Starting phenix.real_space_refine on Sat Jul 4 00:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.map" model { file = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ptu_13638/07_2026/7ptu_13638.cif" } resolution = 3.87 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= 0.001 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 15 5.16 5 C 10210 2.51 5 N 2675 2.21 5 O 4135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17035 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3396 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'BGC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.45, per 1000 atoms: 0.14 Number of scatterers: 17035 At special positions: 0 Unit cell: (147.4, 145.2, 103.4, 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 15 16.00 O 4135 8.00 N 2675 7.00 C 10210 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 811.5 milliseconds 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 40 sheets defined 11.2% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 42 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER A 82 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.539A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.661A pdb=" N LYS A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.703A pdb=" N VAL A 369 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU A 433 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 43 removed outlier: 3.507A pdb=" N ALA B 41 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP B 42 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER B 82 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.703A pdb=" N VAL B 369 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU B 433 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA C 41 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 42 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL C 369 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU C 433 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER C 458 " --> pdb=" O GLY C 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 460 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 496 removed outlier: 3.706A pdb=" N GLY C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 43 removed outlier: 3.509A pdb=" N ALA D 41 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D 42 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER D 82 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL D 181 " --> pdb=" O ILE D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL D 369 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 433 removed outlier: 3.794A pdb=" N GLU D 433 " --> pdb=" O GLY D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 462 removed outlier: 3.820A pdb=" N SER D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 460 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 462 " --> pdb=" O SER D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 43 removed outlier: 3.508A pdb=" N ALA E 41 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 42 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.627A pdb=" N SER E 82 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.540A pdb=" N VAL E 181 " --> pdb=" O ILE E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 287 through 292 removed outlier: 3.660A pdb=" N LYS E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.704A pdb=" N VAL E 369 " --> pdb=" O THR E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.793A pdb=" N GLU E 433 " --> pdb=" O GLY E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 462 removed outlier: 3.821A pdb=" N SER E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU E 462 " --> pdb=" O SER E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 496 removed outlier: 3.705A pdb=" N GLY E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL A 56 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.709A pdb=" N SER A 240 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL A 254 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 375 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP A 355 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 278 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 357 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 274 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 275 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 303 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY A 393 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR A 506 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 395 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 464 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 415 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 401 Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL B 56 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 144 removed outlier: 3.709A pdb=" N SER B 240 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 249 Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL B 254 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN B 375 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASP B 355 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP B 278 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 357 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 274 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 275 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 303 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 388 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.549A pdb=" N GLY B 393 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR B 506 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR B 395 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 464 " --> pdb=" O VAL B 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 415 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 400 through 401 Processing sheet with id=AB8, first strand: chain 'C' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL C 56 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AC1, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER C 240 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 246 through 249 Processing sheet with id=AC3, first strand: chain 'C' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL C 254 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN C 375 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP C 355 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASP C 278 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 357 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL C 274 " --> pdb=" O TYR C 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL C 275 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 303 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 386 through 388 Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY C 393 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR C 506 " --> pdb=" O GLY C 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C 395 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 464 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE C 415 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 400 through 401 Processing sheet with id=AC7, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL D 56 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 125 through 131 Processing sheet with id=AC9, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER D 240 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 246 through 249 Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 255 removed outlier: 6.395A pdb=" N VAL D 254 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN D 375 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP D 355 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP D 278 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 357 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL D 274 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 275 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 303 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 386 through 388 Processing sheet with id=AD4, first strand: chain 'D' and resid 393 through 396 removed outlier: 6.548A pdb=" N GLY D 393 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR D 506 " --> pdb=" O GLY D 393 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR D 395 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 464 " --> pdb=" O VAL D 505 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE D 415 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 400 through 401 Processing sheet with id=AD6, first strand: chain 'E' and resid 55 through 57 removed outlier: 6.064A pdb=" N VAL E 56 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AD8, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.710A pdb=" N SER E 240 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 246 through 249 Processing sheet with id=AE1, first strand: chain 'E' and resid 253 through 255 removed outlier: 6.394A pdb=" N VAL E 254 " --> pdb=" O GLU E 382 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN E 375 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASP E 355 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP E 278 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU E 357 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL E 274 " --> pdb=" O TYR E 359 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 275 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 303 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 386 through 388 Processing sheet with id=AE3, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.547A pdb=" N GLY E 393 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR E 506 " --> pdb=" O GLY E 393 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR E 395 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY E 464 " --> pdb=" O VAL E 505 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE E 415 " --> pdb=" O LEU E 426 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 400 through 401 460 hydrogen bonds defined for protein. 1200 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: 2.74 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6101 1.34 - 1.45: 2062 1.45 - 1.57: 8992 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 17185 Sorted by residual: bond pdb=" CA ASP E 420 " pdb=" CB ASP E 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.86e+00 bond pdb=" CA ASP D 420 " pdb=" CB ASP D 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.84e+00 bond pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.81e+00 bond pdb=" CA ASP B 420 " pdb=" CB ASP B 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.77e+00 bond pdb=" CA ASP C 420 " pdb=" CB ASP C 420 " ideal model delta sigma weight residual 1.529 1.556 -0.027 1.62e-02 3.81e+03 2.68e+00 ... (remaining 17180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 22632 1.90 - 3.79: 736 3.79 - 5.69: 67 5.69 - 7.58: 20 7.58 - 9.48: 10 Bond angle restraints: 23465 Sorted by residual: angle pdb=" N GLN D 242 " pdb=" CA GLN D 242 " pdb=" C GLN D 242 " ideal model delta sigma weight residual 110.80 101.32 9.48 2.13e+00 2.20e-01 1.98e+01 angle pdb=" N GLN A 242 " pdb=" CA GLN A 242 " pdb=" C GLN A 242 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN E 242 " pdb=" CA GLN E 242 " pdb=" C GLN E 242 " ideal model delta sigma weight residual 110.80 101.35 9.45 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN B 242 " pdb=" CA GLN B 242 " pdb=" C GLN B 242 " ideal model delta sigma weight residual 110.80 101.36 9.44 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N GLN C 242 " pdb=" CA GLN C 242 " pdb=" C GLN C 242 " ideal model delta sigma weight residual 110.80 101.36 9.44 2.13e+00 2.20e-01 1.96e+01 ... (remaining 23460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9301 17.92 - 35.84: 674 35.84 - 53.76: 120 53.76 - 71.69: 20 71.69 - 89.61: 20 Dihedral angle restraints: 10135 sinusoidal: 3530 harmonic: 6605 Sorted by residual: dihedral pdb=" N ASP C 420 " pdb=" C ASP C 420 " pdb=" CA ASP C 420 " pdb=" CB ASP C 420 " ideal model delta harmonic sigma weight residual 122.80 131.86 -9.06 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" N ASP A 420 " pdb=" C ASP A 420 " pdb=" CA ASP A 420 " pdb=" CB ASP A 420 " ideal model delta harmonic sigma weight residual 122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" N ASP B 420 " pdb=" C ASP B 420 " pdb=" CA ASP B 420 " pdb=" CB ASP B 420 " ideal model delta harmonic sigma weight residual 122.80 131.81 -9.01 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 10132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2237 0.053 - 0.106: 511 0.106 - 0.159: 107 0.159 - 0.212: 15 0.212 - 0.265: 5 Chirality restraints: 2875 Sorted by residual: chirality pdb=" CA ASP C 420 " pdb=" N ASP C 420 " pdb=" C ASP C 420 " pdb=" CB ASP C 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP B 420 " pdb=" N ASP B 420 " pdb=" C ASP B 420 " pdb=" CB ASP B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASP A 420 " pdb=" N ASP A 420 " pdb=" C ASP A 420 " pdb=" CB ASP A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2872 not shown) Planarity restraints: 3185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 419 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP D 419 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP D 419 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP D 420 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 419 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ASP A 419 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP A 419 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 420 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 419 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ASP C 419 " -0.055 2.00e-02 2.50e+03 pdb=" O ASP C 419 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 420 " 0.019 2.00e-02 2.50e+03 ... (remaining 3182 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1063 2.72 - 3.26: 17930 3.26 - 3.81: 26123 3.81 - 4.35: 31816 4.35 - 4.90: 55036 Nonbonded interactions: 131968 Sorted by model distance: nonbonded pdb=" OG1 THR C 406 " pdb=" O ASP C 440 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR D 406 " pdb=" O ASP D 440 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR E 406 " pdb=" O ASP E 440 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR B 406 " pdb=" O ASP B 440 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR A 406 " pdb=" O ASP A 440 " model vdw 2.174 3.040 ... (remaining 131963 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 group one per residue 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: 2.100 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 : 0.003 0.027 17190 Z= 0.156 Angle : 0.793 9.477 23465 Z= 0.451 Chirality : 0.049 0.265 2875 Planarity : 0.005 0.046 3185 Dihedral : 13.646 89.606 5955 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.48 (0.16), residues: 2360 helix: -1.54 (0.60), residues: 60 sheet: -0.35 (0.18), residues: 810 loop : -1.37 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 124 TYR 0.016 0.002 TYR E 159 PHE 0.020 0.002 PHE E 228 TRP 0.008 0.002 TRP B 423 HIS 0.002 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (17185) covalent geometry : angle 0.79257 / 0.45 (23465) hydrogen bonds : bond 0.12305 / 8.19 ( 460) hydrogen bonds : angle 8.01769 / 5.70 ( 1200) Misc. bond : bond 0.00038 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.577 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 30 average time/residue: 0.1099 time to fit residues: 5.8747 Evaluate side-chains 25 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS B 273 HIS C 273 HIS ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 HIS ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.039638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.028705 restraints weight = 155608.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.029589 restraints weight = 86848.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.030164 restraints weight = 58183.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.030551 restraints weight = 43767.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030813 restraints weight = 35683.784| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17190 Z= 0.229 Angle : 0.624 7.263 23465 Z= 0.342 Chirality : 0.046 0.159 2875 Planarity : 0.004 0.038 3185 Dihedral : 4.944 20.935 2460 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.47 % Allowed : 8.10 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.42 (0.16), residues: 2360 helix: -1.00 (0.46), residues: 125 sheet: -0.09 (0.20), residues: 675 loop : -1.40 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 124 TYR 0.013 0.002 TYR D 466 PHE 0.018 0.002 PHE E 295 TRP 0.017 0.005 TRP B 423 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (17185) covalent geometry : angle 0.62363 / 0.34 (23465) hydrogen bonds : bond 0.04376 / 2.88 ( 460) hydrogen bonds : angle 5.95528 / 4.20 ( 1200) Misc. bond : bond 0.00086 / 0.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.623 Fit side-chains REVERT: D 235 MET cc_start: 0.8216 (mtp) cc_final: 0.7978 (mtp) REVERT: E 235 MET cc_start: 0.7866 (mtp) cc_final: 0.7563 (mtt) outliers start: 9 outliers final: 9 residues processed: 37 average time/residue: 0.0721 time to fit residues: 5.1825 Evaluate side-chains 29 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 165 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 220 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 224 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 229 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.037998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027269 restraints weight = 162131.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.028120 restraints weight = 90234.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028677 restraints weight = 60631.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.029046 restraints weight = 45780.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.029292 restraints weight = 37512.311| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17190 Z= 0.259 Angle : 0.652 7.552 23465 Z= 0.354 Chirality : 0.047 0.170 2875 Planarity : 0.004 0.031 3185 Dihedral : 5.260 19.799 2460 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.40 % Allowed : 11.12 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.37 (0.17), residues: 2360 helix: -0.74 (0.47), residues: 130 sheet: -0.04 (0.19), residues: 765 loop : -1.46 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 36 TYR 0.013 0.002 TYR E 348 PHE 0.017 0.002 PHE A 46 TRP 0.016 0.005 TRP B 423 HIS 0.001 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.26 (17185) covalent geometry : angle 0.65226 / 0.35 (23465) hydrogen bonds : bond 0.04420 / 2.91 ( 460) hydrogen bonds : angle 6.08460 / 4.31 ( 1200) Misc. bond : bond 0.00077 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 27 time to evaluate : 0.615 Fit side-chains outliers start: 27 outliers final: 24 residues processed: 53 average time/residue: 0.0804 time to fit residues: 7.8560 Evaluate side-chains 44 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 505 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 104 optimal weight: 4.9990 chunk 129 optimal weight: 40.0000 chunk 88 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 ASN C 432 ASN D 432 ASN E 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.037752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.026934 restraints weight = 163973.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027766 restraints weight = 93146.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.028305 restraints weight = 63465.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.028665 restraints weight = 48550.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028908 restraints weight = 40148.407| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17190 Z= 0.211 Angle : 0.573 7.670 23465 Z= 0.309 Chirality : 0.045 0.154 2875 Planarity : 0.003 0.029 3185 Dihedral : 5.004 18.430 2460 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.01 % Allowed : 13.04 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.26 (0.18), residues: 2360 helix: -1.36 (0.43), residues: 160 sheet: 0.01 (0.20), residues: 775 loop : -1.29 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 296 TYR 0.009 0.001 TYR E 466 PHE 0.014 0.002 PHE D 295 TRP 0.007 0.003 TRP A 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 (17185) covalent geometry : angle 0.57307 / 0.31 (23465) hydrogen bonds : bond 0.03678 / 2.45 ( 460) hydrogen bonds : angle 5.67699 / 4.02 ( 1200) Misc. bond : bond 0.00080 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 20 time to evaluate : 0.625 Fit side-chains REVERT: A 277 MET cc_start: 0.8929 (tpp) cc_final: 0.8713 (tpp) outliers start: 58 outliers final: 24 residues processed: 77 average time/residue: 0.0833 time to fit residues: 11.8876 Evaluate side-chains 44 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 209 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 201 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 228 optimal weight: 0.0170 chunk 122 optimal weight: 7.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.037652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.026816 restraints weight = 165232.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.027637 restraints weight = 94312.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.028168 restraints weight = 64619.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.028517 restraints weight = 49593.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.028751 restraints weight = 41195.465| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17190 Z= 0.225 Angle : 0.589 7.648 23465 Z= 0.316 Chirality : 0.045 0.158 2875 Planarity : 0.003 0.031 3185 Dihedral : 5.059 18.022 2460 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.06 % Allowed : 15.12 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.28 (0.18), residues: 2360 helix: -1.37 (0.42), residues: 160 sheet: 0.21 (0.21), residues: 735 loop : -1.42 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.011 0.001 TYR D 466 PHE 0.013 0.002 PHE B 295 TRP 0.007 0.003 TRP E 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (17185) covalent geometry : angle 0.58859 / 0.32 (23465) hydrogen bonds : bond 0.03671 / 2.45 ( 460) hydrogen bonds : angle 5.76801 / 4.09 ( 1200) Misc. bond : bond 0.00074 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 20 time to evaluate : 0.539 Fit side-chains outliers start: 59 outliers final: 45 residues processed: 79 average time/residue: 0.0750 time to fit residues: 10.9972 Evaluate side-chains 65 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 20 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 50 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 166 optimal weight: 0.0570 chunk 221 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.037183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.026458 restraints weight = 166651.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.027245 restraints weight = 96266.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.027755 restraints weight = 66366.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.028093 restraints weight = 51087.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.028326 restraints weight = 42588.817| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17190 Z= 0.277 Angle : 0.640 8.041 23465 Z= 0.342 Chirality : 0.046 0.157 2875 Planarity : 0.003 0.034 3185 Dihedral : 5.415 18.670 2460 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.16 % Allowed : 15.01 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.51 (0.18), residues: 2360 helix: -0.55 (0.50), residues: 130 sheet: 0.04 (0.21), residues: 685 loop : -1.63 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 296 TYR 0.012 0.002 TYR A 359 PHE 0.014 0.002 PHE C 295 TRP 0.009 0.003 TRP E 423 HIS 0.002 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.28 (17185) covalent geometry : angle 0.64039 / 0.34 (23465) hydrogen bonds : bond 0.04000 / 2.68 ( 460) hydrogen bonds : angle 5.94619 / 4.22 ( 1200) Misc. bond : bond 0.00105 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 20 time to evaluate : 0.541 Fit side-chains REVERT: A 506 THR cc_start: 0.5951 (OUTLIER) cc_final: 0.5724 (p) REVERT: C 131 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6820 (pp) REVERT: C 506 THR cc_start: 0.6319 (OUTLIER) cc_final: 0.6076 (p) outliers start: 80 outliers final: 60 residues processed: 100 average time/residue: 0.0774 time to fit residues: 14.1537 Evaluate side-chains 83 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 20 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 505 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 15 optimal weight: 4.9990 chunk 198 optimal weight: 0.0010 chunk 71 optimal weight: 0.0770 chunk 60 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 overall best weight: 3.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.037401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.026657 restraints weight = 165291.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.027469 restraints weight = 94872.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.027996 restraints weight = 65038.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.028350 restraints weight = 49888.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.028586 restraints weight = 41400.783| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17190 Z= 0.176 Angle : 0.554 8.267 23465 Z= 0.294 Chirality : 0.045 0.185 2875 Planarity : 0.003 0.030 3185 Dihedral : 4.919 17.708 2460 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.43 % Allowed : 16.47 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.47 (0.18), residues: 2360 helix: -0.52 (0.48), residues: 130 sheet: 0.00 (0.21), residues: 705 loop : -1.58 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 124 TYR 0.009 0.001 TYR D 466 PHE 0.011 0.002 PHE B 295 TRP 0.003 0.002 TRP A 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (17185) covalent geometry : angle 0.55425 / 0.29 (23465) hydrogen bonds : bond 0.03431 / 2.29 ( 460) hydrogen bonds : angle 5.65216 / 4.01 ( 1200) Misc. bond : bond 0.00059 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 20 time to evaluate : 0.652 Fit side-chains REVERT: B 131 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6621 (pp) outliers start: 66 outliers final: 51 residues processed: 86 average time/residue: 0.0917 time to fit residues: 14.5941 Evaluate side-chains 72 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 20 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.037353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.026539 restraints weight = 164174.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.027346 restraints weight = 94963.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.027872 restraints weight = 65483.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.028225 restraints weight = 50458.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.028458 restraints weight = 41949.119| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17190 Z= 0.194 Angle : 0.566 11.424 23465 Z= 0.298 Chirality : 0.045 0.157 2875 Planarity : 0.003 0.031 3185 Dihedral : 4.867 17.381 2460 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.58 % Allowed : 16.62 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.48 (0.18), residues: 2360 helix: -0.53 (0.48), residues: 130 sheet: -0.00 (0.21), residues: 705 loop : -1.59 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 36 TYR 0.010 0.001 TYR B 466 PHE 0.011 0.002 PHE C 295 TRP 0.004 0.002 TRP B 423 HIS 0.002 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (17185) covalent geometry : angle 0.56621 / 0.30 (23465) hydrogen bonds : bond 0.03389 / 2.27 ( 460) hydrogen bonds : angle 5.60501 / 3.98 ( 1200) Misc. bond : bond 0.00067 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 20 time to evaluate : 0.628 Fit side-chains REVERT: B 131 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6793 (pp) REVERT: C 131 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6685 (pp) REVERT: C 506 THR cc_start: 0.6351 (OUTLIER) cc_final: 0.6121 (p) REVERT: E 235 MET cc_start: 0.8380 (mtp) cc_final: 0.7990 (mtt) outliers start: 69 outliers final: 61 residues processed: 88 average time/residue: 0.0855 time to fit residues: 13.9878 Evaluate side-chains 84 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 20 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 197 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 193 optimal weight: 0.6980 chunk 54 optimal weight: 0.0030 chunk 153 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 213 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.038362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027555 restraints weight = 161088.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.028410 restraints weight = 91925.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.028962 restraints weight = 62732.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.029330 restraints weight = 47880.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.029579 restraints weight = 39538.738| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17190 Z= 0.092 Angle : 0.514 12.532 23465 Z= 0.268 Chirality : 0.045 0.158 2875 Planarity : 0.003 0.029 3185 Dihedral : 4.216 15.825 2460 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.18 % Allowed : 18.03 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.33 (0.18), residues: 2360 helix: -0.28 (0.46), residues: 130 sheet: 0.17 (0.21), residues: 680 loop : -1.51 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.008 0.001 TYR D 466 PHE 0.007 0.001 PHE E 57 TRP 0.008 0.002 TRP C 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 (17185) covalent geometry : angle 0.51417 / 0.27 (23465) hydrogen bonds : bond 0.02772 / 1.86 ( 460) hydrogen bonds : angle 5.18184 / 3.67 ( 1200) Misc. bond : bond 0.00004 / 0.00 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 20 time to evaluate : 0.692 Fit side-chains REVERT: B 131 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6299 (pp) REVERT: C 131 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6384 (pp) REVERT: E 235 MET cc_start: 0.8465 (mtp) cc_final: 0.8260 (mtp) outliers start: 42 outliers final: 34 residues processed: 62 average time/residue: 0.0899 time to fit residues: 10.5719 Evaluate side-chains 56 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 20 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 497 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 193 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.037858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.027013 restraints weight = 159822.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.027841 restraints weight = 92386.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028390 restraints weight = 63657.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.028753 restraints weight = 48944.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.028994 restraints weight = 40606.118| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17190 Z= 0.118 Angle : 0.514 12.773 23465 Z= 0.266 Chirality : 0.044 0.155 2875 Planarity : 0.002 0.030 3185 Dihedral : 4.207 15.658 2460 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.18 % Allowed : 18.08 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.31 (0.18), residues: 2360 helix: -0.30 (0.46), residues: 130 sheet: 0.22 (0.21), residues: 710 loop : -1.54 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 124 TYR 0.008 0.001 TYR D 466 PHE 0.008 0.001 PHE E 295 TRP 0.002 0.001 TRP A 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17185) covalent geometry : angle 0.51441 / 0.27 (23465) hydrogen bonds : bond 0.02793 / 1.88 ( 460) hydrogen bonds : angle 5.09951 / 3.62 ( 1200) Misc. bond : bond 0.00033 / 0.02 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 21 time to evaluate : 0.784 Fit side-chains REVERT: B 131 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6422 (pp) REVERT: C 131 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6520 (pp) REVERT: E 235 MET cc_start: 0.8436 (mtp) cc_final: 0.8223 (mtp) REVERT: E 506 THR cc_start: 0.6526 (OUTLIER) cc_final: 0.6308 (p) outliers start: 42 outliers final: 37 residues processed: 63 average time/residue: 0.0917 time to fit residues: 11.0165 Evaluate side-chains 60 residues out of total 1925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 20 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 506 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 183 optimal weight: 0.0370 chunk 224 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.037874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.027092 restraints weight = 161142.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.027924 restraints weight = 93754.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.028463 restraints weight = 64897.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.028831 restraints weight = 50072.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.029072 restraints weight = 41609.320| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17190 Z= 0.097 Angle : 0.508 12.493 23465 Z= 0.262 Chirality : 0.044 0.155 2875 Planarity : 0.002 0.031 3185 Dihedral : 4.003 14.979 2460 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.18 % Allowed : 18.08 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.27 (0.18), residues: 2360 helix: -0.11 (0.45), residues: 130 sheet: 0.21 (0.21), residues: 710 loop : -1.52 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 418 TYR 0.008 0.001 TYR D 466 PHE 0.008 0.001 PHE A 442 TRP 0.004 0.001 TRP A 423 HIS 0.001 0.001 HIS B 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (17185) covalent geometry : angle 0.50777 / 0.26 (23465) hydrogen bonds : bond 0.02627 / 1.77 ( 460) hydrogen bonds : angle 4.94623 / 3.51 ( 1200) Misc. bond : bond 0.00013 / 0.01 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.83 seconds wall clock time: 43 minutes 45.59 seconds (2625.59 seconds total)