Starting phenix.real_space_refine on Mon Aug 25 10:24:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7j_29813/08_2025/8g7j_29813.cif" } resolution = 3.4 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= 0.134 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 98 5.16 5 C 17227 2.51 5 N 4690 2.21 5 O 5446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27461 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "C" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "E" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "G" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Time building chain proxies: 7.22, per 1000 atoms: 0.26 Number of scatterers: 27461 At special positions: 0 Unit cell: (165.933, 160.371, 89.919, 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 98 16.00 O 5446 8.00 N 4690 7.00 C 17227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.4 microseconds 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 28 sheets defined 58.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.987A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.840A pdb=" N ILE A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 removed outlier: 4.297A pdb=" N THR A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 337 through 355 Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.578A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.026A pdb=" N GLU A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.503A pdb=" N ILE A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 516 Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.982A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.527A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 4.406A pdb=" N THR B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.555A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 removed outlier: 4.118A pdb=" N GLU B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.505A pdb=" N ILE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.988A pdb=" N LEU C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 Processing helix chain 'C' and resid 62 through 77 removed outlier: 3.794A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 removed outlier: 4.308A pdb=" N THR C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 337 through 355 Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.595A pdb=" N LEU C 371 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.078A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.504A pdb=" N ILE C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 496 through 516 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.980A pdb=" N LEU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 58 Processing helix chain 'D' and resid 62 through 77 removed outlier: 3.817A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 107 removed outlier: 4.303A pdb=" N THR D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 153 through 168 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 337 through 355 Processing helix chain 'D' and resid 357 through 373 removed outlier: 3.551A pdb=" N LEU D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 409 removed outlier: 4.099A pdb=" N GLU D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 516 Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.975A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 Processing helix chain 'E' and resid 62 through 77 removed outlier: 3.828A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 72 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 107 removed outlier: 4.373A pdb=" N THR E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 231 through 241 Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 337 through 355 Processing helix chain 'E' and resid 357 through 373 removed outlier: 3.570A pdb=" N LEU E 371 " --> pdb=" O ARG E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 removed outlier: 4.046A pdb=" N GLU E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 432 through 446 removed outlier: 3.984A pdb=" N ILE E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 516 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.971A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 58 Processing helix chain 'F' and resid 62 through 77 removed outlier: 3.835A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 107 removed outlier: 3.837A pdb=" N THR F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 231 through 241 Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 337 through 355 Processing helix chain 'F' and resid 357 through 373 removed outlier: 3.595A pdb=" N LEU F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 removed outlier: 4.100A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.500A pdb=" N ILE F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 516 Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.978A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.811A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 107 removed outlier: 4.310A pdb=" N THR G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 231 through 241 Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 279 through 295 Processing helix chain 'G' and resid 337 through 355 Processing helix chain 'G' and resid 357 through 373 removed outlier: 3.586A pdb=" N LEU G 371 " --> pdb=" O ARG G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 409 removed outlier: 4.148A pdb=" N GLU G 390 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 420 Processing helix chain 'G' and resid 421 through 426 Processing helix chain 'G' and resid 432 through 446 removed outlier: 3.508A pdb=" N ILE G 442 " --> pdb=" O GLY G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.540A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU G 522 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.535A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU A 189 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 245 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 274 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.674A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.545A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU C 189 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL C 246 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR C 217 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE C 248 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 219 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.551A pdb=" N THR D 174 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL D 380 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS D 176 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU D 189 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL D 246 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB8, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.517A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU E 189 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL E 246 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU E 245 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL E 274 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE E 247 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC3, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AC4, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AC5, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.527A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLU F 189 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL F 246 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR F 217 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AC8, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.580A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU G 189 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU G 321 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLN G 214 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE G 323 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU G 212 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AD1, first strand: chain 'G' and resid 475 through 478 1757 hydrogen bonds defined for protein. 5058 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: 6.71 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5415 1.31 - 1.44: 5220 1.44 - 1.56: 16830 1.56 - 1.69: 45 1.69 - 1.81: 175 Bond restraints: 27685 Sorted by residual: bond pdb=" CA ILE G 126 " pdb=" CB ILE G 126 " ideal model delta sigma weight residual 1.540 1.493 0.048 1.25e-02 6.40e+03 1.46e+01 bond pdb=" CA ILE B 126 " pdb=" CB ILE B 126 " ideal model delta sigma weight residual 1.540 1.493 0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" CA ILE E 126 " pdb=" CB ILE E 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" CA ILE F 126 " pdb=" CB ILE F 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" CA ILE C 126 " pdb=" CB ILE C 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 27680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 32164 2.02 - 4.04: 4384 4.04 - 6.06: 672 6.06 - 8.07: 85 8.07 - 10.09: 40 Bond angle restraints: 37345 Sorted by residual: angle pdb=" N ILE E 231 " pdb=" CA ILE E 231 " pdb=" C ILE E 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.57e+01 angle pdb=" N ILE G 231 " pdb=" CA ILE G 231 " pdb=" C ILE G 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.57e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.56e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 113.43 103.35 10.08 1.09e+00 8.42e-01 8.55e+01 angle pdb=" N ILE A 231 " pdb=" CA ILE A 231 " pdb=" C ILE A 231 " ideal model delta sigma weight residual 113.43 103.35 10.08 1.09e+00 8.42e-01 8.55e+01 ... (remaining 37340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 16718 15.32 - 30.63: 387 30.63 - 45.95: 78 45.95 - 61.26: 54 61.26 - 76.58: 32 Dihedral angle restraints: 17269 sinusoidal: 6832 harmonic: 10437 Sorted by residual: dihedral pdb=" CA THR D 205 " pdb=" C THR D 205 " pdb=" N SER D 206 " pdb=" CA SER D 206 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA THR E 205 " pdb=" C THR E 205 " pdb=" N SER E 206 " pdb=" CA SER E 206 " ideal model delta harmonic sigma weight residual 180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" C ILE E 422 " pdb=" N ILE E 422 " pdb=" CA ILE E 422 " pdb=" CB ILE E 422 " ideal model delta harmonic sigma weight residual -122.00 -130.47 8.47 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 17266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2967 0.069 - 0.138: 1266 0.138 - 0.207: 289 0.207 - 0.276: 38 0.276 - 0.345: 11 Chirality restraints: 4571 Sorted by residual: chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ILE F 126 " pdb=" N ILE F 126 " pdb=" C ILE F 126 " pdb=" CB ILE F 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 4568 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 73 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C GLN D 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN D 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP D 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 73 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C GLN E 73 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN E 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 73 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLN G 73 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN G 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP G 74 " 0.015 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 9942 2.88 - 3.38: 27147 3.38 - 3.89: 44301 3.89 - 4.39: 50346 4.39 - 4.90: 82812 Nonbonded interactions: 214548 Sorted by model distance: nonbonded pdb=" NZ LYS E 176 " pdb=" OE1 GLU E 321 " model vdw 2.369 3.120 nonbonded pdb=" O ASN F 204 " pdb=" C THR F 205 " model vdw 2.402 3.270 nonbonded pdb=" OD2 ASP E 183 " pdb=" NZ LYS E 391 " model vdw 2.403 3.120 nonbonded pdb=" OD2 ASP A 215 " pdb=" NZ LYS A 243 " model vdw 2.403 3.120 nonbonded pdb=" NZ LYS G 170 " pdb=" OE1 GLU G 407 " model vdw 2.404 3.120 ... (remaining 214543 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.460 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.084 27685 Z= 0.942 Angle : 1.457 10.093 37345 Z= 1.059 Chirality : 0.076 0.345 4571 Planarity : 0.007 0.027 4809 Dihedral : 9.299 76.575 10549 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: 0.22 (0.12), residues: 3668 helix: 0.11 (0.10), residues: 2065 sheet: 0.98 (0.21), residues: 553 loop : 0.11 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 500 TYR 0.029 0.003 TYR B 217 PHE 0.012 0.002 PHE D 213 TRP 0.014 0.006 TRP E 42 HIS 0.003 0.001 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.01515 (27685) covalent geometry : angle 1.45699 (37345) hydrogen bonds : bond 0.18434 ( 1757) hydrogen bonds : angle 6.66408 ( 5058) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 322 VAL cc_start: 0.7001 (t) cc_final: 0.6650 (p) REVERT: A 360 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 487 MET cc_start: 0.7402 (mmt) cc_final: 0.7169 (mpp) REVERT: A 492 ILE cc_start: 0.7573 (mt) cc_final: 0.7313 (mt) REVERT: B 218 VAL cc_start: 0.6822 (t) cc_final: 0.6405 (p) REVERT: B 360 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7075 (mm-30) REVERT: B 464 ILE cc_start: 0.7224 (mm) cc_final: 0.7003 (mm) REVERT: C 218 VAL cc_start: 0.6690 (t) cc_final: 0.6435 (p) REVERT: C 360 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6786 (mm-30) REVERT: D 218 VAL cc_start: 0.6832 (t) cc_final: 0.6486 (p) REVERT: D 285 ASN cc_start: 0.6014 (m-40) cc_final: 0.5202 (t0) REVERT: D 360 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6753 (mm-30) REVERT: D 464 ILE cc_start: 0.7452 (mm) cc_final: 0.7246 (mm) REVERT: D 487 MET cc_start: 0.7201 (mmt) cc_final: 0.6999 (mpp) REVERT: E 285 ASN cc_start: 0.5828 (m-40) cc_final: 0.5222 (t0) REVERT: E 307 ASN cc_start: 0.5077 (t0) cc_final: 0.4385 (m-40) REVERT: E 328 ASP cc_start: 0.6777 (t70) cc_final: 0.6507 (t70) REVERT: E 330 MET cc_start: 0.7502 (ttm) cc_final: 0.6992 (ttt) REVERT: E 360 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7152 (mm-30) REVERT: E 464 ILE cc_start: 0.7417 (mm) cc_final: 0.7160 (mm) REVERT: F 218 VAL cc_start: 0.6808 (t) cc_final: 0.6483 (p) REVERT: F 307 ASN cc_start: 0.5239 (t0) cc_final: 0.4654 (m-40) REVERT: G 285 ASN cc_start: 0.5887 (m-40) cc_final: 0.5201 (t0) REVERT: G 328 ASP cc_start: 0.6970 (t70) cc_final: 0.6615 (t70) REVERT: G 464 ILE cc_start: 0.7455 (mm) cc_final: 0.7227 (mm) REVERT: G 487 MET cc_start: 0.7405 (mmt) cc_final: 0.7040 (mpp) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.2156 time to fit residues: 171.9171 Evaluate side-chains 244 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN C 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.262098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.232970 restraints weight = 26875.213| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 1.22 r_work: 0.4234 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27685 Z= 0.160 Angle : 0.583 11.746 37345 Z= 0.324 Chirality : 0.044 0.166 4571 Planarity : 0.004 0.032 4809 Dihedral : 4.271 28.387 3836 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.38 % Allowed : 5.61 % Favored : 93.01 % 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 aren not related in a simple way. whole: 1.44 (0.13), residues: 3668 helix: 1.78 (0.11), residues: 2016 sheet: 0.94 (0.20), residues: 630 loop : -0.66 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.010 0.002 TYR G 64 PHE 0.017 0.002 PHE E 202 TRP 0.006 0.001 TRP B 42 HIS 0.001 0.000 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00342 (27685) covalent geometry : angle 0.58320 (37345) hydrogen bonds : bond 0.06048 ( 1757) hydrogen bonds : angle 4.84799 ( 5058) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 1.086 Fit side-chains REVERT: A 131 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7424 (ttmt) REVERT: A 223 LYS cc_start: 0.7481 (tttt) cc_final: 0.7108 (mtmm) REVERT: A 322 VAL cc_start: 0.7690 (t) cc_final: 0.7483 (p) REVERT: D 223 LYS cc_start: 0.7390 (tttt) cc_final: 0.7038 (mtmm) REVERT: D 330 MET cc_start: 0.7561 (ttp) cc_final: 0.6936 (ttt) REVERT: D 487 MET cc_start: 0.7297 (mmt) cc_final: 0.6863 (mpp) REVERT: E 328 ASP cc_start: 0.6773 (t70) cc_final: 0.6524 (t0) REVERT: E 330 MET cc_start: 0.7674 (ttm) cc_final: 0.7327 (ttt) REVERT: E 494 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7695 (t0) REVERT: F 131 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7432 (ttmt) REVERT: F 223 LYS cc_start: 0.7398 (tttt) cc_final: 0.7094 (mtmm) REVERT: F 307 ASN cc_start: 0.5231 (t0) cc_final: 0.4661 (m-40) REVERT: G 328 ASP cc_start: 0.7036 (t70) cc_final: 0.6719 (t0) REVERT: G 487 MET cc_start: 0.7514 (mmt) cc_final: 0.6891 (mpp) outliers start: 41 outliers final: 18 residues processed: 339 average time/residue: 0.2167 time to fit residues: 111.5903 Evaluate side-chains 221 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 133 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 146 optimal weight: 0.3980 chunk 42 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 306 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.260992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.237961 restraints weight = 27059.507| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 0.96 r_work: 0.4344 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27685 Z= 0.120 Angle : 0.490 10.639 37345 Z= 0.271 Chirality : 0.042 0.169 4571 Planarity : 0.004 0.038 4809 Dihedral : 4.017 28.304 3836 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.71 % Allowed : 7.33 % Favored : 90.96 % 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 aren not related in a simple way. whole: 1.68 (0.14), residues: 3668 helix: 2.18 (0.11), residues: 2009 sheet: 0.53 (0.20), residues: 644 loop : -0.65 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 344 TYR 0.007 0.001 TYR G 359 PHE 0.020 0.002 PHE E 202 TRP 0.008 0.001 TRP C 42 HIS 0.001 0.000 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00247 (27685) covalent geometry : angle 0.49042 (37345) hydrogen bonds : bond 0.04621 ( 1757) hydrogen bonds : angle 4.44599 ( 5058) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 1.099 Fit side-chains REVERT: A 131 LYS cc_start: 0.7634 (ttmm) cc_final: 0.7368 (ttmt) REVERT: A 185 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6969 (tt) REVERT: D 131 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7347 (ttmt) REVERT: D 330 MET cc_start: 0.7491 (ttp) cc_final: 0.6865 (ttt) REVERT: D 367 ARG cc_start: 0.6517 (mtp85) cc_final: 0.5954 (mtp85) REVERT: D 487 MET cc_start: 0.7339 (mmt) cc_final: 0.6885 (mpp) REVERT: E 330 MET cc_start: 0.7588 (ttm) cc_final: 0.7350 (ttt) REVERT: E 494 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7608 (t0) REVERT: F 131 LYS cc_start: 0.7595 (ttmm) cc_final: 0.7359 (ttmt) REVERT: F 307 ASN cc_start: 0.4936 (t0) cc_final: 0.4479 (m-40) REVERT: G 328 ASP cc_start: 0.6857 (t70) cc_final: 0.6584 (t0) REVERT: G 487 MET cc_start: 0.7388 (mmt) cc_final: 0.6902 (mpp) outliers start: 51 outliers final: 24 residues processed: 278 average time/residue: 0.1964 time to fit residues: 86.8376 Evaluate side-chains 238 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 427 SER Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 161 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 357 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.247704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.223661 restraints weight = 27184.525| |-----------------------------------------------------------------------------| r_work (start): 0.4472 rms_B_bonded: 1.02 r_work: 0.4215 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27685 Z= 0.198 Angle : 0.601 9.827 37345 Z= 0.327 Chirality : 0.046 0.194 4571 Planarity : 0.005 0.042 4809 Dihedral : 4.321 30.462 3836 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.22 % Allowed : 8.13 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.14), residues: 3668 helix: 1.75 (0.12), residues: 2051 sheet: 0.31 (0.20), residues: 630 loop : -1.38 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.010 0.002 TYR D 64 PHE 0.013 0.002 PHE C 202 TRP 0.018 0.003 TRP D 42 HIS 0.002 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00473 (27685) covalent geometry : angle 0.60108 (37345) hydrogen bonds : bond 0.06246 ( 1757) hydrogen bonds : angle 4.53297 ( 5058) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 1.109 Fit side-chains REVERT: A 131 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7445 (ttmt) REVERT: D 131 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7559 (ttmt) REVERT: D 217 TYR cc_start: 0.5006 (m-80) cc_final: 0.4497 (m-80) REVERT: D 487 MET cc_start: 0.7518 (mmt) cc_final: 0.6896 (mpp) REVERT: E 307 ASN cc_start: 0.5647 (t0) cc_final: 0.4609 (m-40) REVERT: E 330 MET cc_start: 0.7583 (ttm) cc_final: 0.7158 (ttt) REVERT: E 367 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6294 (mtp85) REVERT: E 494 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7687 (t0) REVERT: F 131 LYS cc_start: 0.7688 (ttmm) cc_final: 0.7450 (ttmt) REVERT: G 290 MET cc_start: 0.5742 (mtp) cc_final: 0.5483 (mtp) REVERT: G 328 ASP cc_start: 0.7104 (t70) cc_final: 0.6703 (t70) REVERT: G 487 MET cc_start: 0.7598 (mmt) cc_final: 0.6981 (mpp) outliers start: 66 outliers final: 39 residues processed: 314 average time/residue: 0.1904 time to fit residues: 95.2702 Evaluate side-chains 259 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain F residue 515 THR Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 515 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 231 optimal weight: 0.0770 chunk 236 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 300 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.252111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.228792 restraints weight = 26928.421| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 0.99 r_work: 0.4271 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27685 Z= 0.125 Angle : 0.483 8.830 37345 Z= 0.264 Chirality : 0.042 0.155 4571 Planarity : 0.004 0.038 4809 Dihedral : 4.024 29.441 3836 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.42 % Allowed : 9.58 % Favored : 88.00 % 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 aren not related in a simple way. whole: 1.32 (0.14), residues: 3668 helix: 2.09 (0.12), residues: 2030 sheet: 0.31 (0.20), residues: 630 loop : -1.29 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 367 TYR 0.010 0.001 TYR A 477 PHE 0.019 0.002 PHE C 202 TRP 0.010 0.002 TRP D 42 HIS 0.001 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00280 (27685) covalent geometry : angle 0.48285 (37345) hydrogen bonds : bond 0.04592 ( 1757) hydrogen bonds : angle 4.29979 ( 5058) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 231 time to evaluate : 1.054 Fit side-chains REVERT: A 70 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7706 (mtpt) REVERT: A 131 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7444 (ttpt) REVERT: A 367 ARG cc_start: 0.6458 (mtp85) cc_final: 0.6006 (mtp85) REVERT: B 373 ASP cc_start: 0.5812 (t70) cc_final: 0.5590 (t70) REVERT: D 131 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7466 (ttmt) REVERT: D 217 TYR cc_start: 0.4876 (m-80) cc_final: 0.4422 (m-80) REVERT: D 487 MET cc_start: 0.7572 (mmt) cc_final: 0.6950 (mpp) REVERT: E 131 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7579 (ttpt) REVERT: E 330 MET cc_start: 0.7615 (ttm) cc_final: 0.7156 (ttt) REVERT: E 494 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7703 (t0) REVERT: F 131 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7418 (ttmt) REVERT: F 217 TYR cc_start: 0.4946 (m-80) cc_final: 0.4482 (m-80) REVERT: G 328 ASP cc_start: 0.7103 (t70) cc_final: 0.6749 (t0) REVERT: G 487 MET cc_start: 0.7456 (mmt) cc_final: 0.6971 (mpp) outliers start: 72 outliers final: 40 residues processed: 288 average time/residue: 0.1942 time to fit residues: 88.1929 Evaluate side-chains 257 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 79 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 chunk 249 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 321 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.252625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.229582 restraints weight = 26898.380| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 1.01 r_work: 0.4278 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27685 Z= 0.114 Angle : 0.473 8.869 37345 Z= 0.255 Chirality : 0.042 0.149 4571 Planarity : 0.004 0.039 4809 Dihedral : 3.901 28.844 3836 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.15 % Allowed : 10.05 % Favored : 87.80 % 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 aren not related in a simple way. whole: 1.42 (0.14), residues: 3668 helix: 2.20 (0.12), residues: 2030 sheet: 0.33 (0.20), residues: 595 loop : -1.26 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 367 TYR 0.012 0.001 TYR A 477 PHE 0.017 0.002 PHE E 202 TRP 0.008 0.001 TRP D 42 HIS 0.001 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00250 (27685) covalent geometry : angle 0.47322 (37345) hydrogen bonds : bond 0.04286 ( 1757) hydrogen bonds : angle 4.22724 ( 5058) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 1.188 Fit side-chains REVERT: A 70 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7744 (mtmt) REVERT: A 131 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7463 (ttpt) REVERT: D 131 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7445 (ttmt) REVERT: D 217 TYR cc_start: 0.4997 (m-80) cc_final: 0.4537 (m-80) REVERT: D 487 MET cc_start: 0.7538 (mmt) cc_final: 0.6910 (mpp) REVERT: E 131 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7564 (ttpt) REVERT: E 330 MET cc_start: 0.7623 (ttm) cc_final: 0.7154 (ttt) REVERT: E 494 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7719 (t0) REVERT: E 505 ASP cc_start: 0.7214 (m-30) cc_final: 0.7009 (m-30) REVERT: F 131 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7342 (ttmt) REVERT: F 217 TYR cc_start: 0.4931 (m-80) cc_final: 0.4467 (m-80) REVERT: G 328 ASP cc_start: 0.7065 (t70) cc_final: 0.6707 (t0) REVERT: G 487 MET cc_start: 0.7423 (mmt) cc_final: 0.6951 (mpp) outliers start: 64 outliers final: 43 residues processed: 284 average time/residue: 0.1991 time to fit residues: 89.2026 Evaluate side-chains 265 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 57 optimal weight: 0.6980 chunk 346 optimal weight: 0.9980 chunk 300 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.246887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.223289 restraints weight = 26908.500| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 1.02 r_work: 0.4217 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 27685 Z= 0.152 Angle : 0.529 9.274 37345 Z= 0.285 Chirality : 0.044 0.196 4571 Planarity : 0.004 0.039 4809 Dihedral : 4.043 28.965 3836 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 10.59 % Favored : 87.03 % 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 aren not related in a simple way. whole: 1.16 (0.14), residues: 3668 helix: 2.02 (0.12), residues: 2051 sheet: 0.17 (0.20), residues: 595 loop : -1.48 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 367 TYR 0.013 0.001 TYR A 477 PHE 0.017 0.002 PHE C 202 TRP 0.010 0.002 TRP D 42 HIS 0.002 0.001 HIS C 314 Details of bonding type rmsd covalent geometry : bond 0.00363 (27685) covalent geometry : angle 0.52881 (37345) hydrogen bonds : bond 0.05244 ( 1757) hydrogen bonds : angle 4.33458 ( 5058) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 229 time to evaluate : 1.059 Fit side-chains REVERT: A 70 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7719 (mtpt) REVERT: D 131 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7534 (ttmt) REVERT: D 217 TYR cc_start: 0.4948 (m-80) cc_final: 0.4531 (m-80) REVERT: D 307 ASN cc_start: 0.5335 (t0) cc_final: 0.5079 (t0) REVERT: D 487 MET cc_start: 0.7608 (mmt) cc_final: 0.6940 (mpp) REVERT: E 131 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7620 (ttpt) REVERT: E 330 MET cc_start: 0.7605 (ttm) cc_final: 0.7131 (ttt) REVERT: F 131 LYS cc_start: 0.7682 (ttmm) cc_final: 0.7391 (ttmt) REVERT: F 217 TYR cc_start: 0.4996 (m-80) cc_final: 0.4547 (m-80) REVERT: F 487 MET cc_start: 0.6821 (OUTLIER) cc_final: 0.6444 (mpp) REVERT: G 217 TYR cc_start: 0.5012 (m-80) cc_final: 0.4486 (m-80) REVERT: G 328 ASP cc_start: 0.7036 (t70) cc_final: 0.6709 (t0) REVERT: G 487 MET cc_start: 0.7487 (mmt) cc_final: 0.6918 (mpp) outliers start: 71 outliers final: 55 residues processed: 283 average time/residue: 0.2003 time to fit residues: 88.9048 Evaluate side-chains 274 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain G residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 123 optimal weight: 0.0040 chunk 159 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 307 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.250713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.227673 restraints weight = 26999.102| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 1.02 r_work: 0.4265 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27685 Z= 0.109 Angle : 0.477 9.020 37345 Z= 0.255 Chirality : 0.041 0.178 4571 Planarity : 0.004 0.040 4809 Dihedral : 3.884 28.431 3836 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.78 % Allowed : 11.76 % Favored : 86.45 % 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 aren not related in a simple way. whole: 1.41 (0.14), residues: 3668 helix: 2.23 (0.12), residues: 2030 sheet: 0.27 (0.20), residues: 595 loop : -1.32 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 367 TYR 0.011 0.001 TYR A 477 PHE 0.019 0.002 PHE A 299 TRP 0.006 0.001 TRP D 42 HIS 0.001 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00239 (27685) covalent geometry : angle 0.47743 (37345) hydrogen bonds : bond 0.04166 ( 1757) hydrogen bonds : angle 4.21604 ( 5058) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 1.066 Fit side-chains REVERT: A 70 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7763 (mtmt) REVERT: C 328 ASP cc_start: 0.6601 (t0) cc_final: 0.6244 (t70) REVERT: D 131 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7466 (ttmt) REVERT: D 217 TYR cc_start: 0.4969 (m-80) cc_final: 0.4504 (m-80) REVERT: D 487 MET cc_start: 0.7505 (mmt) cc_final: 0.6839 (mpp) REVERT: E 131 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7526 (ttpt) REVERT: E 330 MET cc_start: 0.7581 (ttm) cc_final: 0.7317 (ttt) REVERT: E 494 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7659 (t0) REVERT: F 131 LYS cc_start: 0.7669 (ttmm) cc_final: 0.7369 (ttmt) REVERT: F 217 TYR cc_start: 0.4891 (m-80) cc_final: 0.4447 (m-80) REVERT: G 217 TYR cc_start: 0.4945 (m-80) cc_final: 0.4416 (m-80) REVERT: G 328 ASP cc_start: 0.6964 (t70) cc_final: 0.6632 (t0) REVERT: G 487 MET cc_start: 0.7444 (mmt) cc_final: 0.6944 (mpp) outliers start: 53 outliers final: 41 residues processed: 271 average time/residue: 0.2029 time to fit residues: 85.7457 Evaluate side-chains 264 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 496 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain G residue 494 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.7957 > 50: distance: 33 - 37: 3.966 distance: 37 - 38: 5.978 distance: 38 - 39: 4.866 distance: 38 - 41: 5.986 distance: 39 - 40: 13.554 distance: 39 - 44: 14.017 distance: 41 - 42: 5.536 distance: 41 - 43: 11.142 distance: 44 - 45: 15.184 distance: 45 - 46: 15.192 distance: 45 - 48: 14.289 distance: 46 - 47: 16.370 distance: 46 - 52: 6.848 distance: 48 - 49: 10.627 distance: 49 - 50: 9.897 distance: 49 - 51: 11.635 distance: 52 - 53: 14.925 distance: 53 - 54: 7.443 distance: 53 - 56: 19.886 distance: 54 - 55: 51.940 distance: 54 - 61: 21.524 distance: 56 - 57: 22.645 distance: 58 - 59: 12.257 distance: 58 - 60: 4.247 distance: 61 - 62: 23.175 distance: 62 - 63: 27.724 distance: 62 - 65: 6.037 distance: 63 - 64: 22.358 distance: 63 - 70: 27.446 distance: 65 - 66: 17.850 distance: 66 - 67: 12.662 distance: 67 - 68: 32.161 distance: 67 - 69: 28.792 distance: 70 - 71: 22.432 distance: 71 - 72: 13.682 distance: 71 - 74: 20.564 distance: 72 - 73: 9.860 distance: 72 - 75: 5.627 distance: 75 - 76: 12.631 distance: 76 - 77: 6.556 distance: 77 - 78: 6.491 distance: 77 - 79: 21.054 distance: 79 - 80: 25.522 distance: 80 - 81: 14.051 distance: 80 - 83: 15.566 distance: 81 - 82: 12.074 distance: 81 - 87: 24.157 distance: 83 - 84: 14.682 distance: 84 - 85: 24.851 distance: 84 - 86: 26.449 distance: 87 - 88: 7.270 distance: 88 - 89: 11.915 distance: 89 - 90: 12.651 distance: 89 - 91: 16.427 distance: 90 - 112: 18.584 distance: 91 - 92: 8.179 distance: 92 - 93: 10.186 distance: 92 - 95: 4.102 distance: 93 - 94: 6.639 distance: 93 - 98: 5.201 distance: 94 - 117: 19.542 distance: 95 - 96: 12.102 distance: 95 - 97: 7.100 distance: 98 - 99: 5.805 distance: 99 - 100: 9.082 distance: 99 - 102: 10.460 distance: 100 - 101: 10.807 distance: 100 - 105: 12.290 distance: 101 - 123: 8.474 distance: 102 - 103: 25.787 distance: 102 - 104: 21.218