Starting phenix.real_space_refine on Mon Jun 23 15:49:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7k_29814/06_2025/8g7k_29814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7k_29814/06_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_29814/06_2025/8g7k_29814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7k_29814/06_2025/8g7k_29814.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7k_29814/06_2025/8g7k_29814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7k_29814/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.82, per 1000 atoms: 0.58 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: 6.63 Conformation dependent library (CDL) restraints added in 3.7 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: 3.01 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: 10.44 Time building geometry restraints manager: 7.95 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: 3.000 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: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 59.910 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.270 ------------------------------------------------------------------------------- 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 : 2.988 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: 0.4132 time to fit residues: 507.9853 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 : 2.945 ------------------------------------------------------------------------------- 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 = 0.147617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123401 restraints weight = 43103.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126222 restraints weight = 28784.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128225 restraints weight = 21629.241| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.7514 (mt) cc_final: 0.7221 (pt) REVERT: A 487 MET cc_start: 0.7431 (mmt) cc_final: 0.7197 (tpp) REVERT: B 464 ILE cc_start: 0.9102 (mm) cc_final: 0.8875 (mm) REVERT: C 42 TRP cc_start: 0.7576 (p-90) cc_final: 0.7362 (p90) REVERT: C 61 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7168 (ptmt) REVERT: C 304 LEU cc_start: 0.8453 (tp) cc_final: 0.7717 (pt) REVERT: C 397 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8140 (m-30) REVERT: D 198 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8597 (mm) REVERT: D 213 PHE cc_start: 0.8557 (m-80) cc_final: 0.8318 (m-10) REVERT: D 464 ILE cc_start: 0.8970 (mm) cc_final: 0.8755 (mm) REVERT: E 164 MET cc_start: 0.8650 (mmm) cc_final: 0.8432 (tpp) REVERT: E 191 MET cc_start: 0.6951 (ptm) cc_final: 0.6743 (ptp) REVERT: E 215 ASP cc_start: 0.6407 (t0) cc_final: 0.6203 (t0) REVERT: E 221 SER cc_start: 0.6515 (t) cc_final: 0.6268 (p) REVERT: E 385 ASP cc_start: 0.6096 (p0) cc_final: 0.5766 (m-30) REVERT: E 523 ILE cc_start: 0.8436 (mt) cc_final: 0.8193 (tt) REVERT: F 153 ASP cc_start: 0.8039 (t0) cc_final: 0.7807 (t0) REVERT: F 345 ILE cc_start: 0.8913 (mt) cc_final: 0.8627 (mm) REVERT: G 282 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7314 (m-40) REVERT: G 351 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7416 (mp10) outliers start: 70 outliers final: 39 residues processed: 420 average time/residue: 0.4091 time to fit residues: 278.4383 Evaluate side-chains 292 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 3.187 ------------------------------------------------------------------------------- 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: 7.9990 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: 10.0000 chunk 253 optimal weight: 2.9990 chunk 305 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116974 restraints weight = 44668.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119599 restraints weight = 30556.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121503 restraints weight = 23422.951| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27685 Z= 0.157 Angle : 0.542 6.532 37345 Z= 0.303 Chirality : 0.043 0.201 4571 Planarity : 0.004 0.043 4809 Dihedral : 4.187 32.035 3836 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.49 % Allowed : 10.35 % Favored : 87.16 % 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: 1.58 (0.14), residues: 3668 helix: 2.11 (0.11), residues: 2016 sheet: 0.98 (0.20), residues: 616 loop : -1.08 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 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 0.007 0.001 ARG G 283 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 1782) hydrogen bonds : angle 4.26157 ( 5184) covalent geometry : bond 0.00356 (27685) covalent geometry : angle 0.54172 (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 355 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 281 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.7647 (mt) cc_final: 0.7338 (pt) REVERT: B 119 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7662 (mpp) REVERT: B 487 MET cc_start: 0.8421 (mmt) cc_final: 0.7856 (mmm) REVERT: C 304 LEU cc_start: 0.8514 (tp) cc_final: 0.7789 (pt) REVERT: D 198 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8663 (mm) REVERT: D 213 PHE cc_start: 0.8644 (m-80) cc_final: 0.8423 (m-10) REVERT: E 61 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7713 (ttmt) REVERT: F 153 ASP cc_start: 0.8123 (t0) cc_final: 0.7678 (t70) REVERT: F 202 PHE cc_start: 0.7595 (m-80) cc_final: 0.7362 (m-80) REVERT: F 345 ILE cc_start: 0.8907 (mt) cc_final: 0.8689 (mm) REVERT: F 487 MET cc_start: 0.8394 (tpp) cc_final: 0.7362 (mpp) REVERT: G 9 ASP cc_start: 0.7111 (t0) cc_final: 0.6887 (t0) outliers start: 74 outliers final: 50 residues processed: 345 average time/residue: 0.3538 time to fit residues: 201.4218 Evaluate side-chains 287 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 234 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 282 ASN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain 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: 6.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 287 optimal weight: 20.0000 chunk 343 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 326 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 G 263 ASN G 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118720 restraints weight = 44887.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121520 restraints weight = 30594.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123460 restraints weight = 23181.618| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27685 Z= 0.117 Angle : 0.487 6.429 37345 Z= 0.270 Chirality : 0.042 0.193 4571 Planarity : 0.004 0.047 4809 Dihedral : 4.013 29.926 3836 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.92 % Allowed : 11.87 % Favored : 86.22 % 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: 1.80 (0.14), residues: 3668 helix: 2.42 (0.12), residues: 1998 sheet: 0.78 (0.20), residues: 628 loop : -1.04 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 42 HIS 0.001 0.000 HIS C 314 PHE 0.021 0.002 PHE E 279 TYR 0.011 0.001 TYR E 217 ARG 0.008 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 1782) hydrogen bonds : angle 4.02462 ( 5184) covalent geometry : bond 0.00249 (27685) covalent geometry : angle 0.48714 (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 332 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 275 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LEU cc_start: 0.7558 (mt) cc_final: 0.7324 (pt) REVERT: C 224 LYS cc_start: 0.8418 (tttt) cc_final: 0.8120 (tttm) REVERT: C 304 LEU cc_start: 0.8545 (tp) cc_final: 0.7824 (pt) REVERT: D 260 LEU cc_start: 0.8375 (mm) cc_final: 0.8033 (mt) REVERT: D 269 LEU cc_start: 0.7631 (mp) cc_final: 0.7198 (tp) REVERT: E 290 MET cc_start: 0.7530 (mmt) cc_final: 0.6827 (mtt) REVERT: F 153 ASP cc_start: 0.8111 (t0) cc_final: 0.7796 (t0) REVERT: F 202 PHE cc_start: 0.7457 (m-80) cc_final: 0.7162 (m-80) REVERT: F 345 ILE cc_start: 0.8947 (mt) cc_final: 0.8723 (mm) REVERT: F 487 MET cc_start: 0.8428 (tpp) cc_final: 0.7405 (mpp) REVERT: G 9 ASP cc_start: 0.6929 (t0) cc_final: 0.6680 (t0) REVERT: G 289 ASP cc_start: 0.7556 (m-30) cc_final: 0.7345 (m-30) outliers start: 57 outliers final: 37 residues processed: 326 average time/residue: 0.3255 time to fit residues: 179.2388 Evaluate side-chains 271 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 422 ILE Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 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 523 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 298 optimal weight: 8.9990 chunk 283 optimal weight: 0.0570 chunk 182 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 307 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 309 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 282 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.9104 ------------------------------------------------------------------------------- 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 E 282 ASN F 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113703 restraints weight = 44890.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.116325 restraints weight = 30930.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118205 restraints weight = 23757.530| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 27685 Z= 0.156 Angle : 0.528 9.271 37345 Z= 0.289 Chirality : 0.043 0.185 4571 Planarity : 0.004 0.042 4809 Dihedral : 4.082 28.766 3836 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.96 % Allowed : 12.07 % Favored : 84.97 % 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: 1.57 (0.14), residues: 3668 helix: 2.30 (0.12), residues: 2019 sheet: 1.18 (0.21), residues: 525 loop : -1.48 (0.16), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 42 HIS 0.002 0.001 HIS E 314 PHE 0.023 0.002 PHE D 213 TYR 0.013 0.001 TYR E 217 ARG 0.008 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 1782) hydrogen bonds : angle 4.09543 ( 5184) covalent geometry : bond 0.00362 (27685) covalent geometry : angle 0.52804 (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 334 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 246 time to evaluate : 3.327 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: 0.7648 (mt) cc_final: 0.7377 (pt) REVERT: B 119 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: C 224 LYS cc_start: 0.8417 (tttt) cc_final: 0.8150 (tttm) REVERT: C 304 LEU cc_start: 0.8526 (tp) cc_final: 0.7844 (pt) REVERT: D 195 ARG cc_start: 0.7474 (mmt-90) cc_final: 0.7184 (mmt180) REVERT: D 269 LEU cc_start: 0.7750 (mp) cc_final: 0.7263 (tp) REVERT: E 215 ASP cc_start: 0.6918 (t0) cc_final: 0.5988 (t0) REVERT: E 243 LYS cc_start: 0.6342 (mttp) cc_final: 0.5801 (mmtt) REVERT: E 290 MET cc_start: 0.7716 (mmt) cc_final: 0.7047 (mtt) REVERT: F 153 ASP cc_start: 0.8168 (t0) cc_final: 0.7907 (t0) REVERT: F 202 PHE cc_start: 0.7392 (m-80) cc_final: 0.7023 (m-80) REVERT: F 345 ILE cc_start: 0.8956 (mt) cc_final: 0.8732 (mm) REVERT: F 487 MET cc_start: 0.8503 (tpp) cc_final: 0.7558 (mpp) REVERT: G 9 ASP cc_start: 0.7257 (t0) cc_final: 0.6996 (t0) REVERT: G 119 MET cc_start: 0.7826 (tpp) cc_final: 0.7602 (tpp) REVERT: G 289 ASP cc_start: 0.7671 (m-30) cc_final: 0.7453 (m-30) outliers start: 88 outliers final: 71 residues processed: 316 average time/residue: 0.3500 time to fit residues: 188.2542 Evaluate side-chains 288 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 4.470 ------------------------------------------------------------------------------- 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 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 319 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 72 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN 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 72 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 215 ASP 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 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 F residue 515 THR 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 149 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 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: 0.6980 chunk 290 optimal weight: 0.0670 chunk 132 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 301 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 200 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 E 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118610 restraints weight = 44466.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121314 restraints weight = 30115.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.122981 restraints weight = 22864.966| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27685 Z= 0.104 Angle : 0.475 9.218 37345 Z= 0.259 Chirality : 0.041 0.174 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.881 24.879 3836 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.75 % Allowed : 13.65 % Favored : 84.61 % 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: 2.51 (0.12), residues: 2015 sheet: 0.69 (0.20), residues: 628 loop : -1.21 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 42 HIS 0.001 0.000 HIS B 314 PHE 0.021 0.001 PHE E 279 TYR 0.011 0.001 TYR E 217 ARG 0.005 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1782) hydrogen bonds : angle 3.88956 ( 5184) covalent geometry : bond 0.00213 (27685) covalent geometry : angle 0.47513 (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 299 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7644 (mpp) REVERT: C 224 LYS cc_start: 0.8391 (tttt) cc_final: 0.8166 (tttm) REVERT: C 304 LEU cc_start: 0.8537 (tp) cc_final: 0.7887 (pt) REVERT: D 153 ASP cc_start: 0.7705 (t0) cc_final: 0.7498 (t70) REVERT: D 223 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8135 (mtmm) REVERT: D 269 LEU cc_start: 0.7649 (mp) cc_final: 0.7228 (tp) REVERT: E 215 ASP cc_start: 0.6972 (t0) cc_final: 0.6584 (t0) REVERT: E 290 MET cc_start: 0.7626 (mmt) cc_final: 0.6960 (mtt) REVERT: F 153 ASP cc_start: 0.8067 (t0) cc_final: 0.7762 (t0) REVERT: F 202 PHE cc_start: 0.7285 (m-80) cc_final: 0.6917 (m-80) REVERT: F 487 MET cc_start: 0.8486 (tpp) cc_final: 0.7562 (mpp) REVERT: G 9 ASP cc_start: 0.6846 (t0) cc_final: 0.6629 (t0) REVERT: G 119 MET cc_start: 0.7689 (tpp) cc_final: 0.7471 (tpp) outliers start: 52 outliers final: 38 residues processed: 287 average time/residue: 0.3411 time to fit residues: 165.7187 Evaluate side-chains 269 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 230 time to evaluate : 2.936 ------------------------------------------------------------------------------- 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 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 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 298 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 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 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 314 HIS Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU 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: 5.9990 chunk 351 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 298 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.114019 restraints weight = 44806.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116611 restraints weight = 30844.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118478 restraints weight = 23732.138| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27685 Z= 0.141 Angle : 0.518 9.630 37345 Z= 0.281 Chirality : 0.043 0.189 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.943 25.018 3836 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.69 % Allowed : 13.31 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.14), residues: 3668 helix: 2.35 (0.12), residues: 2048 sheet: 1.15 (0.21), residues: 525 loop : -1.64 (0.16), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 42 HIS 0.002 0.001 HIS E 314 PHE 0.018 0.002 PHE E 279 TYR 0.011 0.001 TYR E 217 ARG 0.003 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.04650 ( 1782) hydrogen bonds : angle 3.97962 ( 5184) covalent geometry : bond 0.00323 (27685) covalent geometry : angle 0.51844 (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 319 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7670 (mpp) REVERT: C 224 LYS cc_start: 0.8414 (tttt) cc_final: 0.8172 (tttm) REVERT: C 304 LEU cc_start: 0.8565 (tp) cc_final: 0.7927 (pt) REVERT: C 487 MET cc_start: 0.8119 (mmt) cc_final: 0.7427 (mpp) REVERT: D 269 LEU cc_start: 0.7707 (mp) cc_final: 0.7177 (tp) REVERT: E 164 MET cc_start: 0.8556 (mmm) cc_final: 0.8293 (tpp) REVERT: E 215 ASP cc_start: 0.7151 (t0) cc_final: 0.6333 (t0) REVERT: E 243 LYS cc_start: 0.6398 (mttp) cc_final: 0.5897 (mmtt) REVERT: E 290 MET cc_start: 0.7709 (mmt) cc_final: 0.7101 (mtt) REVERT: F 100 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7600 (mm-30) REVERT: F 153 ASP cc_start: 0.8182 (t0) cc_final: 0.7927 (t0) REVERT: F 202 PHE cc_start: 0.7347 (m-80) cc_final: 0.6866 (m-80) REVERT: F 444 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6786 (mtm110) REVERT: F 487 MET cc_start: 0.8469 (tpp) cc_final: 0.7554 (mpp) REVERT: G 9 ASP cc_start: 0.7104 (t0) cc_final: 0.6843 (t0) REVERT: G 119 MET cc_start: 0.7843 (tpp) cc_final: 0.7626 (tpp) outliers start: 80 outliers final: 64 residues processed: 303 average time/residue: 0.3981 time to fit residues: 204.2995 Evaluate side-chains 284 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 5.973 ------------------------------------------------------------------------------- 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 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 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 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 61 LYS Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 SER 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 314 HIS 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 212 GLU 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 444 ARG Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 386 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 281 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 210 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 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 = 0.3784 r_free = 0.3784 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113963 restraints weight = 44767.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116559 restraints weight = 30930.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118184 restraints weight = 23830.098| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27685 Z= 0.138 Angle : 0.512 9.355 37345 Z= 0.278 Chirality : 0.043 0.179 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.949 25.102 3836 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.49 % Allowed : 13.95 % Favored : 83.56 % 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: 1.57 (0.14), residues: 3668 helix: 2.34 (0.12), residues: 2050 sheet: 1.12 (0.21), residues: 525 loop : -1.68 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 42 HIS 0.002 0.001 HIS D 241 PHE 0.022 0.002 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.003 0.000 ARG E 283 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 1782) hydrogen bonds : angle 3.96957 ( 5184) covalent geometry : bond 0.00316 (27685) covalent geometry : angle 0.51220 (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 299 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 225 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: C 224 LYS cc_start: 0.8456 (tttt) cc_final: 0.8215 (tttm) REVERT: C 304 LEU cc_start: 0.8593 (tp) cc_final: 0.7969 (pt) REVERT: C 487 MET cc_start: 0.8155 (mmt) cc_final: 0.7464 (mpp) REVERT: D 269 LEU cc_start: 0.7678 (mp) cc_final: 0.7240 (tp) REVERT: E 164 MET cc_start: 0.8564 (mmm) cc_final: 0.8304 (tpp) REVERT: E 215 ASP cc_start: 0.7180 (t0) cc_final: 0.6330 (t0) REVERT: E 243 LYS cc_start: 0.6367 (mttp) cc_final: 0.5857 (mmtt) REVERT: E 290 MET cc_start: 0.7736 (mmt) cc_final: 0.7127 (mtt) REVERT: F 100 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7500 (mm-30) REVERT: F 153 ASP cc_start: 0.8231 (t0) cc_final: 0.7969 (t0) REVERT: F 202 PHE cc_start: 0.7337 (m-80) cc_final: 0.6894 (m-80) REVERT: F 444 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6856 (mtm110) REVERT: F 487 MET cc_start: 0.8495 (tpp) cc_final: 0.7563 (mpp) REVERT: G 9 ASP cc_start: 0.7109 (t0) cc_final: 0.6831 (t0) REVERT: G 119 MET cc_start: 0.7842 (tpp) cc_final: 0.7631 (tpp) outliers start: 74 outliers final: 66 residues processed: 286 average time/residue: 0.3891 time to fit residues: 192.5484 Evaluate side-chains 282 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 214 time to evaluate : 3.406 ------------------------------------------------------------------------------- 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 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 445 THR Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 368 LEU 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 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 221 SER 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 445 THR Chi-restraints excluded: chain E residue 504 LEU 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 212 GLU 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 444 ARG Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 386 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 84 optimal weight: 6.9990 chunk 312 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 185 optimal weight: 0.0770 chunk 195 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 333 optimal weight: 0.0980 chunk 247 optimal weight: 0.9990 chunk 205 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 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 = 0.3854 r_free = 0.3854 target = 0.144643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120597 restraints weight = 44044.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123339 restraints weight = 29795.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125258 restraints weight = 22549.384| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5943 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= 0.101 Angle : 0.475 9.996 37345 Z= 0.258 Chirality : 0.041 0.183 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.771 25.051 3836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.41 % Allowed : 15.13 % Favored : 83.46 % 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: 1.85 (0.14), residues: 3668 helix: 2.66 (0.12), residues: 1990 sheet: 0.65 (0.20), residues: 628 loop : -1.34 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 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 0.005 0.000 ARG F 344 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 1782) hydrogen bonds : angle 3.81773 ( 5184) covalent geometry : bond 0.00205 (27685) covalent geometry : angle 0.47472 (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 286 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 3.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7606 (mpp) REVERT: B 459 VAL cc_start: 0.8202 (m) cc_final: 0.7890 (p) REVERT: C 224 LYS cc_start: 0.8377 (tttt) cc_final: 0.8174 (tttm) REVERT: C 304 LEU cc_start: 0.8524 (tp) cc_final: 0.7989 (pt) REVERT: C 487 MET cc_start: 0.8047 (mmt) cc_final: 0.7448 (mpp) REVERT: D 269 LEU cc_start: 0.7575 (mp) cc_final: 0.7240 (tp) REVERT: E 164 MET cc_start: 0.8492 (mmm) cc_final: 0.8235 (tpp) REVERT: E 215 ASP cc_start: 0.7110 (t0) cc_final: 0.6902 (t0) REVERT: E 290 MET cc_start: 0.7606 (mmt) cc_final: 0.6991 (mtt) REVERT: F 153 ASP cc_start: 0.8147 (t0) cc_final: 0.7843 (t0) REVERT: F 202 PHE cc_start: 0.7169 (m-80) cc_final: 0.6651 (m-80) REVERT: F 487 MET cc_start: 0.8477 (tpp) cc_final: 0.7606 (mpp) REVERT: G 119 MET cc_start: 0.7703 (tpp) cc_final: 0.7492 (tpp) REVERT: G 284 LYS cc_start: 0.8412 (mttt) cc_final: 0.7941 (mtmt) outliers start: 42 outliers final: 34 residues processed: 276 average time/residue: 0.3225 time to fit residues: 151.7199 Evaluate side-chains 260 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 2.981 ------------------------------------------------------------------------------- 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 353 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 119 MET 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 B residue 475 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 185 LEU 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 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 F residue 57 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 87 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 297 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 245 optimal weight: 0.0970 chunk 254 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 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 = 0.3809 r_free = 0.3809 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116413 restraints weight = 44400.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118997 restraints weight = 30340.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120889 restraints weight = 23341.475| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27685 Z= 0.123 Angle : 0.505 10.639 37345 Z= 0.271 Chirality : 0.042 0.195 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.802 25.362 3836 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.38 % Allowed : 15.66 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.89 (0.14), residues: 3668 helix: 2.72 (0.12), residues: 1960 sheet: 0.81 (0.20), residues: 597 loop : -1.32 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 42 HIS 0.001 0.000 HIS D 241 PHE 0.020 0.002 PHE E 279 TYR 0.009 0.001 TYR G 217 ARG 0.003 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 1782) hydrogen bonds : angle 3.86790 ( 5184) covalent geometry : bond 0.00278 (27685) covalent geometry : angle 0.50491 (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 265 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7676 (mpp) REVERT: C 224 LYS cc_start: 0.8410 (tttt) cc_final: 0.8183 (tttm) REVERT: C 304 LEU cc_start: 0.8583 (tp) cc_final: 0.7998 (pt) REVERT: C 487 MET cc_start: 0.8098 (mmt) cc_final: 0.7466 (mpp) REVERT: D 269 LEU cc_start: 0.7643 (mp) cc_final: 0.7157 (tp) REVERT: E 215 ASP cc_start: 0.7164 (t0) cc_final: 0.6178 (t0) REVERT: E 243 LYS cc_start: 0.6263 (mttp) cc_final: 0.5980 (mmtt) REVERT: E 290 MET cc_start: 0.7670 (mmt) cc_final: 0.7092 (mtt) REVERT: F 153 ASP cc_start: 0.8275 (t0) cc_final: 0.7981 (t0) REVERT: F 202 PHE cc_start: 0.7224 (m-80) cc_final: 0.6662 (m-80) REVERT: F 355 THR cc_start: 0.7498 (t) cc_final: 0.7280 (p) REVERT: F 487 MET cc_start: 0.8472 (tpp) cc_final: 0.7534 (mpp) REVERT: G 119 MET cc_start: 0.7799 (tpp) cc_final: 0.7577 (tpp) outliers start: 41 outliers final: 37 residues processed: 257 average time/residue: 0.3147 time to fit residues: 138.5559 Evaluate side-chains 251 residues out of total 2975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 2.884 ------------------------------------------------------------------------------- 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 330 MET Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 459 VAL 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 332 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 494 ASP 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 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 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 F residue 57 SER Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 336 optimal weight: 0.0040 chunk 266 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 285 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 = 0.3860 r_free = 0.3860 target = 0.145187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.121290 restraints weight = 43585.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.124000 restraints weight = 29430.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125894 restraints weight = 22303.262| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27685 Z= 0.103 Angle : 0.488 10.171 37345 Z= 0.262 Chirality : 0.041 0.175 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.716 25.133 3836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.34 % Allowed : 15.97 % Favored : 82.69 % 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: 2.02 (0.14), residues: 3668 helix: 2.88 (0.12), residues: 1936 sheet: 0.66 (0.20), residues: 628 loop : -1.16 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.019 0.001 PHE E 279 TYR 0.009 0.001 TYR E 217 ARG 0.013 0.000 ARG G 264 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 1782) hydrogen bonds : angle 3.79026 ( 5184) covalent geometry : bond 0.00214 (27685) covalent geometry : angle 0.48816 (37345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7714.51 seconds wall clock time: 139 minutes 2.25 seconds (8342.25 seconds total)