 253 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 197 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL C 255 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR C 275 " --> pdb=" O TYR C 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR C 253 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU C 277 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AB4, first strand: chain 'D' and resid 41 through 46 removed outlier: 6.672A pdb=" N TYR D 36 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 45 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP D 34 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 41 through 46 removed outlier: 6.672A pdb=" N TYR D 36 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 45 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP D 34 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N PHE D 31 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS D 23 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 33 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 21 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL D 65 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS D 23 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL D 25 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 64 " --> pdb=" O TRP D 412 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU D 409 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL D 446 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 411 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASP D 415 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG D 440 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 417 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N GLU D 438 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N LEU D 444 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D 455 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL D 446 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 69 through 74 removed outlier: 6.842A pdb=" N GLY D 69 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE D 104 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP D 71 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP D 106 " --> pdb=" O ASP D 71 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS D 73 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 10.627A pdb=" N VAL D 108 " --> pdb=" O HIS D 73 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR D 102 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER D 136 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE D 104 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS D 138 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP D 106 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP D 140 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 108 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER D 163 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR D 167 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE D 164 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS D 198 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 166 " --> pdb=" O HIS D 198 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA D 195 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 253 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 197 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 255 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR D 275 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR D 253 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU D 277 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 80 648 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2584 1.31 - 1.43: 3729 1.43 - 1.55: 8736 1.55 - 1.68: 19 1.68 - 1.80: 116 Bond restraints: 15184 Sorted by residual: bond pdb=" C VAL A 494 " pdb=" N PRO A 495 " ideal model delta sigma weight residual 1.333 1.364 -0.030 1.01e-02 9.80e+03 9.07e+00 bond pdb=" C VAL C 494 " pdb=" N PRO C 495 " ideal model delta sigma weight residual 1.333 1.364 -0.030 1.01e-02 9.80e+03 8.86e+00 bond pdb=" C VAL B 494 " pdb=" N PRO B 495 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.01e-02 9.80e+03 8.58e+00 bond pdb=" C VAL D 494 " pdb=" N PRO D 495 " ideal model delta sigma weight residual 1.333 1.363 -0.029 1.01e-02 9.80e+03 8.37e+00 bond pdb=" CA VAL B 494 " pdb=" C VAL B 494 " ideal model delta sigma weight residual 1.524 1.553 -0.029 1.05e-02 9.07e+03 7.39e+00 ... (remaining 15179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 19949 2.15 - 4.29: 565 4.29 - 6.44: 74 6.44 - 8.58: 8 8.58 - 10.73: 4 Bond angle restraints: 20600 Sorted by residual: angle pdb=" N LEU A 488 " pdb=" CA LEU A 488 " pdb=" C LEU A 488 " ideal model delta sigma weight residual 111.82 117.04 -5.22 1.16e+00 7.43e-01 2.02e+01 angle pdb=" N LEU B 488 " pdb=" CA LEU B 488 " pdb=" C LEU B 488 " ideal model delta sigma weight residual 111.82 117.01 -5.19 1.16e+00 7.43e-01 2.01e+01 angle pdb=" N LEU D 488 " pdb=" CA LEU D 488 " pdb=" C LEU D 488 " ideal model delta sigma weight residual 111.82 117.01 -5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" N LEU C 488 " pdb=" CA LEU C 488 " pdb=" C LEU C 488 " ideal model delta sigma weight residual 111.82 116.98 -5.16 1.16e+00 7.43e-01 1.98e+01 angle pdb=" N GLU C 229 " pdb=" CA GLU C 229 " pdb=" C GLU C 229 " ideal model delta sigma weight residual 112.23 106.63 5.60 1.26e+00 6.30e-01 1.98e+01 ... (remaining 20595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 8396 17.55 - 35.11: 580 35.11 - 52.66: 99 52.66 - 70.21: 29 70.21 - 87.77: 12 Dihedral angle restraints: 9116 sinusoidal: 3588 harmonic: 5528 Sorted by residual: dihedral pdb=" C VAL C 224 " pdb=" N VAL C 224 " pdb=" CA VAL C 224 " pdb=" CB VAL C 224 " ideal model delta harmonic sigma weight residual -122.00 -134.71 12.71 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" C VAL B 224 " pdb=" N VAL B 224 " pdb=" CA VAL B 224 " pdb=" CB VAL B 224 " ideal model delta harmonic sigma weight residual -122.00 -134.68 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" C VAL A 224 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" CB VAL A 224 " ideal model delta harmonic sigma weight residual -122.00 -134.66 12.66 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 9113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1932 0.066 - 0.133: 331 0.133 - 0.199: 45 0.199 - 0.265: 12 0.265 - 0.332: 4 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA VAL B 224 " pdb=" N VAL B 224 " pdb=" C VAL B 224 " pdb=" CB VAL B 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA VAL C 224 " pdb=" N VAL C 224 " pdb=" C VAL C 224 " pdb=" CB VAL C 224 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 2321 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 227 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO C 228 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 227 " 0.062 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO D 228 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO D 228 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 228 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 227 " -0.061 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 228 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.051 5.00e-02 4.00e+02 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2190 2.75 - 3.29: 15410 3.29 - 3.83: 27094 3.83 - 4.36: 34524 4.36 - 4.90: 55753 Nonbonded interactions: 134971 Sorted by model distance: nonbonded pdb=" NZ LYS D 258 " pdb=" OG1 THR D 312 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS A 258 " pdb=" OG1 THR A 312 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS C 258 " pdb=" OG1 THR C 312 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS B 258 " pdb=" OG1 THR B 312 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR C 419 " pdb=" OE1 GLU C 438 " model vdw 2.273 3.040 ... (remaining 134966 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' } 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: 1.370 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: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.440 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.006 0.048 15184 Z= 0.381 Angle : 0.853 10.729 20600 Z= 0.522 Chirality : 0.053 0.332 2324 Planarity : 0.007 0.094 2684 Dihedral : 12.930 87.767 5564 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.86 % Allowed : 1.23 % Favored : 97.90 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 9.09 % 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: -1.12 (0.18), residues: 1924 helix: 0.66 (0.19), residues: 748 sheet: -2.12 (0.27), residues: 304 loop : -1.42 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 412 HIS 0.008 0.002 HIS A 425 PHE 0.009 0.001 PHE C 380 TYR 0.015 0.002 TYR B 275 ARG 0.007 0.001 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 1.571 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 210 average time/residue: 1.8251 time to fit residues: 412.0537 Evaluate side-chains 86 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15184 Z= 0.220 Angle : 0.530 4.944 20600 Z= 0.285 Chirality : 0.043 0.127 2324 Planarity : 0.005 0.053 2684 Dihedral : 4.394 20.660 2060 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.93 % Allowed : 8.15 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.44 (0.19), residues: 1924 helix: 1.16 (0.19), residues: 764 sheet: -1.51 (0.27), residues: 344 loop : -1.08 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.006 0.001 HIS D 145 PHE 0.015 0.001 PHE A 316 TYR 0.012 0.001 TYR C 290 ARG 0.008 0.001 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.775 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 132 average time/residue: 1.7761 time to fit residues: 254.9240 Evaluate side-chains 88 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN B 379 GLN C 379 GLN D 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15184 Z= 0.282 Angle : 0.526 5.088 20600 Z= 0.279 Chirality : 0.043 0.129 2324 Planarity : 0.004 0.034 2684 Dihedral : 4.229 20.653 2060 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.99 % Allowed : 10.19 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.16 (0.19), residues: 1924 helix: 1.33 (0.19), residues: 764 sheet: -1.44 (0.29), residues: 312 loop : -0.84 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.006 0.001 HIS B 425 PHE 0.011 0.001 PHE C 316 TYR 0.010 0.002 TYR A 251 ARG 0.004 0.001 ARG D 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.728 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 116 average time/residue: 1.7865 time to fit residues: 225.1991 Evaluate side-chains 92 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 289 HIS C 289 HIS D 289 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15184 Z= 0.178 Angle : 0.473 4.893 20600 Z= 0.251 Chirality : 0.041 0.120 2324 Planarity : 0.004 0.030 2684 Dihedral : 4.010 20.427 2060 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.17 % Allowed : 10.49 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.36 (0.19), residues: 1924 helix: 1.58 (0.19), residues: 764 sheet: -0.65 (0.31), residues: 268 loop : -0.62 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS D 425 PHE 0.009 0.001 PHE C 316 TYR 0.006 0.001 TYR A 251 ARG 0.003 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.733 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 105 average time/residue: 1.6830 time to fit residues: 192.1898 Evaluate side-chains 88 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15184 Z= 0.208 Angle : 0.488 7.192 20600 Z= 0.255 Chirality : 0.042 0.122 2324 Planarity : 0.004 0.028 2684 Dihedral : 3.960 20.084 2060 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.93 % Allowed : 11.79 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.40 (0.19), residues: 1924 helix: 1.64 (0.19), residues: 768 sheet: -0.94 (0.34), residues: 228 loop : -0.54 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS B 425 PHE 0.007 0.001 PHE B 380 TYR 0.008 0.001 TYR B 251 ARG 0.007 0.001 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.687 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 99 average time/residue: 1.5562 time to fit residues: 169.1313 Evaluate side-chains 85 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 365 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.0570 chunk 167 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15184 Z= 0.162 Angle : 0.466 5.754 20600 Z= 0.244 Chirality : 0.041 0.119 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.854 19.740 2060 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.80 % Allowed : 11.73 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.48 (0.19), residues: 1924 helix: 1.73 (0.19), residues: 768 sheet: -0.88 (0.32), residues: 248 loop : -0.52 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.004 0.001 HIS B 425 PHE 0.007 0.001 PHE C 316 TYR 0.007 0.001 TYR C 251 ARG 0.006 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.763 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 1.4402 time to fit residues: 154.1230 Evaluate side-chains 91 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 15184 Z= 0.352 Angle : 0.529 5.564 20600 Z= 0.279 Chirality : 0.043 0.124 2324 Planarity : 0.004 0.043 2684 Dihedral : 4.073 20.606 2060 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.56 % Allowed : 12.10 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.52 (0.19), residues: 1924 helix: 1.65 (0.19), residues: 764 sheet: -0.85 (0.34), residues: 228 loop : -0.40 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.008 0.001 HIS D 425 PHE 0.009 0.001 PHE B 392 TYR 0.012 0.002 TYR C 251 ARG 0.006 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.711 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 1.5871 time to fit residues: 165.9371 Evaluate side-chains 95 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15184 Z= 0.209 Angle : 0.497 5.396 20600 Z= 0.260 Chirality : 0.042 0.119 2324 Planarity : 0.003 0.053 2684 Dihedral : 3.961 20.605 2060 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.23 % Allowed : 11.73 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.67 (0.19), residues: 1924 helix: 1.72 (0.19), residues: 764 sheet: -0.66 (0.35), residues: 228 loop : -0.29 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS C 425 PHE 0.007 0.001 PHE D 380 TYR 0.007 0.001 TYR B 251 ARG 0.005 0.000 ARG B 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.796 Fit side-chains outliers start: 20 outliers final: 4 residues processed: 107 average time/residue: 1.4561 time to fit residues: 172.6155 Evaluate side-chains 88 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15184 Z= 0.226 Angle : 0.497 5.589 20600 Z= 0.261 Chirality : 0.042 0.120 2324 Planarity : 0.003 0.051 2684 Dihedral : 3.930 20.419 2060 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.56 % Allowed : 12.41 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.63 (0.19), residues: 1924 helix: 1.73 (0.19), residues: 764 sheet: -0.51 (0.34), residues: 248 loop : -0.39 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 295 HIS 0.007 0.001 HIS C 425 PHE 0.007 0.001 PHE D 380 TYR 0.008 0.001 TYR A 251 ARG 0.006 0.000 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.741 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 93 average time/residue: 1.5367 time to fit residues: 157.2003 Evaluate side-chains 90 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15184 Z= 0.209 Angle : 0.497 5.778 20600 Z= 0.261 Chirality : 0.042 0.120 2324 Planarity : 0.003 0.051 2684 Dihedral : 3.901 20.430 2060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.37 % Allowed : 12.72 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.65 (0.19), residues: 1924 helix: 1.70 (0.19), residues: 768 sheet: -0.48 (0.35), residues: 248 loop : -0.35 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 295 HIS 0.006 0.001 HIS C 425 PHE 0.007 0.001 PHE D 380 TYR 0.007 0.001 TYR C 251 ARG 0.007 0.000 ARG B 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.734 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 93 average time/residue: 1.4761 time to fit residues: 151.1298 Evaluate side-chains 88 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.0870 chunk 152 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.063974 restraints weight = 28647.200| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.75 r_work: 0.2783 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15184 Z= 0.180 Angle : 0.482 6.046 20600 Z= 0.254 Chirality : 0.041 0.121 2324 Planarity : 0.003 0.050 2684 Dihedral : 3.847 20.216 2060 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.49 % Allowed : 12.90 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.71 (0.19), residues: 1924 helix: 1.73 (0.19), residues: 768 sheet: -0.43 (0.35), residues: 248 loop : -0.30 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.006 0.001 HIS C 425 PHE 0.007 0.001 PHE D 380 TYR 0.006 0.001 TYR A 251 ARG 0.007 0.000 ARG C 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.60 seconds wall clock time: 74 minutes 0.06 seconds (4440.06 seconds total)