Starting phenix.real_space_refine on Fri Jun 13 09:37:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnm_27574/06_2025/8dnm_27574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnm_27574/06_2025/8dnm_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_27574/06_2025/8dnm_27574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnm_27574/06_2025/8dnm_27574.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnm_27574/06_2025/8dnm_27574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnm_27574/06_2025/8dnm_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.34, per 1000 atoms: 0.63 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: 3.88 Conformation dependent library (CDL) restraints added in 2.0 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: 2.20 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: 5.74 Time building geometry restraints manager: 4.60 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 38.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:15.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- 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= 0.316 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 Details of bonding type rmsd hydrogen bonds : bond 0.19158 ( 620) hydrogen bonds : angle 6.80696 ( 1800) covalent geometry : bond 0.00571 (15184) covalent geometry : angle 0.85312 (20600) *********************** 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 : 1.603 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 210 average time/residue: 1.7222 time to fit residues: 389.4248 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 : 1.587 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.066774 restraints weight = 27768.188| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.71 r_work: 0.2769 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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= 0.149 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 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 620) hydrogen bonds : angle 4.70271 ( 1800) covalent geometry : bond 0.00334 (15184) covalent geometry : angle 0.53016 (20600) *********************** 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 : 3.368 Fit side-chains REVERT: A 78 MET cc_start: 0.9100 (ttt) cc_final: 0.8703 (ptm) REVERT: A 168 MET cc_start: 0.9043 (mmm) cc_final: 0.8780 (mtm) REVERT: A 262 GLU cc_start: 0.8913 (tp30) cc_final: 0.8588 (tp30) REVERT: A 266 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8322 (mp10) REVERT: A 375 MET cc_start: 0.9139 (ptp) cc_final: 0.8921 (ptp) REVERT: B 78 MET cc_start: 0.9099 (ttt) cc_final: 0.8703 (ptm) REVERT: B 262 GLU cc_start: 0.8908 (tp30) cc_final: 0.8596 (tp30) REVERT: B 266 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8300 (mp10) REVERT: B 375 MET cc_start: 0.9138 (ptp) cc_final: 0.8922 (ptp) REVERT: C 78 MET cc_start: 0.9119 (ttt) cc_final: 0.8730 (ptm) REVERT: C 262 GLU cc_start: 0.8910 (tp30) cc_final: 0.8599 (tp30) REVERT: C 266 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8295 (mp10) REVERT: C 375 MET cc_start: 0.9141 (ptp) cc_final: 0.8923 (ptp) REVERT: D 78 MET cc_start: 0.9095 (ttt) cc_final: 0.8705 (ptm) REVERT: D 262 GLU cc_start: 0.8908 (tp30) cc_final: 0.8595 (tp30) REVERT: D 266 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8297 (mp10) REVERT: D 375 MET cc_start: 0.9143 (ptp) cc_final: 0.8925 (ptp) outliers start: 15 outliers final: 0 residues processed: 132 average time/residue: 2.0685 time to fit residues: 299.8508 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 : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.061225 restraints weight = 28585.781| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.73 r_work: 0.2756 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15184 Z= 0.164 Angle : 0.508 5.241 20600 Z= 0.268 Chirality : 0.043 0.130 2324 Planarity : 0.004 0.034 2684 Dihedral : 4.173 20.404 2060 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.93 % Allowed : 10.25 % 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: -0.09 (0.19), residues: 1924 helix: 1.37 (0.19), residues: 764 sheet: -1.40 (0.29), residues: 312 loop : -0.79 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.005 0.001 HIS B 425 PHE 0.010 0.001 PHE C 316 TYR 0.009 0.001 TYR B 251 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 620) hydrogen bonds : angle 4.37911 ( 1800) covalent geometry : bond 0.00381 (15184) covalent geometry : angle 0.50776 (20600) *********************** 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 119 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.948 Fit side-chains REVERT: A 78 MET cc_start: 0.9110 (ttt) cc_final: 0.8773 (ptm) REVERT: A 190 ASP cc_start: 0.9027 (m-30) cc_final: 0.8765 (m-30) REVERT: A 266 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8263 (mp10) REVERT: B 78 MET cc_start: 0.9147 (ttt) cc_final: 0.8775 (ptm) REVERT: B 190 ASP cc_start: 0.9025 (m-30) cc_final: 0.8744 (m-30) REVERT: B 266 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8263 (mp10) REVERT: C 78 MET cc_start: 0.9106 (ttt) cc_final: 0.8742 (ptm) REVERT: C 190 ASP cc_start: 0.9033 (m-30) cc_final: 0.8771 (m-30) REVERT: C 266 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8250 (mp10) REVERT: D 78 MET cc_start: 0.9106 (ttt) cc_final: 0.8768 (ptm) REVERT: D 190 ASP cc_start: 0.9027 (m-30) cc_final: 0.8764 (m-30) REVERT: D 266 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8259 (mp10) outliers start: 15 outliers final: 0 residues processed: 116 average time/residue: 2.0130 time to fit residues: 255.3559 Evaluate side-chains 90 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.063633 restraints weight = 28239.005| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.80 r_work: 0.2700 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15184 Z= 0.163 Angle : 0.492 5.031 20600 Z= 0.261 Chirality : 0.042 0.122 2324 Planarity : 0.004 0.031 2684 Dihedral : 4.069 20.524 2060 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.36 % Allowed : 10.19 % Favored : 88.46 % 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: 0.17 (0.19), residues: 1924 helix: 1.57 (0.19), residues: 764 sheet: -1.06 (0.33), residues: 248 loop : -0.78 (0.19), residues: 912 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 0.008 0.001 PHE C 316 TYR 0.009 0.001 TYR B 251 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 620) hydrogen bonds : angle 4.28561 ( 1800) covalent geometry : bond 0.00380 (15184) covalent geometry : angle 0.49192 (20600) *********************** 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 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.625 Fit side-chains REVERT: A 78 MET cc_start: 0.8979 (ttt) cc_final: 0.8654 (ttp) REVERT: A 190 ASP cc_start: 0.8945 (m-30) cc_final: 0.8661 (m-30) REVERT: A 266 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8243 (mp10) REVERT: A 423 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9094 (mtpp) REVERT: A 440 ARG cc_start: 0.8647 (mtp-110) cc_final: 0.8287 (mtp85) REVERT: B 78 MET cc_start: 0.8994 (ttt) cc_final: 0.8675 (ttp) REVERT: B 190 ASP cc_start: 0.8945 (m-30) cc_final: 0.8656 (m-30) REVERT: B 266 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8235 (mp10) REVERT: B 423 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9100 (mtpp) REVERT: B 440 ARG cc_start: 0.8645 (mtp-110) cc_final: 0.8286 (mtp85) REVERT: C 78 MET cc_start: 0.8978 (ttt) cc_final: 0.8651 (ttp) REVERT: C 190 ASP cc_start: 0.8949 (m-30) cc_final: 0.8663 (m-30) REVERT: C 266 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8217 (mp10) REVERT: C 423 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9101 (mtpp) REVERT: C 440 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8267 (mtp85) REVERT: D 78 MET cc_start: 0.8984 (ttt) cc_final: 0.8659 (ttp) REVERT: D 190 ASP cc_start: 0.8951 (m-30) cc_final: 0.8667 (m-30) REVERT: D 266 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8238 (mp10) REVERT: D 423 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9104 (mtpp) REVERT: D 440 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8292 (mtp85) outliers start: 22 outliers final: 4 residues processed: 101 average time/residue: 2.0314 time to fit residues: 221.6225 Evaluate side-chains 101 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 423 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.075844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.063985 restraints weight = 28544.448| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.84 r_work: 0.2682 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15184 Z= 0.146 Angle : 0.473 4.989 20600 Z= 0.250 Chirality : 0.042 0.122 2324 Planarity : 0.003 0.029 2684 Dihedral : 3.979 20.309 2060 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.62 % Allowed : 11.48 % Favored : 87.90 % 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: 1.62 (0.19), residues: 768 sheet: -1.03 (0.34), residues: 228 loop : -0.50 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.006 0.001 HIS D 425 PHE 0.007 0.001 PHE C 380 TYR 0.009 0.001 TYR B 251 ARG 0.007 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 620) hydrogen bonds : angle 4.20052 ( 1800) covalent geometry : bond 0.00341 (15184) covalent geometry : angle 0.47262 (20600) *********************** 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 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.706 Fit side-chains REVERT: A 146 LYS cc_start: 0.9060 (pptt) cc_final: 0.8825 (pmtt) REVERT: A 190 ASP cc_start: 0.8874 (m-30) cc_final: 0.8600 (m-30) REVERT: A 266 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8263 (mp10) REVERT: A 423 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9092 (mtmm) REVERT: A 440 ARG cc_start: 0.8609 (mtp-110) cc_final: 0.8329 (mtp85) REVERT: B 146 LYS cc_start: 0.9059 (pptt) cc_final: 0.8835 (pmtt) REVERT: B 190 ASP cc_start: 0.8909 (m-30) cc_final: 0.8618 (m-30) REVERT: B 266 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8306 (mp10) REVERT: B 423 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9094 (mtmm) REVERT: B 440 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8318 (mtp85) REVERT: C 146 LYS cc_start: 0.9064 (pptt) cc_final: 0.8830 (pmtt) REVERT: C 190 ASP cc_start: 0.8918 (m-30) cc_final: 0.8632 (m-30) REVERT: C 266 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8264 (mp10) REVERT: C 423 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9095 (mtmm) REVERT: C 440 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8311 (mtp85) REVERT: D 146 LYS cc_start: 0.9064 (pptt) cc_final: 0.8849 (pmtt) REVERT: D 190 ASP cc_start: 0.8922 (m-30) cc_final: 0.8635 (m-30) REVERT: D 266 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8288 (mp10) REVERT: D 423 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9092 (mtmm) REVERT: D 440 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8325 (mtp85) outliers start: 10 outliers final: 8 residues processed: 109 average time/residue: 1.6737 time to fit residues: 199.2496 Evaluate side-chains 94 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 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 121 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3030 r_free = 0.3030 target = 0.073196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.061227 restraints weight = 29057.503| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.88 r_work: 0.2623 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 15184 Z= 0.254 Angle : 0.544 7.622 20600 Z= 0.285 Chirality : 0.044 0.131 2324 Planarity : 0.004 0.029 2684 Dihedral : 4.144 20.662 2060 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.11 % Allowed : 11.11 % Favored : 87.78 % 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: 1.62 (0.19), residues: 764 sheet: -1.18 (0.35), residues: 212 loop : -0.52 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 295 HIS 0.008 0.002 HIS D 425 PHE 0.009 0.001 PHE B 392 TYR 0.013 0.002 TYR B 251 ARG 0.006 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 620) hydrogen bonds : angle 4.33119 ( 1800) covalent geometry : bond 0.00593 (15184) covalent geometry : angle 0.54351 (20600) *********************** 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 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.819 Fit side-chains REVERT: A 78 MET cc_start: 0.8943 (ttt) cc_final: 0.8616 (ptm) REVERT: A 146 LYS cc_start: 0.9046 (pptt) cc_final: 0.8835 (pmtt) REVERT: A 190 ASP cc_start: 0.8940 (m-30) cc_final: 0.8688 (m-30) REVERT: A 266 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8311 (mp10) REVERT: A 423 LYS cc_start: 0.9440 (mtpt) cc_final: 0.9074 (mtmm) REVERT: A 440 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8325 (mtp85) REVERT: B 78 MET cc_start: 0.8998 (ttt) cc_final: 0.8680 (ptm) REVERT: B 146 LYS cc_start: 0.9073 (pptt) cc_final: 0.8840 (pmtt) REVERT: B 190 ASP cc_start: 0.8934 (m-30) cc_final: 0.8663 (m-30) REVERT: B 266 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8312 (mp10) REVERT: B 423 LYS cc_start: 0.9440 (mtpt) cc_final: 0.9075 (mtmm) REVERT: B 440 ARG cc_start: 0.8613 (mtp-110) cc_final: 0.8316 (mtp85) REVERT: C 78 MET cc_start: 0.8944 (ttt) cc_final: 0.8619 (ptm) REVERT: C 146 LYS cc_start: 0.9049 (pptt) cc_final: 0.8838 (pmtt) REVERT: C 190 ASP cc_start: 0.8950 (m-30) cc_final: 0.8683 (m-30) REVERT: C 266 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8311 (mp10) REVERT: C 423 LYS cc_start: 0.9448 (mtpt) cc_final: 0.9085 (mtmm) REVERT: C 440 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8290 (mtp85) REVERT: D 78 MET cc_start: 0.8985 (ttt) cc_final: 0.8666 (ptm) REVERT: D 146 LYS cc_start: 0.9056 (pptt) cc_final: 0.8844 (pmtt) REVERT: D 190 ASP cc_start: 0.8940 (m-30) cc_final: 0.8676 (m-30) REVERT: D 266 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8307 (mp10) REVERT: D 423 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9072 (mtmm) REVERT: D 440 ARG cc_start: 0.8611 (mtp-110) cc_final: 0.8318 (mtp85) outliers start: 18 outliers final: 7 residues processed: 110 average time/residue: 1.5822 time to fit residues: 190.1455 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 109 VAL 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 285 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 188 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3080 r_free = 0.3080 target = 0.075616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.063844 restraints weight = 28635.119| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.84 r_work: 0.2691 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15184 Z= 0.122 Angle : 0.473 6.325 20600 Z= 0.248 Chirality : 0.042 0.122 2324 Planarity : 0.003 0.028 2684 Dihedral : 3.964 20.608 2060 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.62 % Allowed : 11.67 % Favored : 87.72 % 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: 0.51 (0.19), residues: 1924 helix: 1.71 (0.19), residues: 768 sheet: -0.98 (0.34), residues: 232 loop : -0.43 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 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 0.006 0.000 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 620) hydrogen bonds : angle 4.18300 ( 1800) covalent geometry : bond 0.00284 (15184) covalent geometry : angle 0.47334 (20600) *********************** 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 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 1.756 Fit side-chains REVERT: A 78 MET cc_start: 0.9003 (ttt) cc_final: 0.8673 (ptm) REVERT: A 146 LYS cc_start: 0.9027 (pptt) cc_final: 0.8811 (pmtt) REVERT: A 190 ASP cc_start: 0.8880 (m-30) cc_final: 0.8602 (m-30) REVERT: A 266 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8255 (mp10) REVERT: A 423 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9097 (mtmm) REVERT: A 440 ARG cc_start: 0.8597 (mtp-110) cc_final: 0.8294 (mtp85) REVERT: B 78 MET cc_start: 0.8986 (ttt) cc_final: 0.8674 (ptm) REVERT: B 83 MET cc_start: 0.8471 (mtm) cc_final: 0.8034 (ptp) REVERT: B 146 LYS cc_start: 0.9030 (pptt) cc_final: 0.8811 (pmtt) REVERT: B 190 ASP cc_start: 0.8884 (m-30) cc_final: 0.8596 (m-30) REVERT: B 266 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8306 (mp10) REVERT: B 423 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9096 (mtmm) REVERT: B 440 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8289 (mtp85) REVERT: C 78 MET cc_start: 0.8981 (ttt) cc_final: 0.8660 (ptm) REVERT: C 190 ASP cc_start: 0.8891 (m-30) cc_final: 0.8611 (m-30) REVERT: C 266 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8274 (mp10) REVERT: C 423 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9097 (mtmm) REVERT: C 440 ARG cc_start: 0.8556 (mtp-110) cc_final: 0.8248 (mtp85) REVERT: D 78 MET cc_start: 0.8987 (ttt) cc_final: 0.8676 (ptm) REVERT: D 83 MET cc_start: 0.8451 (mtm) cc_final: 0.8007 (ptp) REVERT: D 146 LYS cc_start: 0.9025 (pptt) cc_final: 0.8810 (pmtt) REVERT: D 190 ASP cc_start: 0.8893 (m-30) cc_final: 0.8633 (m-30) REVERT: D 266 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8282 (mp10) REVERT: D 423 LYS cc_start: 0.9456 (mtpt) cc_final: 0.9094 (mtmm) REVERT: D 440 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8291 (mtp85) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 1.6390 time to fit residues: 191.2478 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 365 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 0.7980 chunk 170 optimal weight: 0.0870 chunk 174 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.076334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064375 restraints weight = 28499.481| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.89 r_work: 0.2723 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3564 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= 0.107 Angle : 0.472 5.895 20600 Z= 0.247 Chirality : 0.041 0.121 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.855 19.977 2060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.62 % Allowed : 11.79 % Favored : 87.59 % 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: 1.78 (0.19), residues: 768 sheet: -0.67 (0.33), residues: 248 loop : -0.36 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.005 0.001 HIS B 425 PHE 0.007 0.001 PHE C 380 TYR 0.006 0.001 TYR B 251 ARG 0.006 0.000 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 620) hydrogen bonds : angle 4.13283 ( 1800) covalent geometry : bond 0.00251 (15184) covalent geometry : angle 0.47184 (20600) *********************** 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 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.569 Fit side-chains REVERT: A 78 MET cc_start: 0.9056 (ttt) cc_final: 0.8767 (ptm) REVERT: A 146 LYS cc_start: 0.9017 (pptt) cc_final: 0.8809 (pmtt) REVERT: A 190 ASP cc_start: 0.8907 (m-30) cc_final: 0.8622 (m-30) REVERT: A 266 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8337 (mp10) REVERT: A 423 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9101 (mtmm) REVERT: A 440 ARG cc_start: 0.8611 (mtp-110) cc_final: 0.8304 (mtp85) REVERT: B 78 MET cc_start: 0.9050 (ttt) cc_final: 0.8767 (ptm) REVERT: B 146 LYS cc_start: 0.9033 (pptt) cc_final: 0.8819 (pmtt) REVERT: B 190 ASP cc_start: 0.8910 (m-30) cc_final: 0.8623 (m-30) REVERT: B 266 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8389 (mp10) REVERT: B 423 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9099 (mtmm) REVERT: B 440 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8295 (mtp85) REVERT: C 78 MET cc_start: 0.9049 (ttt) cc_final: 0.8758 (ptm) REVERT: C 190 ASP cc_start: 0.8905 (m-30) cc_final: 0.8619 (m-30) REVERT: C 266 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8339 (mp10) REVERT: C 423 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9101 (mtmm) REVERT: C 440 ARG cc_start: 0.8602 (mtp-110) cc_final: 0.8281 (mtp85) REVERT: D 78 MET cc_start: 0.9057 (ttt) cc_final: 0.8771 (ptm) REVERT: D 83 MET cc_start: 0.8504 (mtm) cc_final: 0.8100 (ptp) REVERT: D 146 LYS cc_start: 0.9021 (pptt) cc_final: 0.8808 (pmtt) REVERT: D 190 ASP cc_start: 0.8902 (m-30) cc_final: 0.8617 (m-30) REVERT: D 266 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8354 (mp10) REVERT: D 423 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9095 (mtmm) REVERT: D 440 ARG cc_start: 0.8607 (mtp-110) cc_final: 0.8299 (mtp85) outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 1.4685 time to fit residues: 175.3937 Evaluate side-chains 98 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR 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 D residue 285 THR Chi-restraints excluded: chain D residue 365 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 0.0370 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.077042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065022 restraints weight = 28274.706| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.91 r_work: 0.2707 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15184 Z= 0.101 Angle : 0.459 5.695 20600 Z= 0.240 Chirality : 0.041 0.123 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.777 19.830 2060 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.49 % Allowed : 12.22 % 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: 0.76 (0.19), residues: 1924 helix: 1.83 (0.19), residues: 768 sheet: -0.51 (0.34), residues: 248 loop : -0.30 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 295 HIS 0.006 0.001 HIS C 425 PHE 0.007 0.001 PHE B 380 TYR 0.006 0.001 TYR B 251 ARG 0.007 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 620) hydrogen bonds : angle 4.11159 ( 1800) covalent geometry : bond 0.00237 (15184) covalent geometry : angle 0.45935 (20600) *********************** 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 103 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.606 Fit side-chains REVERT: A 78 MET cc_start: 0.9010 (ttt) cc_final: 0.8657 (ptm) REVERT: A 146 LYS cc_start: 0.9020 (pptt) cc_final: 0.8806 (pmtt) REVERT: A 190 ASP cc_start: 0.8901 (m-30) cc_final: 0.8618 (m-30) REVERT: A 266 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8318 (mp10) REVERT: A 423 LYS cc_start: 0.9447 (mtpt) cc_final: 0.9090 (mtmm) REVERT: A 440 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.8260 (mtp85) REVERT: B 78 MET cc_start: 0.9005 (ttt) cc_final: 0.8659 (ptm) REVERT: B 146 LYS cc_start: 0.9022 (pptt) cc_final: 0.8802 (pmtt) REVERT: B 190 ASP cc_start: 0.8903 (m-30) cc_final: 0.8615 (m-30) REVERT: B 266 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8361 (mp10) REVERT: B 423 LYS cc_start: 0.9445 (mtpt) cc_final: 0.9089 (mtmm) REVERT: B 440 ARG cc_start: 0.8567 (mtp-110) cc_final: 0.8256 (mtp85) REVERT: C 78 MET cc_start: 0.9006 (ttt) cc_final: 0.8652 (ptm) REVERT: C 146 LYS cc_start: 0.9032 (pptt) cc_final: 0.8817 (pmtt) REVERT: C 190 ASP cc_start: 0.8907 (m-30) cc_final: 0.8623 (m-30) REVERT: C 266 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8344 (mp10) REVERT: C 423 LYS cc_start: 0.9450 (mtpt) cc_final: 0.9091 (mtmm) REVERT: C 440 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8226 (mtp85) REVERT: D 78 MET cc_start: 0.9007 (ttt) cc_final: 0.8661 (ptm) REVERT: D 146 LYS cc_start: 0.9007 (pptt) cc_final: 0.8786 (pmtt) REVERT: D 190 ASP cc_start: 0.8890 (m-30) cc_final: 0.8606 (m-30) REVERT: D 266 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8332 (mp10) REVERT: D 423 LYS cc_start: 0.9445 (mtpt) cc_final: 0.9085 (mtmm) REVERT: D 440 ARG cc_start: 0.8563 (mtp-110) cc_final: 0.8251 (mtp85) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 1.4993 time to fit residues: 169.0053 Evaluate side-chains 97 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.859 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 0.0870 chunk 154 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 52 optimal weight: 0.0870 overall best weight: 0.3714 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.078434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.066370 restraints weight = 28359.118| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.91 r_work: 0.2745 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15184 Z= 0.085 Angle : 0.453 5.390 20600 Z= 0.237 Chirality : 0.041 0.123 2324 Planarity : 0.004 0.044 2684 Dihedral : 3.691 19.494 2060 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.25 % Allowed : 12.47 % 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: 0.88 (0.19), residues: 1924 helix: 1.94 (0.19), residues: 768 sheet: -0.45 (0.35), residues: 248 loop : -0.25 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 295 HIS 0.005 0.001 HIS D 425 PHE 0.006 0.001 PHE C 380 TYR 0.005 0.001 TYR B 251 ARG 0.006 0.000 ARG D 487 Details of bonding type rmsd hydrogen bonds : bond 0.02562 ( 620) hydrogen bonds : angle 4.04836 ( 1800) covalent geometry : bond 0.00195 (15184) covalent geometry : angle 0.45340 (20600) ********************** 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 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 1.571 Fit side-chains REVERT: A 78 MET cc_start: 0.8995 (ttt) cc_final: 0.8710 (ptm) REVERT: A 146 LYS cc_start: 0.9026 (pptt) cc_final: 0.8806 (pmtt) REVERT: A 190 ASP cc_start: 0.8902 (m-30) cc_final: 0.8612 (m-30) REVERT: A 266 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8341 (mp10) REVERT: A 423 LYS cc_start: 0.9454 (mtpt) cc_final: 0.9093 (mtmm) REVERT: A 440 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8268 (mtp85) REVERT: B 78 MET cc_start: 0.8994 (ttt) cc_final: 0.8715 (ptm) REVERT: B 146 LYS cc_start: 0.9032 (pptt) cc_final: 0.8805 (pmtt) REVERT: B 190 ASP cc_start: 0.8896 (m-30) cc_final: 0.8603 (m-30) REVERT: B 266 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8393 (mp10) REVERT: B 423 LYS cc_start: 0.9450 (mtpt) cc_final: 0.9091 (mtmm) REVERT: B 440 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.8258 (mtp85) REVERT: C 59 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8192 (mp0) REVERT: C 78 MET cc_start: 0.8991 (ttt) cc_final: 0.8703 (ptm) REVERT: C 146 LYS cc_start: 0.9020 (pptt) cc_final: 0.8816 (pmtt) REVERT: C 190 ASP cc_start: 0.8898 (m-30) cc_final: 0.8609 (m-30) REVERT: C 266 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8326 (mp10) REVERT: C 423 LYS cc_start: 0.9452 (mtpt) cc_final: 0.9092 (mtmm) REVERT: C 440 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8241 (mtp85) REVERT: C 488 LEU cc_start: 0.8418 (tp) cc_final: 0.8205 (mm) REVERT: D 78 MET cc_start: 0.8993 (ttt) cc_final: 0.8714 (ptm) REVERT: D 83 MET cc_start: 0.8456 (mtm) cc_final: 0.8092 (ptp) REVERT: D 146 LYS cc_start: 0.9030 (pptt) cc_final: 0.8804 (pmtt) REVERT: D 190 ASP cc_start: 0.8894 (m-30) cc_final: 0.8604 (m-30) REVERT: D 266 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8324 (mp10) REVERT: D 423 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9088 (mtmm) REVERT: D 440 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8269 (mtp85) REVERT: D 488 LEU cc_start: 0.8418 (tp) cc_final: 0.8205 (mm) outliers start: 4 outliers final: 5 residues processed: 110 average time/residue: 1.4865 time to fit residues: 179.4174 Evaluate side-chains 98 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.075186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.063201 restraints weight = 28623.665| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.90 r_work: 0.2691 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15184 Z= 0.177 Angle : 0.501 5.401 20600 Z= 0.263 Chirality : 0.043 0.121 2324 Planarity : 0.004 0.057 2684 Dihedral : 3.889 20.324 2060 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.49 % Allowed : 12.47 % 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: 0.76 (0.19), residues: 1924 helix: 1.86 (0.19), residues: 764 sheet: -0.51 (0.35), residues: 248 loop : -0.32 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.007 0.001 HIS C 425 PHE 0.008 0.001 PHE C 380 TYR 0.009 0.001 TYR B 251 ARG 0.006 0.000 ARG B 487 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 620) hydrogen bonds : angle 4.16202 ( 1800) covalent geometry : bond 0.00415 (15184) covalent geometry : angle 0.50096 (20600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7680.61 seconds wall clock time: 135 minutes 26.66 seconds (8126.66 seconds total)