Starting phenix.real_space_refine on Sun May 25 21:00:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7k_29814/05_2025/8g7k_29814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7k_29814/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7k_29814/05_2025/8g7k_29814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7k_29814/05_2025/8g7k_29814.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7k_29814/05_2025/8g7k_29814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7k_29814/05_2025/8g7k_29814.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.19, per 1000 atoms: 0.59 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: 6.53 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 3.53 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: 13.32 Time building geometry restraints manager: 7.60 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: 0.04 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: 2.360 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: 1.080 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 62.860 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.750 ------------------------------------------------------------------------------- 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 : 1.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (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 TRP 0.015 0.004 TRP G 42 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE F 213 TYR 0.028 0.002 TYR E 217 ARG 0.004 0.001 ARG E 500 Details of bonding type rmsd hydrogen bonds : bond 0.18490 ( 1782) hydrogen bonds : angle 6.52341 ( 5184) covalent geometry : bond 0.01480 (27685) covalent geometry : angle 1.43929 (37345) *********************** 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 : 3.321 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: 0.6743 (t0) REVERT: A 244 PRO cc_start: 0.7107 (Cg_exo) cc_final: 0.6868 (Cg_endo) REVERT: A 308 LEU cc_start: 0.7617 (mt) cc_final: 0.6966 (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: 0.7280 (tpp) REVERT: B 231 ILE cc_start: 0.7117 (pt) cc_final: 0.6830 (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: 0.8043 (m) REVERT: C 228 ILE cc_start: 0.7825 (mm) cc_final: 0.7607 (mm) REVERT: C 304 LEU cc_start: 0.8789 (tp) cc_final: 0.7961 (pt) REVERT: C 487 MET cc_start: 0.7723 (mmt) cc_final: 0.6919 (mmm) REVERT: D 213 PHE cc_start: 0.8618 (m-80) cc_final: 0.8306 (m-10) REVERT: D 279 PHE cc_start: 0.6549 (t80) cc_final: 0.6004 (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: 0.6651 (m-30) REVERT: E 523 ILE cc_start: 0.8370 (mt) cc_final: 0.8043 (tt) outliers start: 0 outliers final: 0 residues processed: 805 average time/residue: 0.4080 time to fit residues: 504.1718 Evaluate side-chains 336 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ** 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 204 ASN G 229 GLN G 282 ASN G 351 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123825 restraints weight = 43189.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126508 restraints weight = 29423.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128426 restraints weight = 22384.589| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27685 Z= 0.182 Angle : 0.613 7.316 37345 Z= 0.344 Chirality : 0.046 0.247 4571 Planarity : 0.005 0.048 4809 Dihedral : 4.380 31.938 3836 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.35 % Allowed : 8.50 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.13), residues: 3668 helix: 1.92 (0.11), residues: 2000 sheet: 1.19 (0.20), residues: 616 loop : -0.77 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 42 HIS 0.003 0.001 HIS E 314 PHE 0.021 0.002 PHE A 484 TYR 0.014 0.002 TYR A 477 ARG 0.004 0.001 ARG D 394 Details of bonding type rmsd hydrogen bonds : bond 0.05860 ( 1782) hydrogen bonds : angle 4.65542 ( 5184) covalent geometry : bond 0.00414 (27685) covalent geometry : angle 0.61272 (37345) *********************** 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 434 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 364 time to evaluate : 3.357 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 244 PRO cc_start: 0.7056 (Cg_exo) cc_final: 0.6850 (Cg_endo) REVERT: A 308 LEU cc_start: 0.7553 (mt) cc_final: 0.7219 (pt) REVERT: A 487 MET cc_start: 0.7534 (mmt) cc_final: 0.7279 (tpp) REVERT: B 464 ILE cc_start: 0.9144 (mm) cc_final: 0.8905 (mm) REVERT: C 42 TRP cc_start: 0.7647 (p-90) cc_final: 0.7417 (p90) REVERT: C 61 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7224 (ptmt) REVERT: C 304 LEU cc_start: 0.8512 (tp) cc_final: 0.7746 (pt) REVERT: C 397 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: D 198 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 213 PHE cc_start: 0.8619 (m-80) cc_final: 0.8354 (m-10) REVERT: D 464 ILE cc_start: 0.9001 (mm) cc_final: 0.8784 (mm) REVERT: E 164 MET cc_start: 0.8685 (mmm) cc_final: 0.8462 (tpp) REVERT: E 191 MET cc_start: 0.7018 (ptm) cc_final: 0.6775 (ptp) REVERT: E 215 ASP cc_start: 0.6455 (t0) cc_final: 0.6220 (t0) REVERT: E 221 SER cc_start: 0.6611 (t) cc_final: 0.6368 (p) REVERT: E 385 ASP cc_start: 0.6212 (p0) cc_final: 0.5813 (m-30) REVERT: E 523 ILE cc_start: 0.8424 (mt) cc_final: 0.8197 (tt) REVERT: F 153 ASP cc_start: 0.8083 (t0) cc_final: 0.7802 (t0) REVERT: F 345 ILE cc_start: 0.8946 (mt) cc_final: 0.8656 (mm) REVERT: G 282 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7326 (m-40) REVERT: G 351 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7390 (mp10) outliers start: 70 outliers final: 39 residues processed: 420 average time/residue: 0.3521 time to fit residues: 240.5263 Evaluate side-chains 293 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 515 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 237 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR 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 282 ASN Chi-restraints excluded: chain D residue 292 ILE 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 D residue 515 THR 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 348 ILE Chi-restraints excluded: chain E residue 445 THR 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 322 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 220 LEU 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 Chi-restraints excluded: chain G residue 445 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 199 optimal weight: 6.9990 chunk 308 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116924 restraints weight = 44672.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119588 restraints weight = 30624.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121182 restraints weight = 23403.941| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27685 Z= 0.159 Angle : 0.541 6.527 37345 Z= 0.303 Chirality : 0.043 0.202 4571 Planarity : 0.004 0.044 4809 Dihedral : 4.185 31.905 3836 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.49 % Allowed : 10.22 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 3668 helix: 2.15 (0.12), residues: 2001 sheet: 0.99 (0.20), residues: 616 loop : -1.03 (0.17), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 42 HIS 0.003 0.001 HIS E 314 PHE 0.021 0.002 PHE C 102 TYR 0.012 0.001 TYR G 359 ARG 0.005 0.001 ARG G 283 Details of bonding type rmsd hydrogen bonds : bond 0.05189 ( 1782) hydrogen bonds : angle 4.26048 ( 5184) covalent geometry : bond 0.00359 (27685) covalent geometry : angle 0.54144 (37345) *********************** 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 356 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 282 time to evaluate : 3.138 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: 0.7656 (mt) cc_final: 0.7331 (pt) REVERT: B 119 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7662 (mpp) REVERT: B 223 LYS cc_start: 0.8644 (tptt) cc_final: 0.8436 (mmtt) REVERT: B 487 MET cc_start: 0.8441 (mmt) cc_final: 0.7868 (mmm) REVERT: C 304 LEU cc_start: 0.8531 (tp) cc_final: 0.7801 (pt) REVERT: D 198 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8669 (mm) REVERT: D 213 PHE cc_start: 0.8644 (m-80) cc_final: 0.8430 (m-10) REVERT: E 61 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7721 (ttmt) REVERT: E 290 MET cc_start: 0.7665 (mmt) cc_final: 0.7357 (mmt) REVERT: F 153 ASP cc_start: 0.8139 (t0) cc_final: 0.7684 (t70) REVERT: F 202 PHE cc_start: 0.7597 (m-80) cc_final: 0.7343 (m-80) REVERT: F 345 ILE cc_start: 0.8909 (mt) cc_final: 0.8692 (mm) REVERT: F 487 MET cc_start: 0.8406 (tpp) cc_final: 0.7352 (mpp) REVERT: G 9 ASP cc_start: 0.7110 (t0) cc_final: 0.6882 (t0) outliers start: 74 outliers final: 49 residues processed: 347 average time/residue: 0.3443 time to fit residues: 197.9619 Evaluate side-chains 289 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 194 ASP 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 82 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain D residue 199 SER 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 D residue 515 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 61 LYS 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 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 215 ASP 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 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER 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 445 THR Chi-restraints excluded: chain G residue 515 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 98 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 287 optimal weight: 20.0000 chunk 343 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN G 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.141534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116687 restraints weight = 44887.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119408 restraints weight = 30682.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.121326 restraints weight = 23414.506| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27685 Z= 0.134 Angle : 0.505 6.352 37345 Z= 0.280 Chirality : 0.042 0.191 4571 Planarity : 0.004 0.051 4809 Dihedral : 4.079 30.001 3836 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.66 % Allowed : 11.43 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.14), residues: 3668 helix: 2.29 (0.12), residues: 2019 sheet: 0.92 (0.20), residues: 616 loop : -1.28 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 42 HIS 0.002 0.001 HIS E 314 PHE 0.020 0.002 PHE E 279 TYR 0.012 0.001 TYR E 217 ARG 0.009 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1782) hydrogen bonds : angle 4.08363 ( 5184) covalent geometry : bond 0.00298 (27685) covalent geometry : angle 0.50513 (37345) *********************** 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: 79 poor density : 265 time to evaluate : 3.281 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: 0.7601 (mt) cc_final: 0.7345 (pt) REVERT: B 223 LYS cc_start: 0.8683 (tptt) cc_final: 0.8389 (mmtt) REVERT: C 224 LYS cc_start: 0.8434 (tttt) cc_final: 0.8129 (tttm) REVERT: C 304 LEU cc_start: 0.8528 (tp) cc_final: 0.7813 (pt) REVERT: D 260 LEU cc_start: 0.8394 (mm) cc_final: 0.8036 (mt) REVERT: D 269 LEU cc_start: 0.7650 (mp) cc_final: 0.7177 (tp) REVERT: E 61 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7774 (ttmt) REVERT: F 153 ASP cc_start: 0.8117 (t0) cc_final: 0.7828 (t0) REVERT: F 202 PHE cc_start: 0.7511 (m-80) cc_final: 0.7182 (m-80) REVERT: F 345 ILE cc_start: 0.8970 (mt) cc_final: 0.8748 (mm) REVERT: F 487 MET cc_start: 0.8460 (tpp) cc_final: 0.7496 (mpp) REVERT: G 9 ASP cc_start: 0.7071 (t0) cc_final: 0.6822 (t0) REVERT: G 289 ASP cc_start: 0.7641 (m-30) cc_final: 0.7400 (m-30) outliers start: 79 outliers final: 56 residues processed: 335 average time/residue: 0.3256 time to fit residues: 184.2997 Evaluate side-chains 284 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 232 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 194 ASP 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 187 ILE Chi-restraints excluded: chain D residue 199 SER 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 459 VAL Chi-restraints excluded: chain D residue 509 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 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 215 ASP 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 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 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 298 optimal weight: 0.9990 chunk 283 optimal weight: 0.6980 chunk 182 optimal weight: 0.5980 chunk 258 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119185 restraints weight = 44368.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121971 restraints weight = 30135.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123805 restraints weight = 22882.453| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5144 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= 0.108 Angle : 0.472 8.978 37345 Z= 0.259 Chirality : 0.041 0.185 4571 Planarity : 0.004 0.044 4809 Dihedral : 3.892 28.198 3836 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.92 % Allowed : 12.54 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3668 helix: 2.49 (0.12), residues: 2010 sheet: 0.73 (0.20), residues: 628 loop : -1.17 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.024 0.002 PHE C 102 TYR 0.013 0.001 TYR E 217 ARG 0.004 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 1782) hydrogen bonds : angle 3.92240 ( 5184) covalent geometry : bond 0.00226 (27685) covalent geometry : angle 0.47229 (37345) *********************** 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 318 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 3.207 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: A 308 LEU cc_start: 0.7603 (mt) cc_final: 0.7368 (pt) REVERT: B 119 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7587 (mpp) REVERT: B 223 LYS cc_start: 0.8694 (tptt) cc_final: 0.8363 (mmtt) REVERT: C 224 LYS cc_start: 0.8416 (tttt) cc_final: 0.8209 (tttm) REVERT: C 304 LEU cc_start: 0.8514 (tp) cc_final: 0.7851 (pt) REVERT: C 487 MET cc_start: 0.7956 (mmt) cc_final: 0.7139 (mmm) REVERT: D 269 LEU cc_start: 0.7643 (mp) cc_final: 0.7255 (tp) REVERT: E 215 ASP cc_start: 0.6985 (t0) cc_final: 0.6695 (t0) REVERT: F 153 ASP cc_start: 0.8140 (t0) cc_final: 0.7821 (t0) REVERT: F 202 PHE cc_start: 0.7295 (m-80) cc_final: 0.6970 (m-80) REVERT: F 487 MET cc_start: 0.8495 (tpp) cc_final: 0.7503 (mpp) REVERT: G 9 ASP cc_start: 0.6913 (t0) cc_final: 0.6695 (t0) REVERT: G 119 MET cc_start: 0.7694 (tpp) cc_final: 0.7451 (tpp) REVERT: G 289 ASP cc_start: 0.7645 (m-30) cc_final: 0.7443 (m-30) outliers start: 57 outliers final: 44 residues processed: 310 average time/residue: 0.3237 time to fit residues: 169.6634 Evaluate side-chains 265 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 220 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 194 ASP 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 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 330 MET Chi-restraints excluded: chain D residue 372 SER 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 220 LEU 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 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 282 ASN Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 346 GLN 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 298 VAL 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 250 optimal weight: 5.9990 chunk 290 optimal weight: 0.0570 chunk 132 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 301 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 312 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN F 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.143613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119229 restraints weight = 44285.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.121960 restraints weight = 30090.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123920 restraints weight = 22854.321| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27685 Z= 0.105 Angle : 0.468 9.401 37345 Z= 0.255 Chirality : 0.041 0.174 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.810 24.953 3836 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.95 % Allowed : 13.24 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3668 helix: 2.55 (0.12), residues: 2010 sheet: 0.71 (0.20), residues: 628 loop : -1.18 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.021 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.009 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1782) hydrogen bonds : angle 3.86842 ( 5184) covalent geometry : bond 0.00219 (27685) covalent geometry : angle 0.46829 (37345) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 3.296 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: B 119 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: B 223 LYS cc_start: 0.8729 (tptt) cc_final: 0.8499 (mmtt) REVERT: C 224 LYS cc_start: 0.8389 (tttt) cc_final: 0.8167 (tttm) REVERT: C 290 MET cc_start: 0.6825 (mtt) cc_final: 0.6565 (mtt) REVERT: C 304 LEU cc_start: 0.8489 (tp) cc_final: 0.7849 (pt) REVERT: D 269 LEU cc_start: 0.7525 (mp) cc_final: 0.7181 (tp) REVERT: E 215 ASP cc_start: 0.7001 (t0) cc_final: 0.6620 (t0) REVERT: F 153 ASP cc_start: 0.8108 (t0) cc_final: 0.7819 (t0) REVERT: F 202 PHE cc_start: 0.7230 (m-80) cc_final: 0.6823 (m-80) REVERT: F 487 MET cc_start: 0.8485 (tpp) cc_final: 0.7557 (mpp) REVERT: G 119 MET cc_start: 0.7599 (tpp) cc_final: 0.7368 (tpp) outliers start: 58 outliers final: 43 residues processed: 288 average time/residue: 0.3277 time to fit residues: 159.2269 Evaluate side-chains 274 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU 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 C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 330 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 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU 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 72 ILE 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 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL 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 349 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 337 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 46 optimal weight: 0.0060 chunk 205 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 ** 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 = 0.3749 r_free = 0.3749 target = 0.131700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102197 restraints weight = 46947.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105647 restraints weight = 28566.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108010 restraints weight = 20419.087| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27685 Z= 0.108 Angle : 0.472 8.091 37345 Z= 0.256 Chirality : 0.041 0.179 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.761 24.444 3836 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.02 % Allowed : 13.71 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3668 helix: 2.50 (0.12), residues: 2051 sheet: 0.84 (0.20), residues: 616 loop : -1.42 (0.17), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.019 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.007 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 1782) hydrogen bonds : angle 3.84040 ( 5184) covalent geometry : bond 0.00233 (27685) covalent geometry : angle 0.47197 (37345) *********************** 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 302 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7348 (mpp) REVERT: B 223 LYS cc_start: 0.8521 (tptt) cc_final: 0.8244 (mmtt) REVERT: C 224 LYS cc_start: 0.8713 (tttt) cc_final: 0.8411 (tttm) REVERT: C 290 MET cc_start: 0.7081 (mtt) cc_final: 0.6838 (mtt) REVERT: C 304 LEU cc_start: 0.8896 (tp) cc_final: 0.8114 (pt) REVERT: C 416 CYS cc_start: 0.8049 (m) cc_final: 0.7438 (t) REVERT: C 487 MET cc_start: 0.8192 (mmt) cc_final: 0.7408 (mpp) REVERT: D 269 LEU cc_start: 0.8261 (mp) cc_final: 0.7600 (tp) REVERT: E 215 ASP cc_start: 0.7274 (t0) cc_final: 0.6822 (t0) REVERT: F 153 ASP cc_start: 0.8217 (t0) cc_final: 0.7590 (t0) REVERT: F 202 PHE cc_start: 0.7798 (m-80) cc_final: 0.7109 (m-80) REVERT: F 487 MET cc_start: 0.8496 (tpp) cc_final: 0.7465 (mpp) outliers start: 60 outliers final: 52 residues processed: 290 average time/residue: 0.3110 time to fit residues: 154.9554 Evaluate side-chains 278 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 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 C residue 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER 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 523 ILE 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 314 HIS 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 72 ILE 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 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 445 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 281 optimal weight: 0.0050 chunk 262 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 194 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 268 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103301 restraints weight = 46516.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106758 restraints weight = 28323.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109144 restraints weight = 20284.387| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 27685 Z= 0.101 Angle : 0.463 9.095 37345 Z= 0.252 Chirality : 0.041 0.173 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.702 24.482 3836 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 14.62 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.14), residues: 3668 helix: 2.63 (0.12), residues: 2033 sheet: 0.68 (0.20), residues: 628 loop : -1.27 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.017 0.001 PHE E 279 TYR 0.009 0.001 TYR E 217 ARG 0.006 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 1782) hydrogen bonds : angle 3.78193 ( 5184) covalent geometry : bond 0.00208 (27685) covalent geometry : angle 0.46336 (37345) *********************** 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 295 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7325 (mpp) REVERT: B 223 LYS cc_start: 0.8516 (tptt) cc_final: 0.8294 (mmtt) REVERT: C 224 LYS cc_start: 0.8704 (tttt) cc_final: 0.8410 (tttm) REVERT: C 304 LEU cc_start: 0.8874 (tp) cc_final: 0.8052 (pt) REVERT: C 416 CYS cc_start: 0.8035 (m) cc_final: 0.7456 (t) REVERT: D 269 LEU cc_start: 0.8203 (mp) cc_final: 0.7544 (tp) REVERT: E 191 MET cc_start: 0.8086 (ppp) cc_final: 0.7639 (ppp) REVERT: E 215 ASP cc_start: 0.7294 (t0) cc_final: 0.6848 (t0) REVERT: F 153 ASP cc_start: 0.8267 (t0) cc_final: 0.7570 (t0) REVERT: F 202 PHE cc_start: 0.7782 (m-80) cc_final: 0.7099 (m-80) REVERT: F 487 MET cc_start: 0.8493 (tpp) cc_final: 0.7466 (mpp) outliers start: 51 outliers final: 43 residues processed: 286 average time/residue: 0.3248 time to fit residues: 156.9416 Evaluate side-chains 263 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE 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 B residue 59 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU 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 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 72 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 330 MET 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 247 ILE Chi-restraints excluded: chain E residue 260 LEU 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 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 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 445 THR Chi-restraints excluded: chain G residue 475 VAL 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 84 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 337 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 333 optimal weight: 0.0770 chunk 247 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102241 restraints weight = 47330.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105668 restraints weight = 28827.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108044 restraints weight = 20681.625| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27685 Z= 0.108 Angle : 0.482 9.831 37345 Z= 0.259 Chirality : 0.042 0.174 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.693 24.516 3836 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.65 % Allowed : 14.86 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.14), residues: 3668 helix: 2.72 (0.12), residues: 1996 sheet: 0.64 (0.20), residues: 628 loop : -1.25 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 42 HIS 0.001 0.000 HIS D 241 PHE 0.022 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.006 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1782) hydrogen bonds : angle 3.79253 ( 5184) covalent geometry : bond 0.00236 (27685) covalent geometry : angle 0.48197 (37345) *********************** 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 283 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 TRP cc_start: 0.8258 (p-90) cc_final: 0.7997 (p-90) REVERT: B 119 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7357 (mpp) REVERT: C 224 LYS cc_start: 0.8705 (tttt) cc_final: 0.8414 (tttm) REVERT: C 304 LEU cc_start: 0.8878 (tp) cc_final: 0.8068 (pt) REVERT: C 416 CYS cc_start: 0.8057 (m) cc_final: 0.7443 (t) REVERT: C 487 MET cc_start: 0.8225 (mmt) cc_final: 0.7367 (mpp) REVERT: D 223 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7908 (mtmm) REVERT: D 269 LEU cc_start: 0.8305 (mp) cc_final: 0.7498 (tp) REVERT: E 191 MET cc_start: 0.8142 (ppp) cc_final: 0.7754 (ppp) REVERT: E 215 ASP cc_start: 0.7307 (t0) cc_final: 0.6839 (t0) REVERT: F 153 ASP cc_start: 0.8310 (t0) cc_final: 0.7612 (t0) REVERT: F 202 PHE cc_start: 0.7793 (m-80) cc_final: 0.7116 (m-80) REVERT: F 487 MET cc_start: 0.8501 (tpp) cc_final: 0.7488 (mpp) REVERT: G 284 LYS cc_start: 0.8321 (mttt) cc_final: 0.7750 (mtmt) outliers start: 49 outliers final: 44 residues processed: 273 average time/residue: 0.3208 time to fit residues: 151.5391 Evaluate side-chains 267 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 72 ILE 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 B residue 59 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 175 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 451 MET 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 445 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET 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 247 ILE Chi-restraints excluded: chain E residue 260 LEU 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 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 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL 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 87 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 259 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 297 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098507 restraints weight = 47868.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101786 restraints weight = 29694.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103993 restraints weight = 21570.595| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27685 Z= 0.144 Angle : 0.525 9.984 37345 Z= 0.284 Chirality : 0.043 0.174 4571 Planarity : 0.004 0.045 4809 Dihedral : 3.880 24.703 3836 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 15.16 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.14), residues: 3668 helix: 2.56 (0.12), residues: 2014 sheet: 1.15 (0.21), residues: 525 loop : -1.57 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 42 HIS 0.002 0.001 HIS C 241 PHE 0.023 0.002 PHE E 279 TYR 0.009 0.001 TYR E 217 ARG 0.005 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 1782) hydrogen bonds : angle 3.94691 ( 5184) covalent geometry : bond 0.00334 (27685) covalent geometry : angle 0.52496 (37345) ********************** 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 277 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 2.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 119 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7523 (mpp) REVERT: B 459 VAL cc_start: 0.8203 (m) cc_final: 0.7816 (p) REVERT: C 224 LYS cc_start: 0.8683 (tttt) cc_final: 0.8349 (tttm) REVERT: C 304 LEU cc_start: 0.8928 (tp) cc_final: 0.8136 (pt) REVERT: C 416 CYS cc_start: 0.8165 (m) cc_final: 0.7579 (t) REVERT: C 487 MET cc_start: 0.8263 (mmt) cc_final: 0.7292 (mpp) REVERT: D 434 ASP cc_start: 0.6584 (m-30) cc_final: 0.6364 (m-30) REVERT: E 191 MET cc_start: 0.8094 (ppp) cc_final: 0.7718 (ppp) REVERT: E 215 ASP cc_start: 0.7413 (t0) cc_final: 0.7163 (t0) REVERT: E 284 LYS cc_start: 0.7972 (mttt) cc_final: 0.7575 (mmtm) REVERT: E 385 ASP cc_start: 0.7295 (p0) cc_final: 0.6903 (m-30) REVERT: F 153 ASP cc_start: 0.8506 (t0) cc_final: 0.7847 (t0) REVERT: F 487 MET cc_start: 0.8493 (tpp) cc_final: 0.7437 (mpp) outliers start: 49 outliers final: 44 residues processed: 268 average time/residue: 0.3378 time to fit residues: 156.9114 Evaluate side-chains 262 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 B residue 59 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 175 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 451 MET 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 445 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET 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 247 ILE Chi-restraints excluded: chain E residue 260 LEU 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 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 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL 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 336 optimal weight: 5.9990 chunk 266 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 330 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.129885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100507 restraints weight = 47644.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103799 restraints weight = 29312.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106079 restraints weight = 21154.176| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6056 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= 0.122 Angle : 0.497 10.014 37345 Z= 0.268 Chirality : 0.042 0.172 4571 Planarity : 0.004 0.045 4809 Dihedral : 3.815 24.449 3836 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.71 % Allowed : 15.26 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.14), residues: 3668 helix: 2.60 (0.12), residues: 2014 sheet: 1.11 (0.21), residues: 525 loop : -1.62 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 42 HIS 0.002 0.000 HIS D 241 PHE 0.023 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.005 0.000 ARG F 444 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1782) hydrogen bonds : angle 3.88238 ( 5184) covalent geometry : bond 0.00275 (27685) covalent geometry : angle 0.49710 (37345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7199.38 seconds wall clock time: 127 minutes 41.32 seconds (7661.32 seconds total)