Starting phenix.real_space_refine on Mon Aug 25 10:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7k_29814/08_2025/8g7k_29814.map" } resolution = 3.8 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= -0.001 sd= 0.082 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 26 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: 7.61, per 1000 atoms: 0.28 Number of scatterers: 27461 At special positions: 0 Unit cell: (164.079, 161.298, 91.773, 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: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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 31 sheets defined 58.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.905A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.747A 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 64 through 77 removed outlier: 3.574A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 4.520A pdb=" N THR A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 3.889A 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 removed outlier: 3.517A pdb=" N LEU A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) 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: 3.595A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.036A pdb=" N GLU A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.106A 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 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.502A pdb=" N GLU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) 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: 3.971A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.768A 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 62 through 77 removed outlier: 3.569A pdb=" N ILE B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 4.512A pdb=" N THR B 88 " --> pdb=" O GLY B 84 " (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 280 through 295 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.511A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 removed outlier: 3.681A pdb=" N GLU B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.023A 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: 3.510A 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 removed outlier: 3.521A pdb=" N GLU B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) 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: 3.876A pdb=" N LEU C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.920A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 107 removed outlier: 4.558A pdb=" N THR C 88 " --> pdb=" O GLY C 84 " (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 removed outlier: 3.512A pdb=" N LEU C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) 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: 3.554A pdb=" N LEU C 371 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.061A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.843A 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 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: 3.909A pdb=" N LEU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.762A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 107 removed outlier: 4.350A 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 removed outlier: 4.239A pdb=" N LEU D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 337 through 355 Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 409 removed outlier: 4.031A pdb=" N GLU D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.945A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.897A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 72 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 107 removed outlier: 4.002A pdb=" N THR E 88 " --> pdb=" O GLY E 84 " (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 removed outlier: 3.575A pdb=" N LEU E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) 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: 3.647A pdb=" N LEU E 371 " --> pdb=" O ARG E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 removed outlier: 4.119A pdb=" N GLU E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.949A 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 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: 3.900A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.782A 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: 3.808A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 107 removed outlier: 4.552A pdb=" N THR F 88 " --> pdb=" O GLY F 84 " (cutoff:3.500A) removed outlier: 3.534A 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 removed outlier: 3.563A pdb=" N LEU F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 337 through 355 Processing helix chain 'F' and resid 357 through 373 removed outlier: 3.599A pdb=" N LEU F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 removed outlier: 3.576A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 4.174A 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 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: 3.941A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.846A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 107 removed outlier: 4.530A pdb=" N THR G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 89 " --> pdb=" O ASP G 85 " (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 removed outlier: 3.550A pdb=" N LEU G 235 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 337 through 355 Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 409 removed outlier: 4.042A pdb=" N GLU G 390 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 3.966A 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: 3.512A 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: 6.538A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.239A 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: 6.621A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.356A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.076A pdb=" N ILE A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 177 removed outlier: 8.030A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 321 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 214 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 323 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 212 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 177 removed outlier: 8.030A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 321 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 214 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 323 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 212 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N PHE B 299 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU B 220 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.544A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 190 through 193 removed outlier: 6.387A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.066A 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: 6.634A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB7, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AB8, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 177 removed outlier: 8.069A pdb=" N GLU D 189 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU D 321 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN D 214 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 323 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU D 212 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AC3, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AC4, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.667A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU E 189 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC6, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AC7, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AC8, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.648A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLU F 189 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU F 321 " --> pdb=" O GLN F 214 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN F 214 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE F 323 " --> pdb=" O GLU F 212 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU F 212 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AD1, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AD2, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.720A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU G 189 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU G 321 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN G 214 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE G 323 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU G 212 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AD4, first strand: chain 'G' and resid 475 through 478 1807 hydrogen bonds defined for protein. 5184 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: 6.41 Time building geometry restraints manager: 3.45 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: 5476 1.31 - 1.44: 5180 1.44 - 1.56: 16810 1.56 - 1.69: 44 1.69 - 1.81: 175 Bond restraints: 27685 Sorted by residual: bond pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE G 448 " pdb=" CA ILE G 448 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE D 448 " pdb=" CA ILE D 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.23e+01 bond pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.21e+01 ... (remaining 27680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 32374 2.01 - 4.03: 4199 4.03 - 6.04: 643 6.04 - 8.06: 88 8.06 - 10.07: 41 Bond angle restraints: 37345 Sorted by residual: angle pdb=" N ILE D 231 " pdb=" CA ILE D 231 " pdb=" C ILE D 231 " ideal model delta sigma weight residual 112.90 103.43 9.47 9.60e-01 1.09e+00 9.72e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.43 103.36 10.07 1.09e+00 8.42e-01 8.54e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 113.43 103.36 10.07 1.09e+00 8.42e-01 8.53e+01 angle pdb=" N ILE G 231 " pdb=" CA ILE G 231 " pdb=" C ILE G 231 " ideal model delta sigma weight residual 113.43 103.38 10.05 1.09e+00 8.42e-01 8.51e+01 angle pdb=" C ALA F 276 " pdb=" N PRO F 277 " pdb=" CA PRO F 277 " ideal model delta sigma weight residual 119.56 128.47 -8.91 1.01e+00 9.80e-01 7.79e+01 ... (remaining 37340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 16746 15.67 - 31.33: 369 31.33 - 47.00: 85 47.00 - 62.67: 41 62.67 - 78.33: 28 Dihedral angle restraints: 17269 sinusoidal: 6832 harmonic: 10437 Sorted by residual: dihedral pdb=" CA THR C 205 " pdb=" C THR C 205 " pdb=" N SER C 206 " pdb=" CA SER C 206 " ideal model delta harmonic sigma weight residual 180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA THR A 205 " pdb=" C THR A 205 " pdb=" N SER A 206 " pdb=" CA SER A 206 " ideal model delta harmonic sigma weight residual 180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+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 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 17266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2448 0.052 - 0.104: 1523 0.104 - 0.156: 408 0.156 - 0.208: 167 0.208 - 0.260: 25 Chirality restraints: 4571 Sorted by residual: chirality pdb=" CA PRO A 277 " pdb=" N PRO A 277 " pdb=" C PRO A 277 " pdb=" CB PRO A 277 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLU A 408 " pdb=" N GLU A 408 " pdb=" C GLU A 408 " pdb=" CB GLU A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLU D 408 " pdb=" N GLU D 408 " pdb=" C GLU D 408 " pdb=" CB GLU D 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4568 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 73 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN C 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN C 73 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 73 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C GLN D 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN D 73 " 0.017 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 A 73 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C GLN A 73 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN A 73 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 74 " -0.015 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9755 2.87 - 3.38: 27152 3.38 - 3.88: 44041 3.88 - 4.39: 50232 4.39 - 4.90: 82929 Nonbonded interactions: 214109 Sorted by model distance: nonbonded pdb=" NZ LYS C 176 " pdb=" OE1 GLU C 321 " model vdw 2.362 3.120 nonbonded pdb=" N ASP C 281 " pdb=" OD1 ASP C 281 " model vdw 2.386 3.120 nonbonded pdb=" NZ LYS B 192 " pdb=" OD1 ASP B 328 " model vdw 2.386 3.120 nonbonded pdb=" OD2 ASP F 183 " pdb=" NZ LYS F 391 " model vdw 2.386 3.120 nonbonded pdb=" NZ LYS D 192 " pdb=" OD1 ASP D 328 " model vdw 2.390 3.120 ... (remaining 214104 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.020 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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= 0.932 Angle : 1.439 10.074 37345 Z= 1.052 Chirality : 0.072 0.260 4571 Planarity : 0.007 0.026 4809 Dihedral : 9.236 78.332 10549 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.82 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.30 (0.12), residues: 3668 helix: 0.21 (0.10), residues: 2023 sheet: 0.99 (0.21), residues: 553 loop : 0.08 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 500 TYR 0.028 0.002 TYR E 217 PHE 0.012 0.001 PHE F 213 TRP 0.015 0.004 TRP G 42 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.01480 (27685) covalent geometry : angle 1.43929 (37345) hydrogen bonds : bond 0.18490 ( 1782) hydrogen bonds : angle 6.52341 ( 5184) *********************** 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 805 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 805 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7009 (t70) cc_final: 0.6744 (t0) REVERT: A 244 PRO cc_start: 0.7107 (Cg_exo) cc_final: 0.6858 (Cg_endo) REVERT: A 271 VAL cc_start: 0.7239 (p) cc_final: 0.6877 (t) REVERT: A 308 LEU cc_start: 0.7617 (mt) cc_final: 0.6961 (pt) REVERT: A 464 ILE cc_start: 0.8416 (mm) cc_final: 0.8194 (mm) REVERT: A 487 MET cc_start: 0.7500 (mmt) cc_final: 0.7281 (tpp) REVERT: B 231 ILE cc_start: 0.7117 (pt) cc_final: 0.6826 (pt) REVERT: B 464 ILE cc_start: 0.8734 (mm) cc_final: 0.8522 (mm) REVERT: C 211 CYS cc_start: 0.8635 (t) cc_final: 0.8042 (m) REVERT: C 228 ILE cc_start: 0.7825 (mm) cc_final: 0.7608 (mm) REVERT: C 304 LEU cc_start: 0.8789 (tp) cc_final: 0.7959 (pt) REVERT: C 487 MET cc_start: 0.7723 (mmt) cc_final: 0.6917 (mmm) REVERT: D 213 PHE cc_start: 0.8618 (m-80) cc_final: 0.8305 (m-10) REVERT: D 279 PHE cc_start: 0.6549 (t80) cc_final: 0.6017 (t80) REVERT: E 338 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7452 (ttmt) REVERT: E 385 ASP cc_start: 0.6998 (p0) cc_final: 0.6667 (m-30) REVERT: E 523 ILE cc_start: 0.8370 (mt) cc_final: 0.8042 (tt) REVERT: G 205 THR cc_start: 0.8058 (p) cc_final: 0.7833 (t) REVERT: G 244 PRO cc_start: 0.7417 (Cg_exo) cc_final: 0.7062 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 805 average time/residue: 0.2046 time to fit residues: 252.1537 Evaluate side-chains 342 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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: 0.8980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 346 GLN B 77 ASN B 282 ASN C 77 ASN D 214 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN F 78 ASN F 340 GLN G 229 GLN G 282 ASN G 351 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125192 restraints weight = 44557.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128417 restraints weight = 28846.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130664 restraints weight = 21107.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132240 restraints weight = 16774.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133197 restraints weight = 14087.420| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27685 Z= 0.153 Angle : 0.576 7.283 37345 Z= 0.323 Chirality : 0.044 0.263 4571 Planarity : 0.004 0.047 4809 Dihedral : 4.273 31.358 3836 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.95 % Allowed : 8.87 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.76 (0.13), residues: 3668 helix: 2.08 (0.11), residues: 1979 sheet: 1.01 (0.20), residues: 629 loop : -0.49 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 367 TYR 0.014 0.002 TYR A 477 PHE 0.021 0.002 PHE A 484 TRP 0.021 0.002 TRP B 42 HIS 0.002 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00330 (27685) covalent geometry : angle 0.57580 (37345) hydrogen bonds : bond 0.05377 ( 1782) hydrogen bonds : angle 4.57699 ( 5184) *********************** 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 447 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 389 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.7579 (mt) cc_final: 0.7259 (pt) REVERT: B 464 ILE cc_start: 0.9049 (mm) cc_final: 0.8787 (mm) REVERT: B 487 MET cc_start: 0.8314 (mmt) cc_final: 0.7649 (mmm) REVERT: C 61 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7023 (ptmt) REVERT: C 228 ILE cc_start: 0.8383 (mm) cc_final: 0.8179 (mm) REVERT: C 304 LEU cc_start: 0.8433 (tp) cc_final: 0.7677 (pt) REVERT: C 397 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: D 198 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8471 (mm) REVERT: D 213 PHE cc_start: 0.8544 (m-80) cc_final: 0.8310 (m-10) REVERT: E 74 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7951 (t0) REVERT: E 191 MET cc_start: 0.6999 (ptm) cc_final: 0.6782 (ptp) REVERT: E 215 ASP cc_start: 0.6598 (t0) cc_final: 0.6310 (t0) REVERT: E 221 SER cc_start: 0.6459 (t) cc_final: 0.6241 (p) REVERT: E 385 ASP cc_start: 0.6344 (p0) cc_final: 0.5779 (p0) REVERT: F 153 ASP cc_start: 0.7912 (t0) cc_final: 0.7610 (t0) REVERT: F 345 ILE cc_start: 0.8903 (mt) cc_final: 0.8603 (mm) REVERT: F 487 MET cc_start: 0.8137 (tpp) cc_final: 0.7850 (tpp) REVERT: G 282 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7166 (m-40) REVERT: G 351 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7370 (mp10) outliers start: 58 outliers final: 29 residues processed: 433 average time/residue: 0.1759 time to fit residues: 123.5188 Evaluate side-chains 284 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 290 MET Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 351 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 133 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 232 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 306 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN D 282 ASN E 282 ASN G 282 ASN G 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.147087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123125 restraints weight = 44836.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125951 restraints weight = 30075.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127939 restraints weight = 22642.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129352 restraints weight = 18357.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130298 restraints weight = 15671.196| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27685 Z= 0.124 Angle : 0.506 7.228 37345 Z= 0.281 Chirality : 0.042 0.207 4571 Planarity : 0.004 0.045 4809 Dihedral : 4.021 31.120 3836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.08 % Allowed : 10.69 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.93 (0.14), residues: 3668 helix: 2.40 (0.12), residues: 1980 sheet: 0.88 (0.20), residues: 628 loop : -0.67 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 367 TYR 0.011 0.001 TYR G 359 PHE 0.024 0.002 PHE C 102 TRP 0.025 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00262 (27685) covalent geometry : angle 0.50562 (37345) hydrogen bonds : bond 0.04510 ( 1782) hydrogen bonds : angle 4.16710 ( 5184) *********************** 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 354 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.7489 (mt) cc_final: 0.7210 (pt) REVERT: B 464 ILE cc_start: 0.9047 (mm) cc_final: 0.8755 (mm) REVERT: C 304 LEU cc_start: 0.8335 (tp) cc_final: 0.7660 (pt) REVERT: D 198 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8546 (mm) REVERT: D 213 PHE cc_start: 0.8587 (m-80) cc_final: 0.8364 (m-10) REVERT: E 290 MET cc_start: 0.7516 (mmt) cc_final: 0.7205 (mmt) REVERT: E 385 ASP cc_start: 0.5984 (p0) cc_final: 0.5550 (p0) REVERT: F 153 ASP cc_start: 0.7972 (t0) cc_final: 0.7674 (t0) REVERT: F 191 MET cc_start: 0.7660 (ptm) cc_final: 0.6874 (ptp) REVERT: F 345 ILE cc_start: 0.8904 (mt) cc_final: 0.8663 (mm) REVERT: G 284 LYS cc_start: 0.8404 (mttt) cc_final: 0.7945 (mttt) outliers start: 62 outliers final: 41 residues processed: 345 average time/residue: 0.1703 time to fit residues: 97.0538 Evaluate side-chains 278 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 161 optimal weight: 0.9990 chunk 349 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 233 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 200 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 chunk 357 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN E 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117917 restraints weight = 44831.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120708 restraints weight = 30461.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122538 restraints weight = 23158.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123998 restraints weight = 19044.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124906 restraints weight = 16428.024| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27685 Z= 0.143 Angle : 0.512 6.385 37345 Z= 0.282 Chirality : 0.043 0.191 4571 Planarity : 0.004 0.044 4809 Dihedral : 4.030 29.636 3836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.59 % Allowed : 11.63 % Favored : 85.78 % 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: 1.80 (0.14), residues: 3668 helix: 2.38 (0.12), residues: 1998 sheet: 1.00 (0.20), residues: 616 loop : -1.08 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 283 TYR 0.008 0.001 TYR G 217 PHE 0.018 0.002 PHE E 279 TRP 0.025 0.002 TRP D 42 HIS 0.002 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00325 (27685) covalent geometry : angle 0.51195 (37345) hydrogen bonds : bond 0.04666 ( 1782) hydrogen bonds : angle 4.08150 ( 5184) *********************** 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 344 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 267 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.6070 (mtt) cc_final: 0.5795 (mtt) REVERT: C 290 MET cc_start: 0.6886 (mtt) cc_final: 0.6615 (mtt) REVERT: C 304 LEU cc_start: 0.8450 (tp) cc_final: 0.7737 (pt) REVERT: D 269 LEU cc_start: 0.7441 (mp) cc_final: 0.7123 (tp) REVERT: E 215 ASP cc_start: 0.6782 (t0) cc_final: 0.5512 (t0) REVERT: E 385 ASP cc_start: 0.6241 (p0) cc_final: 0.5925 (m-30) REVERT: F 153 ASP cc_start: 0.7977 (t0) cc_final: 0.7702 (t0) REVERT: F 202 PHE cc_start: 0.7558 (m-80) cc_final: 0.7261 (m-80) REVERT: G 9 ASP cc_start: 0.7039 (t0) cc_final: 0.6801 (t0) outliers start: 77 outliers final: 59 residues processed: 332 average time/residue: 0.1639 time to fit residues: 91.2952 Evaluate side-chains 285 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 226 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR 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: 10.0000 chunk 236 optimal weight: 0.9980 chunk 225 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 268 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 282 ASN D 282 ASN E 77 ASN E 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.143282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118984 restraints weight = 44400.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121775 restraints weight = 30097.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123760 restraints weight = 22765.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125106 restraints weight = 18601.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126073 restraints weight = 15993.722| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27685 Z= 0.119 Angle : 0.481 9.133 37345 Z= 0.263 Chirality : 0.042 0.214 4571 Planarity : 0.004 0.062 4809 Dihedral : 3.918 28.101 3836 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.55 % Allowed : 12.00 % Favored : 85.45 % 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: 1.90 (0.14), residues: 3668 helix: 2.54 (0.12), residues: 1998 sheet: 0.81 (0.20), residues: 628 loop : -1.07 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 367 TYR 0.008 0.001 TYR G 359 PHE 0.024 0.002 PHE C 102 TRP 0.027 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00255 (27685) covalent geometry : angle 0.48077 (37345) hydrogen bonds : bond 0.04133 ( 1782) hydrogen bonds : angle 3.94968 ( 5184) *********************** 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 334 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 258 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.6099 (mtt) cc_final: 0.5827 (mtt) REVERT: C 224 LYS cc_start: 0.8440 (tttt) cc_final: 0.8181 (tttm) REVERT: C 304 LEU cc_start: 0.8411 (tp) cc_final: 0.7730 (pt) REVERT: D 260 LEU cc_start: 0.8347 (mm) cc_final: 0.8084 (mt) REVERT: E 215 ASP cc_start: 0.6862 (t0) cc_final: 0.6288 (t0) REVERT: F 153 ASP cc_start: 0.8015 (t0) cc_final: 0.7731 (t0) REVERT: F 202 PHE cc_start: 0.7294 (m-80) cc_final: 0.7070 (m-80) REVERT: F 487 MET cc_start: 0.8425 (tpp) cc_final: 0.7383 (mpp) REVERT: G 9 ASP cc_start: 0.6937 (t0) cc_final: 0.6689 (t0) REVERT: G 194 ASP cc_start: 0.6651 (t0) cc_final: 0.6442 (t0) REVERT: G 223 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8106 (pttm) REVERT: G 289 ASP cc_start: 0.7582 (m-30) cc_final: 0.7376 (m-30) outliers start: 76 outliers final: 60 residues processed: 320 average time/residue: 0.1609 time to fit residues: 86.6351 Evaluate side-chains 286 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 226 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 79 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 249 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 321 optimal weight: 0.9980 chunk 208 optimal weight: 10.0000 chunk 296 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117191 restraints weight = 44591.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119927 restraints weight = 30446.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121749 restraints weight = 23235.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123170 restraints weight = 19103.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124144 restraints weight = 16515.850| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27685 Z= 0.123 Angle : 0.486 7.352 37345 Z= 0.265 Chirality : 0.042 0.188 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.877 25.256 3836 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.59 % Allowed : 12.30 % Favored : 85.11 % 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: 1.78 (0.14), residues: 3668 helix: 2.45 (0.12), residues: 2034 sheet: 0.93 (0.20), residues: 616 loop : -1.40 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 444 TYR 0.009 0.001 TYR G 217 PHE 0.020 0.002 PHE E 279 TRP 0.029 0.002 TRP D 42 HIS 0.002 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00273 (27685) covalent geometry : angle 0.48602 (37345) hydrogen bonds : bond 0.04213 ( 1782) hydrogen bonds : angle 3.91631 ( 5184) *********************** 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 319 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.6140 (mtt) cc_final: 0.5910 (mtt) REVERT: B 74 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7938 (t0) REVERT: B 119 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: C 224 LYS cc_start: 0.8408 (tttt) cc_final: 0.8156 (tttm) REVERT: C 304 LEU cc_start: 0.8431 (tp) cc_final: 0.7758 (pt) REVERT: E 61 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7829 (ttmt) REVERT: E 215 ASP cc_start: 0.6919 (t0) cc_final: 0.6696 (t0) REVERT: F 153 ASP cc_start: 0.8040 (t0) cc_final: 0.7768 (t0) REVERT: F 202 PHE cc_start: 0.7232 (m-80) cc_final: 0.6959 (m-80) REVERT: F 205 THR cc_start: 0.8384 (t) cc_final: 0.7996 (t) REVERT: F 487 MET cc_start: 0.8419 (tpp) cc_final: 0.7399 (mpp) REVERT: G 9 ASP cc_start: 0.6976 (t0) cc_final: 0.6727 (t0) REVERT: G 119 MET cc_start: 0.7638 (tpp) cc_final: 0.7431 (tpp) REVERT: G 284 LYS cc_start: 0.8451 (mttt) cc_final: 0.7923 (mtmt) REVERT: G 289 ASP cc_start: 0.7439 (m-30) cc_final: 0.7219 (m-30) outliers start: 77 outliers final: 58 residues processed: 301 average time/residue: 0.1619 time to fit residues: 82.1458 Evaluate side-chains 285 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 57 optimal weight: 0.9980 chunk 346 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 255 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN F 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116699 restraints weight = 44254.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119381 restraints weight = 30271.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121273 restraints weight = 23200.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122525 restraints weight = 19077.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123528 restraints weight = 16541.444| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27685 Z= 0.129 Angle : 0.493 7.904 37345 Z= 0.269 Chirality : 0.042 0.168 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.874 25.090 3836 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 12.87 % Favored : 84.47 % 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: 1.75 (0.14), residues: 3668 helix: 2.50 (0.12), residues: 2009 sheet: 0.88 (0.20), residues: 616 loop : -1.45 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 344 TYR 0.007 0.001 TYR A 64 PHE 0.018 0.002 PHE G 193 TRP 0.032 0.002 TRP D 42 HIS 0.002 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00289 (27685) covalent geometry : angle 0.49348 (37345) hydrogen bonds : bond 0.04322 ( 1782) hydrogen bonds : angle 3.93468 ( 5184) *********************** 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 311 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 232 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.5986 (mtt) cc_final: 0.5782 (mtt) REVERT: B 74 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7991 (t0) REVERT: B 119 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7781 (mpp) REVERT: C 224 LYS cc_start: 0.8423 (tttt) cc_final: 0.8178 (tttm) REVERT: C 304 LEU cc_start: 0.8447 (tp) cc_final: 0.7838 (pt) REVERT: D 195 ARG cc_start: 0.7378 (mmt-90) cc_final: 0.7117 (mmt180) REVERT: E 215 ASP cc_start: 0.6969 (t0) cc_final: 0.6713 (t0) REVERT: F 153 ASP cc_start: 0.8042 (t0) cc_final: 0.7802 (t0) REVERT: F 202 PHE cc_start: 0.7253 (m-80) cc_final: 0.6938 (m-80) REVERT: F 487 MET cc_start: 0.8456 (tpp) cc_final: 0.7502 (mpp) REVERT: G 9 ASP cc_start: 0.7007 (t0) cc_final: 0.6753 (t0) REVERT: G 289 ASP cc_start: 0.7546 (m-30) cc_final: 0.7297 (m-30) outliers start: 79 outliers final: 66 residues processed: 298 average time/residue: 0.1634 time to fit residues: 82.3141 Evaluate side-chains 287 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 123 optimal weight: 0.0770 chunk 159 optimal weight: 0.7980 chunk 327 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN E 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118735 restraints weight = 44384.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121480 restraints weight = 30165.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123440 restraints weight = 22915.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124586 restraints weight = 18728.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125720 restraints weight = 16262.483| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 27685 Z= 0.103 Angle : 0.472 10.375 37345 Z= 0.256 Chirality : 0.041 0.166 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.786 25.160 3836 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.88 % Allowed : 14.08 % Favored : 84.03 % 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: 1.92 (0.14), residues: 3668 helix: 2.69 (0.12), residues: 1987 sheet: 0.74 (0.20), residues: 628 loop : -1.28 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 283 TYR 0.008 0.001 TYR A 477 PHE 0.015 0.001 PHE G 193 TRP 0.032 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00214 (27685) covalent geometry : angle 0.47161 (37345) hydrogen bonds : bond 0.03720 ( 1782) hydrogen bonds : angle 3.82639 ( 5184) *********************** 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: 56 poor density : 230 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 TRP cc_start: 0.7734 (p-90) cc_final: 0.7526 (p-90) REVERT: B 119 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7763 (mpp) REVERT: C 224 LYS cc_start: 0.8415 (tttt) cc_final: 0.8204 (tttm) REVERT: C 304 LEU cc_start: 0.8437 (tp) cc_final: 0.7817 (pt) REVERT: C 487 MET cc_start: 0.7606 (mmt) cc_final: 0.7287 (mpp) REVERT: D 223 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7958 (mtmm) REVERT: F 153 ASP cc_start: 0.8000 (t0) cc_final: 0.7759 (t0) REVERT: F 202 PHE cc_start: 0.7198 (m-80) cc_final: 0.6857 (m-80) REVERT: F 487 MET cc_start: 0.8380 (tpp) cc_final: 0.7403 (mpp) REVERT: G 9 ASP cc_start: 0.6898 (t0) cc_final: 0.6666 (t0) outliers start: 56 outliers final: 46 residues processed: 276 average time/residue: 0.1552 time to fit residues: 72.6737 Evaluate side-chains 267 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 179 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 302 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112815 restraints weight = 44930.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115385 restraints weight = 30926.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.117185 restraints weight = 23737.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118363 restraints weight = 19714.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119302 restraints weight = 17245.077| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27685 Z= 0.170 Angle : 0.555 9.780 37345 Z= 0.300 Chirality : 0.044 0.204 4571 Planarity : 0.004 0.046 4809 Dihedral : 3.990 25.618 3836 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 13.95 % Favored : 83.63 % 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: 1.58 (0.14), residues: 3668 helix: 2.40 (0.12), residues: 2018 sheet: 1.16 (0.21), residues: 525 loop : -1.66 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 283 TYR 0.010 0.001 TYR A 64 PHE 0.017 0.002 PHE B 193 TRP 0.031 0.002 TRP D 42 HIS 0.003 0.001 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00401 (27685) covalent geometry : angle 0.55514 (37345) hydrogen bonds : bond 0.05058 ( 1782) hydrogen bonds : angle 4.07113 ( 5184) *********************** REFINEMENT MACRO_CYCLE 9 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 296 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 224 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8170 (t0) REVERT: B 119 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7770 (mpp) REVERT: C 224 LYS cc_start: 0.8499 (tttt) cc_final: 0.8264 (tttm) REVERT: C 304 LEU cc_start: 0.8503 (tp) cc_final: 0.7863 (pt) REVERT: F 202 PHE cc_start: 0.7323 (m-80) cc_final: 0.6930 (m-80) REVERT: F 487 MET cc_start: 0.8459 (tpp) cc_final: 0.7511 (mpp) REVERT: G 9 ASP cc_start: 0.7239 (t0) cc_final: 0.6959 (t0) outliers start: 72 outliers final: 59 residues processed: 284 average time/residue: 0.1595 time to fit residues: 75.9625 Evaluate side-chains 268 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 266 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 137 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 chunk 287 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.118380 restraints weight = 44334.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.121075 restraints weight = 30072.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122756 restraints weight = 22787.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124280 restraints weight = 18843.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125087 restraints weight = 16189.102| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5959 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 : 0.494 10.389 37345 Z= 0.265 Chirality : 0.041 0.174 4571 Planarity : 0.004 0.046 4809 Dihedral : 3.825 25.029 3836 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 14.89 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.14), residues: 3668 helix: 2.68 (0.12), residues: 1993 sheet: 0.68 (0.20), residues: 628 loop : -1.38 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 264 TYR 0.009 0.001 TYR A 217 PHE 0.017 0.002 PHE E 279 TRP 0.029 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 Details of bonding type rmsd covalent geometry : bond 0.00232 (27685) covalent geometry : angle 0.49437 (37345) hydrogen bonds : bond 0.03831 ( 1782) hydrogen bonds : angle 3.87485 ( 5184) ********************** REFINEMENT MACRO_CYCLE 10 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 269 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7754 (mpp) REVERT: C 224 LYS cc_start: 0.8397 (tttt) cc_final: 0.8190 (tttm) REVERT: C 304 LEU cc_start: 0.8467 (tp) cc_final: 0.7912 (pt) REVERT: F 202 PHE cc_start: 0.7239 (m-80) cc_final: 0.6764 (m-80) REVERT: F 487 MET cc_start: 0.8415 (tpp) cc_final: 0.7496 (mpp) REVERT: G 9 ASP cc_start: 0.6939 (t0) cc_final: 0.6675 (t0) REVERT: G 119 MET cc_start: 0.7327 (tpp) cc_final: 0.7114 (mmm) outliers start: 50 outliers final: 45 residues processed: 261 average time/residue: 0.1584 time to fit residues: 70.6671 Evaluate side-chains 259 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 130 optimal weight: 0.9990 chunk 123 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 321 optimal weight: 0.6980 chunk 158 optimal weight: 0.0040 chunk 275 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 overall best weight: 0.5512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.118798 restraints weight = 43929.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121509 restraints weight = 29885.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.123474 restraints weight = 22712.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124615 restraints weight = 18501.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.125671 restraints weight = 16133.350| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27685 Z= 0.105 Angle : 0.499 10.232 37345 Z= 0.268 Chirality : 0.041 0.167 4571 Planarity : 0.004 0.046 4809 Dihedral : 3.819 25.023 3836 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.38 % Allowed : 15.29 % Favored : 83.33 % 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: 1.89 (0.14), residues: 3668 helix: 2.69 (0.12), residues: 1993 sheet: 0.70 (0.21), residues: 628 loop : -1.36 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 242 TYR 0.011 0.001 TYR A 217 PHE 0.024 0.002 PHE A 202 TRP 0.027 0.002 TRP D 42 HIS 0.002 0.000 HIS F 241 Details of bonding type rmsd covalent geometry : bond 0.00214 (27685) covalent geometry : angle 0.49890 (37345) hydrogen bonds : bond 0.03760 ( 1782) hydrogen bonds : angle 3.84796 ( 5184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.38 seconds wall clock time: 70 minutes 14.74 seconds (4214.74 seconds total)