Starting phenix.real_space_refine on Sat Aug 23 21:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnm_27574/08_2025/8dnm_27574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnm_27574/08_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_27574/08_2025/8dnm_27574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnm_27574/08_2025/8dnm_27574.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnm_27574/08_2025/8dnm_27574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnm_27574/08_2025/8dnm_27574.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.55, per 1000 atoms: 0.24 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: 1.36 Conformation dependent library (CDL) restraints added in 708.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.78 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: 2.85 Time building geometry restraints manager: 1.79 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.670 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- 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 : 8.39 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A 496 TYR 0.015 0.002 TYR B 275 PHE 0.009 0.001 PHE C 380 TRP 0.016 0.002 TRP B 412 HIS 0.008 0.002 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00571 (15184) covalent geometry : angle 0.85312 (20600) hydrogen bonds : bond 0.19158 ( 620) hydrogen bonds : angle 6.80696 ( 1800) *********************** 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 : 0.674 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 210 average time/residue: 0.8877 time to fit residues: 200.0371 Evaluate side-chains 87 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.077044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.065675 restraints weight = 28000.152| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.72 r_work: 0.2743 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15184 Z= 0.166 Angle : 0.546 5.011 20600 Z= 0.294 Chirality : 0.043 0.129 2324 Planarity : 0.005 0.053 2684 Dihedral : 4.419 20.381 2060 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.68 % Allowed : 8.64 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.19), residues: 1924 helix: 1.11 (0.19), residues: 764 sheet: -1.53 (0.27), residues: 344 loop : -1.12 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 440 TYR 0.010 0.001 TYR C 290 PHE 0.015 0.002 PHE C 316 TRP 0.009 0.002 TRP C 295 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00384 (15184) covalent geometry : angle 0.54556 (20600) hydrogen bonds : bond 0.04105 ( 620) hydrogen bonds : angle 4.72799 ( 1800) *********************** 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 135 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.613 Fit side-chains REVERT: A 78 MET cc_start: 0.9141 (ttt) cc_final: 0.8835 (ptm) REVERT: A 262 GLU cc_start: 0.8923 (tp30) cc_final: 0.8609 (tp30) REVERT: A 266 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8282 (mp10) REVERT: A 375 MET cc_start: 0.9172 (ptp) cc_final: 0.8951 (ptp) REVERT: A 440 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8545 (mtp85) REVERT: B 78 MET cc_start: 0.9139 (ttt) cc_final: 0.8834 (ptm) REVERT: B 262 GLU cc_start: 0.8919 (tp30) cc_final: 0.8620 (tp30) REVERT: B 266 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8339 (mp10) REVERT: B 375 MET cc_start: 0.9175 (ptp) cc_final: 0.8956 (ptp) REVERT: B 440 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8512 (mtp85) REVERT: C 78 MET cc_start: 0.9139 (ttt) cc_final: 0.8841 (ptm) REVERT: C 262 GLU cc_start: 0.8920 (tp30) cc_final: 0.8624 (tp30) REVERT: C 266 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8338 (mp10) REVERT: C 375 MET cc_start: 0.9182 (ptp) cc_final: 0.8959 (ptp) REVERT: C 440 ARG cc_start: 0.8767 (mtp-110) cc_final: 0.8541 (mtp85) REVERT: D 78 MET cc_start: 0.9139 (ttt) cc_final: 0.8835 (ptm) REVERT: D 262 GLU cc_start: 0.8921 (tp30) cc_final: 0.8618 (tp30) REVERT: D 266 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8314 (mp10) REVERT: D 375 MET cc_start: 0.9179 (ptp) cc_final: 0.8957 (ptp) outliers start: 11 outliers final: 0 residues processed: 127 average time/residue: 0.8484 time to fit residues: 116.4865 Evaluate side-chains 91 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 119 optimal weight: 0.0570 chunk 86 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 379 GLN B 289 HIS B 379 GLN C 289 HIS C 379 GLN D 289 HIS D 379 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.073817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.062382 restraints weight = 28734.338| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.73 r_work: 0.2727 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15184 Z= 0.134 Angle : 0.492 5.573 20600 Z= 0.259 Chirality : 0.042 0.121 2324 Planarity : 0.004 0.036 2684 Dihedral : 4.145 20.525 2060 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.48 % Allowed : 9.38 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.19), residues: 1924 helix: 1.40 (0.19), residues: 764 sheet: -1.40 (0.29), residues: 312 loop : -0.81 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 440 TYR 0.008 0.001 TYR B 251 PHE 0.011 0.001 PHE C 316 TRP 0.010 0.001 TRP C 295 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00311 (15184) covalent geometry : angle 0.49153 (20600) hydrogen bonds : bond 0.03460 ( 620) hydrogen bonds : angle 4.33657 ( 1800) *********************** 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 135 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.614 Fit side-chains REVERT: A 78 MET cc_start: 0.9124 (ttt) cc_final: 0.8736 (ptm) REVERT: A 190 ASP cc_start: 0.9044 (m-30) cc_final: 0.8764 (m-30) REVERT: A 266 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8253 (mp10) REVERT: A 327 GLN cc_start: 0.8458 (pm20) cc_final: 0.8242 (pm20) REVERT: A 440 ARG cc_start: 0.8792 (mtp-110) cc_final: 0.8497 (mtp85) REVERT: B 78 MET cc_start: 0.9118 (ttt) cc_final: 0.8727 (ptm) REVERT: B 190 ASP cc_start: 0.9033 (m-30) cc_final: 0.8749 (m-30) REVERT: B 266 GLN cc_start: 0.8660 (mm-40) cc_final: 0.8233 (mp10) REVERT: B 327 GLN cc_start: 0.8458 (pm20) cc_final: 0.8239 (pm20) REVERT: B 440 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8505 (mtp85) REVERT: C 78 MET cc_start: 0.9119 (ttt) cc_final: 0.8737 (ptm) REVERT: C 190 ASP cc_start: 0.9041 (m-30) cc_final: 0.8760 (m-30) REVERT: C 266 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8198 (mp10) REVERT: C 327 GLN cc_start: 0.8466 (pm20) cc_final: 0.8247 (pm20) REVERT: C 440 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8500 (mtp85) REVERT: D 78 MET cc_start: 0.9115 (ttt) cc_final: 0.8726 (ptm) REVERT: D 190 ASP cc_start: 0.9042 (m-30) cc_final: 0.8761 (m-30) REVERT: D 266 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8200 (mp10) REVERT: D 327 GLN cc_start: 0.8466 (pm20) cc_final: 0.8248 (pm20) outliers start: 24 outliers final: 4 residues processed: 131 average time/residue: 0.8300 time to fit residues: 117.5550 Evaluate side-chains 104 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.076923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065308 restraints weight = 28252.646| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.82 r_work: 0.2731 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15184 Z= 0.120 Angle : 0.466 4.906 20600 Z= 0.247 Chirality : 0.041 0.120 2324 Planarity : 0.004 0.030 2684 Dihedral : 3.975 19.986 2060 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.23 % Allowed : 10.37 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.19), residues: 1924 helix: 1.61 (0.19), residues: 764 sheet: -1.12 (0.29), residues: 312 loop : -0.56 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 440 TYR 0.008 0.001 TYR B 251 PHE 0.009 0.001 PHE B 316 TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00277 (15184) covalent geometry : angle 0.46564 (20600) hydrogen bonds : bond 0.03139 ( 620) hydrogen bonds : angle 4.21413 ( 1800) *********************** 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 122 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.701 Fit side-chains REVERT: A 78 MET cc_start: 0.9028 (ttt) cc_final: 0.8648 (ptm) REVERT: A 146 LYS cc_start: 0.9044 (pptt) cc_final: 0.8834 (pmtt) REVERT: A 190 ASP cc_start: 0.8956 (m-30) cc_final: 0.8650 (m-30) REVERT: A 266 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8221 (mp10) REVERT: A 423 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9088 (mtpp) REVERT: A 440 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8262 (mtp85) REVERT: B 78 MET cc_start: 0.9024 (ttt) cc_final: 0.8642 (ptm) REVERT: B 190 ASP cc_start: 0.8963 (m-30) cc_final: 0.8657 (m-30) REVERT: B 266 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8248 (mp10) REVERT: B 423 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9084 (mtpp) REVERT: B 440 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8259 (mtp85) REVERT: C 78 MET cc_start: 0.9027 (ttt) cc_final: 0.8648 (ptm) REVERT: C 190 ASP cc_start: 0.8962 (m-30) cc_final: 0.8656 (m-30) REVERT: C 266 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8233 (mp10) REVERT: C 423 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9086 (mtpp) REVERT: C 440 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8239 (mtp85) REVERT: D 78 MET cc_start: 0.9033 (ttt) cc_final: 0.8654 (ptm) REVERT: D 190 ASP cc_start: 0.8956 (m-30) cc_final: 0.8649 (m-30) REVERT: D 266 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8234 (mp10) REVERT: D 423 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9083 (mtpp) outliers start: 20 outliers final: 4 residues processed: 110 average time/residue: 0.8481 time to fit residues: 101.1560 Evaluate side-chains 95 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 86 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.074920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063096 restraints weight = 28847.436| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.87 r_work: 0.2691 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3203 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= 0.192 Angle : 0.501 7.038 20600 Z= 0.265 Chirality : 0.043 0.124 2324 Planarity : 0.003 0.029 2684 Dihedral : 4.036 20.470 2060 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.74 % Allowed : 11.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1924 helix: 1.63 (0.19), residues: 764 sheet: -1.04 (0.34), residues: 228 loop : -0.56 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 487 TYR 0.010 0.001 TYR C 251 PHE 0.008 0.001 PHE C 392 TRP 0.010 0.001 TRP C 295 HIS 0.007 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00447 (15184) covalent geometry : angle 0.50055 (20600) hydrogen bonds : bond 0.03479 ( 620) hydrogen bonds : angle 4.26391 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.751 Fit side-chains REVERT: A 78 MET cc_start: 0.8958 (ttt) cc_final: 0.8624 (ttp) REVERT: A 146 LYS cc_start: 0.9043 (pptt) cc_final: 0.8822 (pmtt) REVERT: A 190 ASP cc_start: 0.8941 (m-30) cc_final: 0.8660 (m-30) REVERT: A 266 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8266 (mp10) REVERT: A 423 LYS cc_start: 0.9466 (mtpt) cc_final: 0.9100 (mtpp) REVERT: A 440 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8356 (mtp85) REVERT: B 78 MET cc_start: 0.8963 (ttt) cc_final: 0.8629 (ttp) REVERT: B 146 LYS cc_start: 0.9057 (pptt) cc_final: 0.8848 (pmtt) REVERT: B 190 ASP cc_start: 0.8938 (m-30) cc_final: 0.8658 (m-30) REVERT: B 266 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8267 (mp10) REVERT: B 423 LYS cc_start: 0.9463 (mtpt) cc_final: 0.9097 (mtpp) REVERT: B 440 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8345 (mtp85) REVERT: C 78 MET cc_start: 0.8966 (ttt) cc_final: 0.8632 (ttp) REVERT: C 146 LYS cc_start: 0.9069 (pptt) cc_final: 0.8863 (pmtt) REVERT: C 190 ASP cc_start: 0.8945 (m-30) cc_final: 0.8664 (m-30) REVERT: C 266 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8278 (mp10) REVERT: C 423 LYS cc_start: 0.9462 (mtpt) cc_final: 0.9097 (mtpp) REVERT: C 440 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8333 (mtp85) REVERT: D 78 MET cc_start: 0.8966 (ttt) cc_final: 0.8633 (ttp) REVERT: D 146 LYS cc_start: 0.9059 (pptt) cc_final: 0.8853 (pmtt) REVERT: D 190 ASP cc_start: 0.8943 (m-30) cc_final: 0.8660 (m-30) REVERT: D 266 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8285 (mp10) REVERT: D 423 LYS cc_start: 0.9462 (mtpt) cc_final: 0.9096 (mtpp) REVERT: D 440 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8348 (mtp85) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.8763 time to fit residues: 98.7251 Evaluate side-chains 92 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 185 optimal weight: 5.9990 chunk 187 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.075874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.064190 restraints weight = 28400.564| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.84 r_work: 0.2698 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3316 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= 0.120 Angle : 0.455 6.041 20600 Z= 0.240 Chirality : 0.041 0.121 2324 Planarity : 0.003 0.028 2684 Dihedral : 3.915 20.310 2060 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.99 % Allowed : 11.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1924 helix: 1.73 (0.19), residues: 764 sheet: -0.91 (0.34), residues: 228 loop : -0.39 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 487 TYR 0.007 0.001 TYR C 251 PHE 0.006 0.001 PHE B 380 TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00280 (15184) covalent geometry : angle 0.45532 (20600) hydrogen bonds : bond 0.02986 ( 620) hydrogen bonds : angle 4.15719 ( 1800) *********************** 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: 16 poor density : 97 time to evaluate : 0.632 Fit side-chains REVERT: A 146 LYS cc_start: 0.9036 (pptt) cc_final: 0.8812 (pmtt) REVERT: A 190 ASP cc_start: 0.8896 (m-30) cc_final: 0.8614 (m-30) REVERT: A 266 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8267 (mp10) REVERT: A 423 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9100 (mtpp) REVERT: A 440 ARG cc_start: 0.8628 (mtp-110) cc_final: 0.8342 (mtp85) REVERT: B 146 LYS cc_start: 0.9076 (pptt) cc_final: 0.8824 (pmtt) REVERT: B 190 ASP cc_start: 0.8886 (m-30) cc_final: 0.8599 (m-30) REVERT: B 266 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8277 (mp10) REVERT: B 423 LYS cc_start: 0.9466 (mtpt) cc_final: 0.9099 (mtpp) REVERT: B 440 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8337 (mtp85) REVERT: C 146 LYS cc_start: 0.9052 (pptt) cc_final: 0.8826 (pmtt) REVERT: C 190 ASP cc_start: 0.8895 (m-30) cc_final: 0.8618 (m-30) REVERT: C 266 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8288 (mp10) REVERT: C 423 LYS cc_start: 0.9465 (mtpt) cc_final: 0.9099 (mtpp) REVERT: C 440 ARG cc_start: 0.8603 (mtp-110) cc_final: 0.8312 (mtp85) REVERT: D 146 LYS cc_start: 0.9073 (pptt) cc_final: 0.8836 (pmtt) REVERT: D 190 ASP cc_start: 0.8891 (m-30) cc_final: 0.8606 (m-30) REVERT: D 266 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8296 (mp10) REVERT: D 423 LYS cc_start: 0.9464 (mtpt) cc_final: 0.9098 (mtpp) REVERT: D 440 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8308 (mtp85) outliers start: 16 outliers final: 12 residues processed: 113 average time/residue: 0.7780 time to fit residues: 96.0418 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 456 ASP Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 456 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3078 r_free = 0.3078 target = 0.075681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.063842 restraints weight = 28457.729| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.86 r_work: 0.2687 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15184 Z= 0.138 Angle : 0.474 7.643 20600 Z= 0.247 Chirality : 0.042 0.123 2324 Planarity : 0.003 0.029 2684 Dihedral : 3.918 20.245 2060 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.23 % Allowed : 11.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.19), residues: 1924 helix: 1.72 (0.19), residues: 768 sheet: -0.78 (0.32), residues: 248 loop : -0.40 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 487 TYR 0.008 0.001 TYR C 251 PHE 0.007 0.001 PHE D 380 TRP 0.010 0.001 TRP D 295 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00323 (15184) covalent geometry : angle 0.47359 (20600) hydrogen bonds : bond 0.03085 ( 620) hydrogen bonds : angle 4.16789 ( 1800) *********************** 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 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.625 Fit side-chains REVERT: A 78 MET cc_start: 0.8995 (ttt) cc_final: 0.8733 (ptm) REVERT: A 146 LYS cc_start: 0.9029 (pptt) cc_final: 0.8793 (pmtt) REVERT: A 190 ASP cc_start: 0.8901 (m-30) cc_final: 0.8617 (m-30) REVERT: A 266 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8259 (mp10) REVERT: A 423 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9104 (mtmm) REVERT: A 440 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8330 (mtp85) REVERT: B 78 MET cc_start: 0.8994 (ttt) cc_final: 0.8734 (ptm) REVERT: B 146 LYS cc_start: 0.9029 (pptt) cc_final: 0.8805 (pmtt) REVERT: B 190 ASP cc_start: 0.8893 (m-30) cc_final: 0.8607 (m-30) REVERT: B 266 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8288 (mp10) REVERT: B 423 LYS cc_start: 0.9464 (mtpt) cc_final: 0.9100 (mtmm) REVERT: B 440 ARG cc_start: 0.8659 (mtp-110) cc_final: 0.8328 (mtp85) REVERT: C 78 MET cc_start: 0.8990 (ttt) cc_final: 0.8726 (ptm) REVERT: C 146 LYS cc_start: 0.9035 (pptt) cc_final: 0.8832 (pmtt) REVERT: C 190 ASP cc_start: 0.8899 (m-30) cc_final: 0.8617 (m-30) REVERT: C 266 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8280 (mp10) REVERT: C 423 LYS cc_start: 0.9466 (mtpt) cc_final: 0.9102 (mtmm) REVERT: C 440 ARG cc_start: 0.8651 (mtp-110) cc_final: 0.8309 (mtp85) REVERT: D 78 MET cc_start: 0.8998 (ttt) cc_final: 0.8737 (ptm) REVERT: D 146 LYS cc_start: 0.9043 (pptt) cc_final: 0.8816 (pmtt) REVERT: D 190 ASP cc_start: 0.8901 (m-30) cc_final: 0.8617 (m-30) REVERT: D 266 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8290 (mp10) REVERT: D 423 LYS cc_start: 0.9465 (mtpt) cc_final: 0.9101 (mtmm) REVERT: D 440 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8281 (mtp85) outliers start: 20 outliers final: 4 residues processed: 110 average time/residue: 0.7463 time to fit residues: 89.8621 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.076674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.064952 restraints weight = 28371.682| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.84 r_work: 0.2716 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15184 Z= 0.104 Angle : 0.453 6.270 20600 Z= 0.236 Chirality : 0.041 0.120 2324 Planarity : 0.003 0.028 2684 Dihedral : 3.823 19.924 2060 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.49 % Allowed : 12.16 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.19), residues: 1924 helix: 1.77 (0.19), residues: 768 sheet: -0.57 (0.33), residues: 248 loop : -0.31 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 487 TYR 0.007 0.001 TYR C 251 PHE 0.006 0.001 PHE B 380 TRP 0.010 0.001 TRP B 295 HIS 0.004 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00243 (15184) covalent geometry : angle 0.45287 (20600) hydrogen bonds : bond 0.02803 ( 620) hydrogen bonds : angle 4.11979 ( 1800) *********************** 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 108 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.603 Fit side-chains REVERT: A 78 MET cc_start: 0.9057 (ttt) cc_final: 0.8794 (ptm) REVERT: A 146 LYS cc_start: 0.9018 (pptt) cc_final: 0.8800 (pmtt) REVERT: A 190 ASP cc_start: 0.8900 (m-30) cc_final: 0.8614 (m-30) REVERT: A 266 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8320 (mp10) REVERT: A 423 LYS cc_start: 0.9465 (mtpt) cc_final: 0.9105 (mtmm) REVERT: A 440 ARG cc_start: 0.8619 (mtp-110) cc_final: 0.8284 (mtp85) REVERT: B 78 MET cc_start: 0.9053 (ttt) cc_final: 0.8823 (ptm) REVERT: B 146 LYS cc_start: 0.9031 (pptt) cc_final: 0.8809 (pmtt) REVERT: B 190 ASP cc_start: 0.8902 (m-30) cc_final: 0.8606 (m-30) REVERT: B 266 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8323 (mp10) REVERT: B 423 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9096 (mtmm) REVERT: B 440 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8282 (mtp85) REVERT: C 78 MET cc_start: 0.9048 (ttt) cc_final: 0.8790 (ptm) REVERT: C 146 LYS cc_start: 0.9018 (pptt) cc_final: 0.8818 (pmtt) REVERT: C 190 ASP cc_start: 0.8903 (m-30) cc_final: 0.8615 (m-30) REVERT: C 266 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8379 (mp10) REVERT: C 423 LYS cc_start: 0.9466 (mtpt) cc_final: 0.9107 (mtmm) REVERT: C 440 ARG cc_start: 0.8616 (mtp-110) cc_final: 0.8278 (mtp85) REVERT: D 78 MET cc_start: 0.9054 (ttt) cc_final: 0.8821 (ptm) REVERT: D 146 LYS cc_start: 0.9036 (pptt) cc_final: 0.8812 (pmtt) REVERT: D 190 ASP cc_start: 0.8903 (m-30) cc_final: 0.8608 (m-30) REVERT: D 266 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8358 (mp10) REVERT: D 423 LYS cc_start: 0.9462 (mtpt) cc_final: 0.9102 (mtmm) REVERT: D 440 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8303 (mtp85) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.7459 time to fit residues: 88.1448 Evaluate side-chains 100 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 142 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.074432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062756 restraints weight = 28771.797| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.84 r_work: 0.2658 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15184 Z= 0.186 Angle : 0.498 6.224 20600 Z= 0.261 Chirality : 0.043 0.125 2324 Planarity : 0.003 0.028 2684 Dihedral : 3.962 20.378 2060 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.49 % Allowed : 12.28 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.19), residues: 1924 helix: 1.76 (0.19), residues: 764 sheet: -0.61 (0.35), residues: 228 loop : -0.25 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 487 TYR 0.010 0.001 TYR D 251 PHE 0.008 0.001 PHE B 392 TRP 0.010 0.001 TRP C 295 HIS 0.008 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00436 (15184) covalent geometry : angle 0.49782 (20600) hydrogen bonds : bond 0.03315 ( 620) hydrogen bonds : angle 4.21533 ( 1800) *********************** 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 108 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.642 Fit side-chains REVERT: A 78 MET cc_start: 0.9060 (ttt) cc_final: 0.8754 (ptm) REVERT: A 146 LYS cc_start: 0.9032 (pptt) cc_final: 0.8809 (pmtt) REVERT: A 190 ASP cc_start: 0.8957 (m-30) cc_final: 0.8676 (m-30) REVERT: A 266 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8347 (mp10) REVERT: A 423 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9105 (mtmm) REVERT: A 440 ARG cc_start: 0.8641 (mtp-110) cc_final: 0.8307 (mtp85) REVERT: B 78 MET cc_start: 0.9054 (ttt) cc_final: 0.8744 (ptm) REVERT: B 146 LYS cc_start: 0.9030 (pptt) cc_final: 0.8818 (pmtt) REVERT: B 190 ASP cc_start: 0.8951 (m-30) cc_final: 0.8663 (m-30) REVERT: B 266 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8354 (mp10) REVERT: B 423 LYS cc_start: 0.9454 (mtpt) cc_final: 0.9105 (mtmm) REVERT: B 440 ARG cc_start: 0.8637 (mtp-110) cc_final: 0.8303 (mtp85) REVERT: C 78 MET cc_start: 0.9059 (ttt) cc_final: 0.8753 (ptm) REVERT: C 146 LYS cc_start: 0.9031 (pptt) cc_final: 0.8820 (pmtt) REVERT: C 190 ASP cc_start: 0.8952 (m-30) cc_final: 0.8673 (m-30) REVERT: C 266 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8354 (mp10) REVERT: C 423 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9106 (mtmm) REVERT: C 440 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8289 (mtp85) REVERT: D 78 MET cc_start: 0.9056 (ttt) cc_final: 0.8745 (ptm) REVERT: D 146 LYS cc_start: 0.9031 (pptt) cc_final: 0.8818 (pmtt) REVERT: D 190 ASP cc_start: 0.8952 (m-30) cc_final: 0.8670 (m-30) REVERT: D 266 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8361 (mp10) REVERT: D 423 LYS cc_start: 0.9453 (mtpt) cc_final: 0.9104 (mtmm) REVERT: D 440 ARG cc_start: 0.8623 (mtp-110) cc_final: 0.8317 (mtp85) outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.8028 time to fit residues: 94.5374 Evaluate side-chains 104 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 90 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.077311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065431 restraints weight = 28507.373| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.89 r_work: 0.2726 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15184 Z= 0.091 Angle : 0.466 6.143 20600 Z= 0.243 Chirality : 0.041 0.124 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.798 19.969 2060 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.25 % Allowed : 12.59 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), residues: 1924 helix: 1.85 (0.19), residues: 768 sheet: -0.37 (0.35), residues: 248 loop : -0.27 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.006 0.001 TYR A 251 PHE 0.006 0.001 PHE D 316 TRP 0.010 0.001 TRP C 295 HIS 0.005 0.001 HIS D 425 Details of bonding type rmsd covalent geometry : bond 0.00212 (15184) covalent geometry : angle 0.46586 (20600) hydrogen bonds : bond 0.02693 ( 620) hydrogen bonds : angle 4.10748 ( 1800) ********************** 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 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.621 Fit side-chains REVERT: A 78 MET cc_start: 0.9048 (ttt) cc_final: 0.8818 (ptm) REVERT: A 146 LYS cc_start: 0.9019 (pptt) cc_final: 0.8797 (pmtt) REVERT: A 190 ASP cc_start: 0.8901 (m-30) cc_final: 0.8614 (m-30) REVERT: A 266 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8302 (mp10) REVERT: A 423 LYS cc_start: 0.9459 (mtpt) cc_final: 0.9100 (mtmm) REVERT: A 440 ARG cc_start: 0.8596 (mtp-110) cc_final: 0.8240 (mtp85) REVERT: B 78 MET cc_start: 0.9047 (ttt) cc_final: 0.8810 (ptm) REVERT: B 146 LYS cc_start: 0.9046 (pptt) cc_final: 0.8819 (pmtt) REVERT: B 190 ASP cc_start: 0.8887 (m-30) cc_final: 0.8593 (m-30) REVERT: B 266 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8331 (mp10) REVERT: B 423 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9099 (mtmm) REVERT: B 440 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8239 (mtp85) REVERT: C 78 MET cc_start: 0.9043 (ttt) cc_final: 0.8810 (ptm) REVERT: C 146 LYS cc_start: 0.9027 (pptt) cc_final: 0.8803 (pmtt) REVERT: C 190 ASP cc_start: 0.8891 (m-30) cc_final: 0.8600 (m-30) REVERT: C 266 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8368 (mp10) REVERT: C 423 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9098 (mtmm) REVERT: C 440 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8237 (mtp85) REVERT: D 78 MET cc_start: 0.9046 (ttt) cc_final: 0.8808 (ptm) REVERT: D 146 LYS cc_start: 0.9049 (pptt) cc_final: 0.8819 (pmtt) REVERT: D 190 ASP cc_start: 0.8901 (m-30) cc_final: 0.8607 (m-30) REVERT: D 266 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8375 (mp10) REVERT: D 423 LYS cc_start: 0.9457 (mtpt) cc_final: 0.9096 (mtmm) REVERT: D 440 ARG cc_start: 0.8546 (mtp-110) cc_final: 0.8252 (mtp85) outliers start: 4 outliers final: 4 residues processed: 111 average time/residue: 0.7942 time to fit residues: 96.2213 Evaluate side-chains 102 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 285 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 187 optimal weight: 0.3980 chunk 43 optimal weight: 0.0770 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.078521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.066541 restraints weight = 28328.238| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.91 r_work: 0.2745 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15184 Z= 0.085 Angle : 0.440 5.833 20600 Z= 0.229 Chirality : 0.041 0.127 2324 Planarity : 0.003 0.027 2684 Dihedral : 3.673 19.195 2060 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.31 % Allowed : 12.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.19), residues: 1924 helix: 1.94 (0.19), residues: 768 sheet: -0.32 (0.35), residues: 248 loop : -0.25 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 487 TYR 0.006 0.001 TYR B 251 PHE 0.006 0.001 PHE B 380 TRP 0.009 0.001 TRP D 295 HIS 0.005 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00196 (15184) covalent geometry : angle 0.44024 (20600) hydrogen bonds : bond 0.02585 ( 620) hydrogen bonds : angle 4.06005 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3742.36 seconds wall clock time: 65 minutes 30.71 seconds (3930.71 seconds total)