Starting phenix.real_space_refine on Sun Aug 24 20:31:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9la3_62918/08_2025/9la3_62918.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 100 5.16 5 C 14236 2.51 5 N 3656 2.21 5 O 3952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21944 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "B" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "C" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain: "D" Number of atoms: 5486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5486 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Time building chain proxies: 6.65, per 1000 atoms: 0.30 Number of scatterers: 21944 At special positions: 0 Unit cell: (122.928, 125.292, 183.604, 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 100 16.00 O 3952 8.00 N 3656 7.00 C 14236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5072 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 14 sheets defined 70.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 62 through 89 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 97 through 115 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 143 through 152 removed outlier: 3.951A pdb=" N ASP A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.089A pdb=" N ARG A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 164 through 169' Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 195 through 226 removed outlier: 4.043A pdb=" N LEU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 253 through 270 Processing helix chain 'A' and resid 281 through 313 Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.582A pdb=" N ASP A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 4.057A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.899A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.567A pdb=" N CYS A 461 " --> pdb=" O ILE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.817A pdb=" N GLY A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 516 through 542 removed outlier: 3.696A pdb=" N ILE A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 609 through 619 Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.600A pdb=" N VAL A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 696 through 705 Processing helix chain 'A' and resid 706 through 724 Processing helix chain 'B' and resid 62 through 82 Processing helix chain 'B' and resid 82 through 89 Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 143 through 150 removed outlier: 3.917A pdb=" N ASP B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 195 through 226 removed outlier: 4.035A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 Processing helix chain 'B' and resid 253 through 270 Processing helix chain 'B' and resid 281 through 313 Processing helix chain 'B' and resid 314 through 334 removed outlier: 3.538A pdb=" N ARG B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 353 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.865A pdb=" N MET B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.688A pdb=" N LYS B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.596A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 461 removed outlier: 3.606A pdb=" N ILE B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 492 through 510 removed outlier: 4.223A pdb=" N GLU B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 542 Processing helix chain 'B' and resid 543 through 554 Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.647A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 587 Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 627 through 639 removed outlier: 3.503A pdb=" N GLY B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 658 through 662 Processing helix chain 'B' and resid 663 through 672 Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.800A pdb=" N ALA B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 705 Processing helix chain 'B' and resid 706 through 724 Processing helix chain 'C' and resid 62 through 90 Proline residue: C 84 - end of helix removed outlier: 3.534A pdb=" N PHE C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.601A pdb=" N PHE C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 195 through 226 removed outlier: 4.181A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 removed outlier: 4.445A pdb=" N GLY C 232 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 270 Processing helix chain 'C' and resid 281 through 313 removed outlier: 3.596A pdb=" N VAL C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 334 Processing helix chain 'C' and resid 336 through 351 Processing helix chain 'C' and resid 354 through 362 removed outlier: 3.898A pdb=" N THR C 358 " --> pdb=" O HIS C 354 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 removed outlier: 4.089A pdb=" N LEU C 378 " --> pdb=" O GLN C 374 " (cutoff:3.500A) Proline residue: C 379 - end of helix Processing helix chain 'C' and resid 385 through 388 removed outlier: 3.656A pdb=" N LYS C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 455 through 461 Processing helix chain 'C' and resid 482 through 490 Processing helix chain 'C' and resid 492 through 510 removed outlier: 3.681A pdb=" N GLU C 506 " --> pdb=" O ASN C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 3.961A pdb=" N LYS C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 Processing helix chain 'C' and resid 526 through 542 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 586 Processing helix chain 'C' and resid 599 through 607 removed outlier: 4.173A pdb=" N GLU C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 619 Processing helix chain 'C' and resid 627 through 639 Processing helix chain 'C' and resid 640 through 651 Processing helix chain 'C' and resid 663 through 671 Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 696 through 705 Processing helix chain 'C' and resid 706 through 721 Processing helix chain 'D' and resid 51 through 55 removed outlier: 3.502A pdb=" N LYS D 55 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 90 Proline residue: D 84 - end of helix removed outlier: 3.681A pdb=" N PHE D 90 " --> pdb=" O GLU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 117 Processing helix chain 'D' and resid 131 through 143 removed outlier: 3.909A pdb=" N PHE D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.195A pdb=" N ARG D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 164 through 169' Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 177 through 191 removed outlier: 4.365A pdb=" N VAL D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 225 Processing helix chain 'D' and resid 227 through 234 removed outlier: 3.555A pdb=" N GLU D 231 " --> pdb=" O PRO D 228 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLY D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.627A pdb=" N THR D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 313 removed outlier: 3.737A pdb=" N GLY D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 333 Processing helix chain 'D' and resid 336 through 354 Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.868A pdb=" N MET D 360 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D 362 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 4.319A pdb=" N LEU D 378 " --> pdb=" O GLN D 374 " (cutoff:3.500A) Proline residue: D 379 - end of helix removed outlier: 3.676A pdb=" N LYS D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 391 through 401 Processing helix chain 'D' and resid 455 through 461 removed outlier: 3.645A pdb=" N CYS D 461 " --> pdb=" O ILE D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 494 through 507 removed outlier: 3.672A pdb=" N ASN D 501 " --> pdb=" O ARG D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 542 removed outlier: 4.099A pdb=" N ASP D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.817A pdb=" N HIS D 569 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 586 Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 627 through 638 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 663 through 671 removed outlier: 3.541A pdb=" N VAL D 667 " --> pdb=" O THR D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 696 through 705 Processing helix chain 'D' and resid 706 through 724 removed outlier: 4.605A pdb=" N SER D 722 " --> pdb=" O ASN D 718 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.833A pdb=" N TYR A 120 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 127 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 407 Processing sheet with id=AA3, first strand: chain 'A' and resid 442 through 446 removed outlier: 7.021A pdb=" N ALA A 433 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'B' and resid 403 through 405 Processing sheet with id=AA6, first strand: chain 'B' and resid 444 through 448 removed outlier: 5.256A pdb=" N THR B 446 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA B 433 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.554A pdb=" N TYR C 120 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AA9, first strand: chain 'C' and resid 403 through 407 removed outlier: 6.716A pdb=" N HIS C 476 " --> pdb=" O CYS C 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.662A pdb=" N VAL C 412 " --> pdb=" O VAL C 471 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL C 471 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 414 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 121 removed outlier: 3.712A pdb=" N TYR D 120 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 240 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 403 through 405 removed outlier: 3.556A pdb=" N TYR D 424 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 454 " --> pdb=" O TYR D 424 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR D 452 " --> pdb=" O VAL D 426 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 411 through 414 removed outlier: 6.596A pdb=" N VAL D 469 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 446 " --> pdb=" O ALA D 433 " (cutoff:3.500A) 1362 hydrogen bonds defined for protein. 3861 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: 5.17 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6462 1.34 - 1.46: 3924 1.46 - 1.58: 11918 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 22460 Sorted by residual: bond pdb=" N VAL C 272 " pdb=" CA VAL C 272 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.23e-02 6.61e+03 9.20e+00 bond pdb=" N VAL B 272 " pdb=" CA VAL B 272 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.18e+00 bond pdb=" N VAL D 272 " pdb=" CA VAL D 272 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N ILE D 266 " pdb=" CA ILE D 266 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.92e+00 bond pdb=" N VAL D 426 " pdb=" CA VAL D 426 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 8.88e+00 ... (remaining 22455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 29370 2.10 - 4.20: 886 4.20 - 6.30: 87 6.30 - 8.40: 35 8.40 - 10.50: 6 Bond angle restraints: 30384 Sorted by residual: angle pdb=" CA GLY D 429 " pdb=" C GLY D 429 " pdb=" O GLY D 429 " ideal model delta sigma weight residual 122.57 118.36 4.21 9.20e-01 1.18e+00 2.09e+01 angle pdb=" N LEU B 81 " pdb=" CA LEU B 81 " pdb=" C LEU B 81 " ideal model delta sigma weight residual 113.72 107.84 5.88 1.30e+00 5.92e-01 2.05e+01 angle pdb=" N ASP D 563 " pdb=" CA ASP D 563 " pdb=" C ASP D 563 " ideal model delta sigma weight residual 113.21 108.18 5.03 1.15e+00 7.56e-01 1.91e+01 angle pdb=" CA GLN B 397 " pdb=" CB GLN B 397 " pdb=" CG GLN B 397 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 angle pdb=" N CYS D 427 " pdb=" CA CYS D 427 " pdb=" C CYS D 427 " ideal model delta sigma weight residual 113.97 108.86 5.11 1.28e+00 6.10e-01 1.59e+01 ... (remaining 30379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 11477 17.71 - 35.41: 1368 35.41 - 53.12: 367 53.12 - 70.83: 81 70.83 - 88.53: 11 Dihedral angle restraints: 13304 sinusoidal: 5396 harmonic: 7908 Sorted by residual: dihedral pdb=" CA VAL C 272 " pdb=" C VAL C 272 " pdb=" N GLY C 273 " pdb=" CA GLY C 273 " ideal model delta harmonic sigma weight residual 180.00 150.84 29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA VAL A 272 " pdb=" C VAL A 272 " pdb=" N GLY A 273 " pdb=" CA GLY A 273 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA TYR D 355 " pdb=" C TYR D 355 " pdb=" N THR D 356 " pdb=" CA THR D 356 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 13301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3093 0.087 - 0.175: 259 0.175 - 0.262: 22 0.262 - 0.350: 1 0.350 - 0.437: 1 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CG LEU C 713 " pdb=" CB LEU C 713 " pdb=" CD1 LEU C 713 " pdb=" CD2 LEU C 713 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CG LEU B 665 " pdb=" CB LEU B 665 " pdb=" CD1 LEU B 665 " pdb=" CD2 LEU B 665 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ILE C 277 " pdb=" N ILE C 277 " pdb=" C ILE C 277 " pdb=" CB ILE C 277 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3373 not shown) Planarity restraints: 3832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 139 " 0.018 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR D 139 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR D 139 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 139 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR D 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 139 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 139 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 493 " -0.020 2.00e-02 2.50e+03 2.26e-02 8.90e+00 pdb=" CG PHE B 493 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 493 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 493 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 493 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 493 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 493 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 432 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU A 432 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU A 432 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 433 " -0.014 2.00e-02 2.50e+03 ... (remaining 3829 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3104 2.75 - 3.29: 24624 3.29 - 3.83: 40314 3.83 - 4.36: 49150 4.36 - 4.90: 77025 Nonbonded interactions: 194217 Sorted by model distance: nonbonded pdb=" O HIS C 494 " pdb=" OG1 THR C 498 " model vdw 2.215 3.040 nonbonded pdb=" O ILE B 194 " pdb=" NH2 ARG C 320 " model vdw 2.216 3.120 nonbonded pdb=" O PHE D 87 " pdb=" NH2 ARG D 168 " model vdw 2.223 3.120 nonbonded pdb=" O PHE C 87 " pdb=" NH2 ARG C 168 " model vdw 2.244 3.120 nonbonded pdb=" OD1 ASN D 331 " pdb=" NH1 ARG D 340 " model vdw 2.246 3.120 ... (remaining 194212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.290 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.005 0.056 22460 Z= 0.295 Angle : 0.814 10.499 30384 Z= 0.481 Chirality : 0.051 0.437 3376 Planarity : 0.005 0.078 3832 Dihedral : 16.466 88.533 8232 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.27 % Allowed : 23.45 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 2696 helix: 0.09 (0.11), residues: 1718 sheet: -2.15 (0.48), residues: 96 loop : -0.43 (0.23), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 479 TYR 0.063 0.002 TYR D 139 PHE 0.052 0.002 PHE B 493 TRP 0.037 0.002 TRP A 693 HIS 0.016 0.001 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00491 (22460) covalent geometry : angle 0.81372 (30384) hydrogen bonds : bond 0.14551 ( 1362) hydrogen bonds : angle 6.65310 ( 3861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 502 time to evaluate : 1.026 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: 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 330 MET cc_start: 0.8179 (mtm) cc_final: 0.7941 (mmm) REVERT: A 500 LEU cc_start: 0.8336 (mm) cc_final: 0.7909 (pp) REVERT: A 591 ASN cc_start: 0.8775 (m-40) cc_final: 0.8558 (m-40) REVERT: B 55 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7831 (ptpp) REVERT: B 56 TYR cc_start: 0.7346 (p90) cc_final: 0.7082 (p90) REVERT: B 348 ARG cc_start: 0.8045 (tmm-80) cc_final: 0.7776 (mmm-85) REVERT: B 349 LEU cc_start: 0.9062 (tp) cc_final: 0.8766 (tt) REVERT: B 386 LEU cc_start: 0.8352 (mm) cc_final: 0.7502 (tp) REVERT: B 402 LEU cc_start: 0.8590 (mt) cc_final: 0.7799 (mm) REVERT: B 424 TYR cc_start: 0.5643 (m-80) cc_final: 0.5393 (m-80) REVERT: B 493 PHE cc_start: 0.7921 (t80) cc_final: 0.7500 (p90) REVERT: B 500 LEU cc_start: 0.8690 (mp) cc_final: 0.8192 (mt) REVERT: B 512 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6182 (mtp180) REVERT: B 519 ASP cc_start: 0.8167 (t0) cc_final: 0.7927 (m-30) REVERT: B 644 LEU cc_start: 0.6458 (tp) cc_final: 0.6237 (mt) REVERT: B 676 MET cc_start: 0.5250 (ptp) cc_final: 0.4861 (ptt) REVERT: C 70 MET cc_start: 0.7941 (tpp) cc_final: 0.7607 (tpt) REVERT: C 127 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7436 (tpp-160) REVERT: C 315 ASN cc_start: 0.8354 (m-40) cc_final: 0.8119 (t0) REVERT: C 330 MET cc_start: 0.8605 (mtm) cc_final: 0.8197 (mtm) REVERT: C 351 TYR cc_start: 0.7209 (t80) cc_final: 0.6239 (t80) REVERT: C 406 TYR cc_start: 0.8206 (m-80) cc_final: 0.7410 (m-80) REVERT: C 497 ARG cc_start: 0.8632 (ptt90) cc_final: 0.8273 (ptt-90) REVERT: C 533 LEU cc_start: 0.8356 (mt) cc_final: 0.8148 (mp) REVERT: C 562 TYR cc_start: 0.7790 (p90) cc_final: 0.7424 (p90) REVERT: C 652 MET cc_start: 0.4788 (tpp) cc_final: 0.4023 (tpp) REVERT: C 679 MET cc_start: 0.7056 (mmm) cc_final: 0.6384 (mmm) REVERT: D 266 ILE cc_start: 0.8900 (mm) cc_final: 0.8637 (mm) REVERT: D 423 LEU cc_start: 0.9018 (tp) cc_final: 0.8816 (tp) REVERT: D 491 ILE cc_start: 0.7072 (mt) cc_final: 0.6780 (mm) REVERT: D 534 LYS cc_start: 0.9025 (mttt) cc_final: 0.8785 (ptpp) REVERT: D 540 PHE cc_start: 0.7877 (t80) cc_final: 0.7630 (t80) REVERT: D 550 LEU cc_start: 0.7932 (mt) cc_final: 0.7577 (mt) REVERT: D 581 LEU cc_start: 0.8485 (pp) cc_final: 0.8153 (tp) REVERT: D 624 ASN cc_start: 0.7760 (m-40) cc_final: 0.7079 (p0) outliers start: 78 outliers final: 38 residues processed: 550 average time/residue: 0.1781 time to fit residues: 148.4134 Evaluate side-chains 366 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 676 MET Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 380 TYR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 475 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN B 630 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN C 362 GLN C 403 HIS ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS C 523 HIS C 585 GLN C 609 GLN ** D 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 403 HIS ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS D 465 GLN D 483 GLN D 487 ASN D 510 ASN D 695 ASN D 706 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.170615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110058 restraints weight = 42949.602| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.01 r_work: 0.3396 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22460 Z= 0.233 Angle : 0.725 11.235 30384 Z= 0.372 Chirality : 0.046 0.205 3376 Planarity : 0.004 0.038 3832 Dihedral : 7.001 59.364 3065 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.90 % Allowed : 21.02 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.16), residues: 2696 helix: 0.41 (0.11), residues: 1736 sheet: -1.84 (0.51), residues: 94 loop : -0.38 (0.23), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 479 TYR 0.025 0.002 TYR A 562 PHE 0.030 0.003 PHE D 319 TRP 0.020 0.002 TRP B 75 HIS 0.012 0.002 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00525 (22460) covalent geometry : angle 0.72477 (30384) hydrogen bonds : bond 0.05790 ( 1362) hydrogen bonds : angle 5.54465 ( 3861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 357 time to evaluate : 1.038 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: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8941 (mm) REVERT: A 320 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7697 (tpt-90) REVERT: A 360 MET cc_start: 0.8000 (mmt) cc_final: 0.7553 (mmt) REVERT: A 368 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8778 (tp) REVERT: A 375 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 386 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8277 (tp) REVERT: A 470 ARG cc_start: 0.8620 (mtp180) cc_final: 0.8344 (ttt-90) REVERT: A 528 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7980 (pt0) REVERT: A 576 TYR cc_start: 0.5833 (m-10) cc_final: 0.5590 (m-10) REVERT: B 55 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7868 (ptpp) REVERT: B 165 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: B 301 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7712 (t80) REVERT: B 348 ARG cc_start: 0.7976 (tmm-80) cc_final: 0.7668 (mmm-85) REVERT: B 386 LEU cc_start: 0.8420 (mm) cc_final: 0.7538 (tp) REVERT: B 493 PHE cc_start: 0.7848 (t80) cc_final: 0.7316 (p90) REVERT: B 500 LEU cc_start: 0.8562 (mp) cc_final: 0.8217 (mt) REVERT: B 512 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.5825 (tpt170) REVERT: B 519 ASP cc_start: 0.8200 (t0) cc_final: 0.7948 (m-30) REVERT: B 524 ILE cc_start: 0.7935 (mt) cc_final: 0.7715 (mt) REVERT: B 644 LEU cc_start: 0.6280 (tp) cc_final: 0.6053 (mt) REVERT: B 676 MET cc_start: 0.5001 (ptp) cc_final: 0.4661 (ptp) REVERT: B 718 ASN cc_start: 0.5739 (t0) cc_final: 0.5506 (m-40) REVERT: C 70 MET cc_start: 0.7976 (tpp) cc_final: 0.7576 (tpt) REVERT: C 127 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7370 (tpp-160) REVERT: C 130 TYR cc_start: 0.7550 (m-80) cc_final: 0.7289 (m-10) REVERT: C 202 LEU cc_start: 0.9028 (mt) cc_final: 0.8803 (mm) REVERT: C 315 ASN cc_start: 0.8359 (m-40) cc_final: 0.8115 (t0) REVERT: C 330 MET cc_start: 0.8723 (mtm) cc_final: 0.8437 (mtm) REVERT: C 406 TYR cc_start: 0.8492 (m-80) cc_final: 0.8159 (m-80) REVERT: C 470 ARG cc_start: 0.7456 (ptm160) cc_final: 0.7131 (ptt90) REVERT: C 582 PHE cc_start: 0.6941 (OUTLIER) cc_final: 0.6414 (t80) REVERT: C 652 MET cc_start: 0.5337 (tpp) cc_final: 0.3942 (tpp) REVERT: C 679 MET cc_start: 0.7231 (mmm) cc_final: 0.6911 (mmm) REVERT: D 90 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: D 175 LEU cc_start: 0.8436 (mt) cc_final: 0.7672 (tp) REVERT: D 252 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8523 (mt) REVERT: D 315 ASN cc_start: 0.8509 (m-40) cc_final: 0.8221 (p0) REVERT: D 534 LYS cc_start: 0.9046 (mttt) cc_final: 0.8786 (ptpp) REVERT: D 546 GLN cc_start: 0.8336 (tp-100) cc_final: 0.8088 (tp-100) REVERT: D 550 LEU cc_start: 0.7760 (mt) cc_final: 0.7286 (mt) REVERT: D 581 LEU cc_start: 0.8515 (pp) cc_final: 0.8208 (tp) REVERT: D 638 LYS cc_start: 0.7362 (pttp) cc_final: 0.7078 (tptt) outliers start: 141 outliers final: 78 residues processed: 465 average time/residue: 0.1658 time to fit residues: 119.9074 Evaluate side-chains 391 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 302 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 573 CYS Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 224 optimal weight: 0.9980 chunk 223 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 108 optimal weight: 0.0060 chunk 150 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 451 HIS A 527 GLN A 536 ASN B 501 ASN B 502 ASN B 523 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN D 624 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.173286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115592 restraints weight = 42863.772| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.47 r_work: 0.3452 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22460 Z= 0.146 Angle : 0.643 12.336 30384 Z= 0.325 Chirality : 0.042 0.251 3376 Planarity : 0.004 0.040 3832 Dihedral : 6.338 59.181 3036 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.40 % Allowed : 20.94 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.16), residues: 2696 helix: 0.71 (0.12), residues: 1738 sheet: -1.82 (0.53), residues: 88 loop : -0.32 (0.23), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 479 TYR 0.022 0.002 TYR A 562 PHE 0.026 0.002 PHE D 425 TRP 0.015 0.001 TRP B 75 HIS 0.015 0.001 HIS C 523 Details of bonding type rmsd covalent geometry : bond 0.00306 (22460) covalent geometry : angle 0.64344 (30384) hydrogen bonds : bond 0.05168 ( 1362) hydrogen bonds : angle 5.17734 ( 3861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 339 time to evaluate : 0.915 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASP cc_start: 0.8379 (t0) cc_final: 0.7906 (t0) REVERT: A 139 TYR cc_start: 0.7562 (t80) cc_final: 0.7253 (t80) REVERT: A 197 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7048 (mp) REVERT: A 330 MET cc_start: 0.8347 (mtm) cc_final: 0.8051 (tpp) REVERT: A 360 MET cc_start: 0.7975 (mmt) cc_final: 0.7517 (mmt) REVERT: A 368 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8817 (tp) REVERT: A 375 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 386 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8100 (tp) REVERT: A 431 LEU cc_start: 0.8912 (tp) cc_final: 0.8695 (mm) REVERT: A 528 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8007 (pt0) REVERT: B 55 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7932 (ptpp) REVERT: B 165 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: B 168 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7759 (ttp80) REVERT: B 170 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8925 (mm) REVERT: B 301 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7458 (t80) REVERT: B 386 LEU cc_start: 0.8564 (mm) cc_final: 0.7699 (tp) REVERT: B 398 ILE cc_start: 0.8845 (mm) cc_final: 0.8611 (mm) REVERT: B 402 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7634 (mm) REVERT: B 411 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: B 465 GLN cc_start: 0.8891 (tt0) cc_final: 0.8505 (tm-30) REVERT: B 512 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6418 (mtp180) REVERT: B 519 ASP cc_start: 0.8072 (t0) cc_final: 0.7868 (m-30) REVERT: C 70 MET cc_start: 0.7798 (tpp) cc_final: 0.7367 (tpt) REVERT: C 127 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7361 (tpp-160) REVERT: C 130 TYR cc_start: 0.7608 (m-80) cc_final: 0.6834 (m-10) REVERT: C 202 LEU cc_start: 0.8778 (mt) cc_final: 0.8493 (mm) REVERT: C 330 MET cc_start: 0.8590 (mtm) cc_final: 0.8291 (mtm) REVERT: C 406 TYR cc_start: 0.7988 (m-80) cc_final: 0.7229 (m-80) REVERT: C 451 HIS cc_start: 0.7278 (m-70) cc_final: 0.7022 (m-70) REVERT: C 470 ARG cc_start: 0.7436 (ptm160) cc_final: 0.7087 (ptt90) REVERT: C 643 PHE cc_start: 0.8376 (t80) cc_final: 0.7929 (t80) REVERT: C 652 MET cc_start: 0.4877 (tpp) cc_final: 0.3839 (tpp) REVERT: C 679 MET cc_start: 0.7188 (mmm) cc_final: 0.6855 (mmm) REVERT: D 175 LEU cc_start: 0.8392 (mt) cc_final: 0.7210 (tp) REVERT: D 315 ASN cc_start: 0.8496 (m-40) cc_final: 0.8167 (p0) REVERT: D 465 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: D 527 GLN cc_start: 0.9113 (pt0) cc_final: 0.8842 (pp30) REVERT: D 534 LYS cc_start: 0.9046 (mttt) cc_final: 0.8781 (ptpp) REVERT: D 546 GLN cc_start: 0.8316 (tp-100) cc_final: 0.8042 (tp-100) REVERT: D 550 LEU cc_start: 0.7706 (mt) cc_final: 0.7108 (mt) REVERT: D 581 LEU cc_start: 0.8476 (pp) cc_final: 0.8220 (tp) REVERT: D 679 MET cc_start: 0.5702 (mmp) cc_final: 0.5493 (mpp) outliers start: 129 outliers final: 64 residues processed: 437 average time/residue: 0.1622 time to fit residues: 111.1579 Evaluate side-chains 360 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 0.6980 chunk 259 optimal weight: 30.0000 chunk 179 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.169092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.108761 restraints weight = 42877.208| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.35 r_work: 0.3346 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22460 Z= 0.271 Angle : 0.701 11.795 30384 Z= 0.357 Chirality : 0.046 0.281 3376 Planarity : 0.004 0.044 3832 Dihedral : 6.256 58.310 3029 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.99 % Allowed : 20.64 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.16), residues: 2696 helix: 0.59 (0.12), residues: 1737 sheet: -1.85 (0.56), residues: 85 loop : -0.35 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 320 TYR 0.030 0.002 TYR A 351 PHE 0.029 0.002 PHE C 287 TRP 0.016 0.002 TRP D 75 HIS 0.007 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00627 (22460) covalent geometry : angle 0.70112 (30384) hydrogen bonds : bond 0.05217 ( 1362) hydrogen bonds : angle 5.19306 ( 3861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 317 time to evaluate : 0.868 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: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7194 (mmp80) REVERT: A 147 ASP cc_start: 0.8440 (m-30) cc_final: 0.8207 (m-30) REVERT: A 335 LEU cc_start: 0.8169 (mp) cc_final: 0.7943 (mp) REVERT: A 431 LEU cc_start: 0.8980 (tp) cc_final: 0.8724 (mm) REVERT: A 576 TYR cc_start: 0.6205 (m-10) cc_final: 0.5858 (m-10) REVERT: B 55 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7890 (ptpp) REVERT: B 165 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8212 (tp30) REVERT: B 170 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8998 (mm) REVERT: B 282 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7990 (mp) REVERT: B 301 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7531 (t80) REVERT: B 411 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6430 (mp0) REVERT: B 465 GLN cc_start: 0.8971 (tt0) cc_final: 0.8421 (tm-30) REVERT: B 493 PHE cc_start: 0.7743 (t80) cc_final: 0.7185 (p90) REVERT: B 500 LEU cc_start: 0.8489 (mp) cc_final: 0.7885 (mt) REVERT: C 70 MET cc_start: 0.7882 (tpp) cc_final: 0.7464 (tpt) REVERT: C 127 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7218 (tpp-160) REVERT: C 130 TYR cc_start: 0.7714 (m-80) cc_final: 0.6871 (m-10) REVERT: C 202 LEU cc_start: 0.8795 (mt) cc_final: 0.8460 (mm) REVERT: C 406 TYR cc_start: 0.8082 (m-80) cc_final: 0.7281 (m-80) REVERT: C 451 HIS cc_start: 0.7395 (m-70) cc_final: 0.7076 (m-70) REVERT: C 470 ARG cc_start: 0.7431 (ptm160) cc_final: 0.7049 (ptt90) REVERT: C 643 PHE cc_start: 0.8416 (t80) cc_final: 0.8021 (t80) REVERT: C 652 MET cc_start: 0.4893 (tpp) cc_final: 0.3899 (tpp) REVERT: C 679 MET cc_start: 0.7316 (mmm) cc_final: 0.6998 (mmm) REVERT: D 64 TRP cc_start: 0.7629 (m100) cc_final: 0.7010 (m-10) REVERT: D 315 ASN cc_start: 0.8550 (m-40) cc_final: 0.8275 (p0) REVERT: D 323 MET cc_start: 0.8776 (mmt) cc_final: 0.8552 (mmt) REVERT: D 527 GLN cc_start: 0.9100 (pt0) cc_final: 0.8856 (pp30) REVERT: D 534 LYS cc_start: 0.8994 (mttt) cc_final: 0.8710 (ptpp) REVERT: D 550 LEU cc_start: 0.7615 (mt) cc_final: 0.7237 (mt) REVERT: D 581 LEU cc_start: 0.8524 (pp) cc_final: 0.8264 (tp) REVERT: D 652 MET cc_start: 0.1946 (mmm) cc_final: 0.1609 (mmt) outliers start: 143 outliers final: 101 residues processed: 419 average time/residue: 0.1610 time to fit residues: 105.6512 Evaluate side-chains 388 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 280 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 512 ARG Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 425 PHE Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 573 CYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 687 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 221 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 265 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 237 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN ** D 281 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 = 0.4474 r_free = 0.4474 target = 0.172142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114750 restraints weight = 43499.663| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.61 r_work: 0.3416 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22460 Z= 0.142 Angle : 0.621 11.270 30384 Z= 0.314 Chirality : 0.043 0.278 3376 Planarity : 0.004 0.046 3832 Dihedral : 5.949 59.335 3024 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.86 % Allowed : 22.11 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.16), residues: 2696 helix: 0.82 (0.12), residues: 1737 sheet: -1.70 (0.53), residues: 94 loop : -0.22 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 565 TYR 0.020 0.002 TYR D 380 PHE 0.024 0.002 PHE A 485 TRP 0.014 0.001 TRP B 75 HIS 0.007 0.001 HIS C 523 Details of bonding type rmsd covalent geometry : bond 0.00306 (22460) covalent geometry : angle 0.62083 (30384) hydrogen bonds : bond 0.04762 ( 1362) hydrogen bonds : angle 4.96428 ( 3861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 318 time to evaluate : 0.899 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8475 (m-30) cc_final: 0.8119 (m-30) REVERT: A 197 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7072 (mp) REVERT: A 403 HIS cc_start: 0.7489 (m90) cc_final: 0.7266 (m90) REVERT: A 404 GLU cc_start: 0.7589 (pp20) cc_final: 0.7243 (pm20) REVERT: A 431 LEU cc_start: 0.8996 (tp) cc_final: 0.8717 (mm) REVERT: A 528 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8013 (pt0) REVERT: A 576 TYR cc_start: 0.6377 (m-10) cc_final: 0.6045 (m-10) REVERT: B 55 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (ptpp) REVERT: B 165 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8155 (tp30) REVERT: B 170 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9008 (mm) REVERT: B 301 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7469 (t80) REVERT: B 398 ILE cc_start: 0.8784 (mm) cc_final: 0.8482 (mm) REVERT: B 411 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: B 465 GLN cc_start: 0.8910 (tt0) cc_final: 0.8441 (tm-30) REVERT: B 500 LEU cc_start: 0.8521 (mp) cc_final: 0.7926 (mt) REVERT: C 70 MET cc_start: 0.7847 (tpp) cc_final: 0.7423 (tpt) REVERT: C 127 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7238 (tpp-160) REVERT: C 129 VAL cc_start: 0.5131 (OUTLIER) cc_final: 0.4810 (t) REVERT: C 130 TYR cc_start: 0.7602 (m-80) cc_final: 0.6871 (m-10) REVERT: C 177 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7823 (mtp180) REVERT: C 189 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: C 202 LEU cc_start: 0.8760 (mt) cc_final: 0.8490 (mm) REVERT: C 406 TYR cc_start: 0.8141 (m-80) cc_final: 0.7380 (m-80) REVERT: C 451 HIS cc_start: 0.7489 (m-70) cc_final: 0.7277 (m-70) REVERT: C 470 ARG cc_start: 0.7387 (ptm160) cc_final: 0.6972 (ptt90) REVERT: C 643 PHE cc_start: 0.8378 (t80) cc_final: 0.7945 (t80) REVERT: C 652 MET cc_start: 0.4943 (tpp) cc_final: 0.3969 (tpp) REVERT: C 679 MET cc_start: 0.7355 (mmm) cc_final: 0.7049 (mmm) REVERT: D 64 TRP cc_start: 0.7600 (m100) cc_final: 0.6998 (m-10) REVERT: D 315 ASN cc_start: 0.8539 (m-40) cc_final: 0.8228 (p0) REVERT: D 355 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6964 (p90) REVERT: D 435 VAL cc_start: 0.7031 (m) cc_final: 0.6655 (p) REVERT: D 534 LYS cc_start: 0.8995 (mttt) cc_final: 0.8650 (ptpp) REVERT: D 581 LEU cc_start: 0.8486 (pp) cc_final: 0.8234 (tp) outliers start: 116 outliers final: 81 residues processed: 400 average time/residue: 0.1651 time to fit residues: 102.8906 Evaluate side-chains 379 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 288 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 562 TYR Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 645 LYS Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 687 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 227 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 237 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN D 527 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.172160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115411 restraints weight = 42949.084| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.91 r_work: 0.3415 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22460 Z= 0.143 Angle : 0.617 11.543 30384 Z= 0.311 Chirality : 0.042 0.294 3376 Planarity : 0.004 0.048 3832 Dihedral : 5.794 59.558 3018 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.98 % Allowed : 23.07 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2696 helix: 0.90 (0.12), residues: 1738 sheet: -1.66 (0.52), residues: 104 loop : -0.15 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 512 TYR 0.023 0.001 TYR B 424 PHE 0.024 0.002 PHE A 485 TRP 0.012 0.001 TRP D 75 HIS 0.006 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00315 (22460) covalent geometry : angle 0.61736 (30384) hydrogen bonds : bond 0.04624 ( 1362) hydrogen bonds : angle 4.90971 ( 3861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 310 time to evaluate : 0.876 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7215 (mmp80) REVERT: A 197 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7054 (mp) REVERT: A 206 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7563 (t80) REVERT: A 368 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8761 (tp) REVERT: A 403 HIS cc_start: 0.7564 (m90) cc_final: 0.7362 (m90) REVERT: A 404 GLU cc_start: 0.7623 (pp20) cc_final: 0.7280 (pm20) REVERT: A 431 LEU cc_start: 0.8999 (tp) cc_final: 0.8723 (mm) REVERT: A 470 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8364 (ttt-90) REVERT: A 528 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7968 (pt0) REVERT: A 576 TYR cc_start: 0.6522 (m-10) cc_final: 0.6216 (m-10) REVERT: A 676 MET cc_start: 0.4674 (tpt) cc_final: 0.3617 (mmt) REVERT: B 55 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7821 (ptpp) REVERT: B 165 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: B 170 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8972 (mm) REVERT: B 301 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7353 (t80) REVERT: B 411 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: B 465 GLN cc_start: 0.8914 (tt0) cc_final: 0.8478 (tm-30) REVERT: C 70 MET cc_start: 0.7843 (tpp) cc_final: 0.7415 (tpt) REVERT: C 127 ARG cc_start: 0.7625 (tpp80) cc_final: 0.7220 (tpp-160) REVERT: C 129 VAL cc_start: 0.5106 (OUTLIER) cc_final: 0.4740 (t) REVERT: C 130 TYR cc_start: 0.7596 (m-80) cc_final: 0.6964 (m-10) REVERT: C 177 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: C 202 LEU cc_start: 0.8746 (mt) cc_final: 0.8481 (mm) REVERT: C 401 ARG cc_start: 0.9022 (mtt90) cc_final: 0.8593 (mtm-85) REVERT: C 406 TYR cc_start: 0.8141 (m-80) cc_final: 0.7419 (m-80) REVERT: C 451 HIS cc_start: 0.7681 (m-70) cc_final: 0.7462 (m-70) REVERT: C 470 ARG cc_start: 0.7420 (ptm160) cc_final: 0.7011 (ptt90) REVERT: C 643 PHE cc_start: 0.8373 (t80) cc_final: 0.7947 (t80) REVERT: C 652 MET cc_start: 0.4937 (tpp) cc_final: 0.3970 (tpp) REVERT: C 679 MET cc_start: 0.7345 (mmm) cc_final: 0.7056 (mmm) REVERT: D 64 TRP cc_start: 0.7592 (m100) cc_final: 0.7008 (m-10) REVERT: D 315 ASN cc_start: 0.8523 (m-40) cc_final: 0.8260 (p0) REVERT: D 355 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6930 (p90) REVERT: D 534 LYS cc_start: 0.8955 (mttt) cc_final: 0.8606 (ptpp) REVERT: D 581 LEU cc_start: 0.8475 (pp) cc_final: 0.8219 (tp) REVERT: D 679 MET cc_start: 0.5669 (mmp) cc_final: 0.4958 (mtt) outliers start: 119 outliers final: 91 residues processed: 393 average time/residue: 0.1585 time to fit residues: 97.0573 Evaluate side-chains 394 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 291 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 645 LYS Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 562 TYR Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain D residue 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 134 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 209 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN B 655 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** C 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 GLN D 569 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.172792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114490 restraints weight = 42887.920| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.71 r_work: 0.3445 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22460 Z= 0.137 Angle : 0.614 12.515 30384 Z= 0.310 Chirality : 0.042 0.284 3376 Planarity : 0.004 0.048 3832 Dihedral : 5.718 59.914 3016 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.98 % Allowed : 23.58 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2696 helix: 0.98 (0.12), residues: 1739 sheet: -1.54 (0.54), residues: 99 loop : -0.08 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 565 TYR 0.029 0.001 TYR B 424 PHE 0.028 0.002 PHE C 394 TRP 0.012 0.001 TRP D 75 HIS 0.006 0.001 HIS D 346 Details of bonding type rmsd covalent geometry : bond 0.00299 (22460) covalent geometry : angle 0.61402 (30384) hydrogen bonds : bond 0.04522 ( 1362) hydrogen bonds : angle 4.84016 ( 3861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 305 time to evaluate : 0.959 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7283 (mmp80) REVERT: A 156 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7722 (mm) REVERT: A 197 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7026 (mp) REVERT: A 206 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 368 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 384 VAL cc_start: 0.8807 (t) cc_final: 0.8606 (t) REVERT: A 404 GLU cc_start: 0.7605 (pp20) cc_final: 0.7358 (pm20) REVERT: A 431 LEU cc_start: 0.9033 (tp) cc_final: 0.8703 (mm) REVERT: A 528 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7913 (pt0) REVERT: A 676 MET cc_start: 0.4565 (tpt) cc_final: 0.3648 (mmt) REVERT: B 55 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (ptpp) REVERT: B 170 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8974 (mm) REVERT: B 282 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 301 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7310 (t80) REVERT: B 386 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 402 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 411 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: B 451 HIS cc_start: 0.7266 (m90) cc_final: 0.6737 (m-70) REVERT: B 465 GLN cc_start: 0.8911 (tt0) cc_final: 0.8506 (tm-30) REVERT: B 500 LEU cc_start: 0.8394 (mp) cc_final: 0.7982 (mt) REVERT: C 70 MET cc_start: 0.7838 (tpp) cc_final: 0.7417 (tpt) REVERT: C 127 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7228 (tpp-160) REVERT: C 129 VAL cc_start: 0.5220 (OUTLIER) cc_final: 0.4892 (t) REVERT: C 130 TYR cc_start: 0.7534 (m-80) cc_final: 0.6964 (m-10) REVERT: C 177 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7784 (mtp180) REVERT: C 202 LEU cc_start: 0.8746 (mt) cc_final: 0.8484 (mm) REVERT: C 401 ARG cc_start: 0.9020 (mtt90) cc_final: 0.8579 (mtm-85) REVERT: C 406 TYR cc_start: 0.8172 (m-80) cc_final: 0.7482 (m-80) REVERT: C 451 HIS cc_start: 0.7671 (m-70) cc_final: 0.7369 (m-70) REVERT: C 470 ARG cc_start: 0.7397 (ptm160) cc_final: 0.6987 (ptt90) REVERT: C 497 ARG cc_start: 0.8582 (ptt-90) cc_final: 0.8301 (mtm-85) REVERT: C 643 PHE cc_start: 0.8402 (t80) cc_final: 0.7967 (t80) REVERT: C 652 MET cc_start: 0.4975 (tpp) cc_final: 0.4027 (tpp) REVERT: C 679 MET cc_start: 0.7416 (mmm) cc_final: 0.7136 (mmm) REVERT: D 64 TRP cc_start: 0.7583 (m100) cc_final: 0.7007 (m-10) REVERT: D 315 ASN cc_start: 0.8511 (m-40) cc_final: 0.8222 (p0) REVERT: D 355 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6880 (p90) REVERT: D 425 PHE cc_start: 0.7434 (m-80) cc_final: 0.7222 (m-80) REVERT: D 534 LYS cc_start: 0.8945 (mttt) cc_final: 0.8593 (ptpp) REVERT: D 562 TYR cc_start: 0.6779 (p90) cc_final: 0.6200 (p90) REVERT: D 581 LEU cc_start: 0.8463 (pp) cc_final: 0.8197 (tp) REVERT: D 679 MET cc_start: 0.5711 (mmp) cc_final: 0.5015 (mtt) outliers start: 119 outliers final: 88 residues processed: 388 average time/residue: 0.1630 time to fit residues: 98.7806 Evaluate side-chains 391 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 288 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 631 PHE Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 582 PHE Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 GLN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115130 restraints weight = 42455.754| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.24 r_work: 0.3434 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22460 Z= 0.198 Angle : 0.643 11.885 30384 Z= 0.327 Chirality : 0.044 0.320 3376 Planarity : 0.004 0.047 3832 Dihedral : 5.771 59.309 3016 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.82 % Allowed : 24.12 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2696 helix: 0.94 (0.12), residues: 1733 sheet: -1.32 (0.53), residues: 104 loop : -0.12 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 401 TYR 0.042 0.002 TYR A 351 PHE 0.025 0.002 PHE A 485 TRP 0.014 0.001 TRP D 75 HIS 0.023 0.001 HIS C 523 Details of bonding type rmsd covalent geometry : bond 0.00457 (22460) covalent geometry : angle 0.64288 (30384) hydrogen bonds : bond 0.04684 ( 1362) hydrogen bonds : angle 4.86004 ( 3861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 303 time to evaluate : 0.932 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: 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 156 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7985 (mm) REVERT: A 197 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 206 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7875 (t80) REVERT: A 368 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 384 VAL cc_start: 0.8792 (t) cc_final: 0.8590 (t) REVERT: A 404 GLU cc_start: 0.7482 (pp20) cc_final: 0.7210 (pm20) REVERT: A 431 LEU cc_start: 0.9028 (tp) cc_final: 0.8752 (mm) REVERT: A 528 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7901 (pt0) REVERT: A 576 TYR cc_start: 0.6354 (m-10) cc_final: 0.5989 (m-10) REVERT: A 676 MET cc_start: 0.4434 (tpt) cc_final: 0.3411 (mmt) REVERT: B 55 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7793 (ptpp) REVERT: B 165 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8112 (tp30) REVERT: B 170 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 282 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8036 (mp) REVERT: B 301 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7605 (t80) REVERT: B 386 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 411 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: B 451 HIS cc_start: 0.7265 (m90) cc_final: 0.6953 (m-70) REVERT: B 500 LEU cc_start: 0.8375 (mp) cc_final: 0.8037 (mt) REVERT: C 70 MET cc_start: 0.8110 (tpp) cc_final: 0.7718 (tpt) REVERT: C 127 ARG cc_start: 0.7609 (tpp80) cc_final: 0.7152 (tpp-160) REVERT: C 130 TYR cc_start: 0.7454 (m-80) cc_final: 0.7049 (m-10) REVERT: C 177 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7931 (mtp180) REVERT: C 401 ARG cc_start: 0.9056 (mtt90) cc_final: 0.8646 (mtm-85) REVERT: C 406 TYR cc_start: 0.8422 (m-80) cc_final: 0.7704 (m-80) REVERT: C 451 HIS cc_start: 0.7838 (m-70) cc_final: 0.7564 (m-70) REVERT: C 470 ARG cc_start: 0.7337 (ptm160) cc_final: 0.6983 (ptt90) REVERT: C 643 PHE cc_start: 0.8333 (t80) cc_final: 0.7850 (t80) REVERT: C 652 MET cc_start: 0.5515 (tpp) cc_final: 0.4520 (tpp) REVERT: C 679 MET cc_start: 0.7526 (mmm) cc_final: 0.7252 (mmm) REVERT: D 64 TRP cc_start: 0.7686 (m100) cc_final: 0.7163 (m-10) REVERT: D 126 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6419 (m-10) REVERT: D 315 ASN cc_start: 0.8498 (m-40) cc_final: 0.8246 (p0) REVERT: D 355 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6806 (p90) REVERT: D 534 LYS cc_start: 0.8927 (mttt) cc_final: 0.8552 (ptpp) REVERT: D 581 LEU cc_start: 0.8444 (pp) cc_final: 0.8156 (tp) REVERT: D 679 MET cc_start: 0.5800 (mmp) cc_final: 0.5068 (mtt) outliers start: 115 outliers final: 87 residues processed: 379 average time/residue: 0.1569 time to fit residues: 92.9362 Evaluate side-chains 390 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 289 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 411 GLU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 103 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS D 281 ASN D 465 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.168883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112394 restraints weight = 42705.129| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.33 r_work: 0.3376 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22460 Z= 0.247 Angle : 0.694 11.628 30384 Z= 0.354 Chirality : 0.045 0.381 3376 Planarity : 0.004 0.050 3832 Dihedral : 5.860 59.541 3016 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.07 % Allowed : 24.33 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2696 helix: 0.81 (0.12), residues: 1734 sheet: -1.65 (0.55), residues: 97 loop : -0.17 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 320 TYR 0.020 0.002 TYR B 258 PHE 0.030 0.002 PHE B 407 TRP 0.014 0.002 TRP D 75 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00574 (22460) covalent geometry : angle 0.69421 (30384) hydrogen bonds : bond 0.04857 ( 1362) hydrogen bonds : angle 4.97089 ( 3861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 297 time to evaluate : 0.598 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8001 (mm) REVERT: A 197 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7366 (mp) REVERT: A 206 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 362 GLN cc_start: 0.8719 (mm110) cc_final: 0.8426 (mt0) REVERT: A 384 VAL cc_start: 0.8828 (t) cc_final: 0.8610 (t) REVERT: A 431 LEU cc_start: 0.9039 (tp) cc_final: 0.8787 (mm) REVERT: A 470 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8416 (tpt-90) REVERT: A 528 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7914 (pt0) REVERT: A 586 GLU cc_start: 0.7842 (tp30) cc_final: 0.7456 (tp30) REVERT: A 676 MET cc_start: 0.4602 (tpt) cc_final: 0.3635 (mmt) REVERT: B 55 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7692 (ptpp) REVERT: B 165 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: B 282 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 301 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7752 (t80) REVERT: B 386 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7814 (tp) REVERT: B 398 ILE cc_start: 0.8791 (mm) cc_final: 0.8455 (mm) REVERT: B 451 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6955 (m-70) REVERT: B 476 HIS cc_start: 0.8307 (m-70) cc_final: 0.8079 (m-70) REVERT: B 500 LEU cc_start: 0.8443 (mp) cc_final: 0.8065 (mt) REVERT: C 70 MET cc_start: 0.8126 (tpp) cc_final: 0.7738 (tpt) REVERT: C 127 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7077 (tpp-160) REVERT: C 130 TYR cc_start: 0.7571 (m-80) cc_final: 0.7014 (m-10) REVERT: C 177 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7961 (mtp180) REVERT: C 401 ARG cc_start: 0.9076 (mtt90) cc_final: 0.8663 (mtm-85) REVERT: C 406 TYR cc_start: 0.8419 (m-80) cc_final: 0.7606 (m-80) REVERT: C 451 HIS cc_start: 0.7843 (m-70) cc_final: 0.7527 (m-70) REVERT: C 643 PHE cc_start: 0.8331 (t80) cc_final: 0.7831 (t80) REVERT: C 652 MET cc_start: 0.5599 (tpp) cc_final: 0.4644 (tpp) REVERT: C 679 MET cc_start: 0.7505 (mmm) cc_final: 0.7209 (mmm) REVERT: D 64 TRP cc_start: 0.7717 (m100) cc_final: 0.7191 (m-10) REVERT: D 126 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6628 (m-10) REVERT: D 315 ASN cc_start: 0.8553 (m-40) cc_final: 0.8221 (p0) REVERT: D 355 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6793 (p90) REVERT: D 534 LYS cc_start: 0.8890 (mttt) cc_final: 0.8575 (ptpp) REVERT: D 581 LEU cc_start: 0.8454 (pp) cc_final: 0.8172 (tp) REVERT: D 679 MET cc_start: 0.5765 (mmp) cc_final: 0.5075 (mtt) outliers start: 121 outliers final: 97 residues processed: 379 average time/residue: 0.1348 time to fit residues: 81.1226 Evaluate side-chains 393 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 284 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 504 MET Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 339 LEU Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 467 PHE Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 509 SER Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 126 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 206 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 151 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS D 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.172187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.117816 restraints weight = 43003.601| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.31 r_work: 0.3444 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22460 Z= 0.142 Angle : 0.657 13.295 30384 Z= 0.331 Chirality : 0.043 0.346 3376 Planarity : 0.004 0.047 3832 Dihedral : 5.683 59.543 3014 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.10 % Allowed : 25.34 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.16), residues: 2696 helix: 0.90 (0.12), residues: 1737 sheet: -1.56 (0.56), residues: 96 loop : -0.10 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.030 0.001 TYR A 351 PHE 0.032 0.002 PHE A 485 TRP 0.013 0.001 TRP B 75 HIS 0.008 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00308 (22460) covalent geometry : angle 0.65656 (30384) hydrogen bonds : bond 0.04655 ( 1362) hydrogen bonds : angle 4.87505 ( 3861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 296 time to evaluate : 0.846 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7919 (mm) REVERT: A 197 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7084 (mp) REVERT: A 206 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7645 (t80) REVERT: A 360 MET cc_start: 0.7725 (mmt) cc_final: 0.7468 (mmt) REVERT: A 368 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8821 (tp) REVERT: A 384 VAL cc_start: 0.8829 (t) cc_final: 0.8615 (t) REVERT: A 431 LEU cc_start: 0.9001 (tp) cc_final: 0.8777 (mm) REVERT: A 470 ARG cc_start: 0.8618 (mtp180) cc_final: 0.8399 (tpt-90) REVERT: A 528 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7859 (pt0) REVERT: A 586 GLU cc_start: 0.7748 (tp30) cc_final: 0.7429 (tp30) REVERT: A 676 MET cc_start: 0.4572 (tpt) cc_final: 0.3609 (mmt) REVERT: B 165 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7934 (tp30) REVERT: B 301 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7410 (t80) REVERT: B 451 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6927 (m-70) REVERT: B 465 GLN cc_start: 0.8923 (tt0) cc_final: 0.8613 (tm-30) REVERT: B 476 HIS cc_start: 0.8254 (m-70) cc_final: 0.7821 (m-70) REVERT: B 500 LEU cc_start: 0.8429 (mp) cc_final: 0.7890 (mt) REVERT: B 504 MET cc_start: 0.8099 (tmm) cc_final: 0.7433 (mmp) REVERT: C 70 MET cc_start: 0.7930 (tpp) cc_final: 0.7546 (tpt) REVERT: C 127 ARG cc_start: 0.7584 (tpp80) cc_final: 0.7247 (tpp-160) REVERT: C 130 TYR cc_start: 0.7363 (m-80) cc_final: 0.7063 (m-10) REVERT: C 177 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7855 (mtp180) REVERT: C 401 ARG cc_start: 0.9035 (mtt90) cc_final: 0.8526 (mtm-85) REVERT: C 406 TYR cc_start: 0.8229 (m-80) cc_final: 0.7589 (m-80) REVERT: C 451 HIS cc_start: 0.7735 (m-70) cc_final: 0.7356 (m-70) REVERT: C 497 ARG cc_start: 0.8430 (ptt-90) cc_final: 0.8218 (mtm-85) REVERT: C 643 PHE cc_start: 0.8308 (t80) cc_final: 0.7822 (t80) REVERT: C 652 MET cc_start: 0.5448 (tpp) cc_final: 0.4505 (tpp) REVERT: C 679 MET cc_start: 0.7497 (mmm) cc_final: 0.7253 (mmm) REVERT: D 64 TRP cc_start: 0.7566 (m100) cc_final: 0.7097 (m-10) REVERT: D 126 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: D 315 ASN cc_start: 0.8460 (m-40) cc_final: 0.8161 (p0) REVERT: D 317 GLU cc_start: 0.8779 (tp30) cc_final: 0.8487 (tp30) REVERT: D 355 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6430 (p90) REVERT: D 534 LYS cc_start: 0.8878 (mttt) cc_final: 0.8581 (ptpp) REVERT: D 581 LEU cc_start: 0.8415 (pp) cc_final: 0.8124 (tp) REVERT: D 679 MET cc_start: 0.5748 (mmp) cc_final: 0.5181 (mtt) outliers start: 98 outliers final: 81 residues processed: 361 average time/residue: 0.1343 time to fit residues: 76.2676 Evaluate side-chains 376 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 285 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 494 HIS Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain B residue 56 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 301 TYR Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 515 LYS Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 676 MET Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 143 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 545 TYR Chi-restraints excluded: chain C residue 631 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 126 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 338 ASP Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 530 GLU Chi-restraints excluded: chain D residue 540 PHE Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 558 ASN Chi-restraints excluded: chain D residue 573 CYS Chi-restraints excluded: chain D residue 655 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 706 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.171472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.109995 restraints weight = 44203.491| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.20 r_work: 0.3553 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 22460 Z= 0.182 Angle : 0.657 12.854 30384 Z= 0.331 Chirality : 0.044 0.332 3376 Planarity : 0.004 0.048 3832 Dihedral : 5.551 59.859 3008 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.23 % Allowed : 25.21 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2696 helix: 0.89 (0.12), residues: 1737 sheet: -1.60 (0.56), residues: 97 loop : -0.07 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 283 TYR 0.020 0.002 TYR B 424 PHE 0.029 0.002 PHE C 394 TRP 0.013 0.001 TRP D 75 HIS 0.007 0.001 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00419 (22460) covalent geometry : angle 0.65662 (30384) hydrogen bonds : bond 0.04650 ( 1362) hydrogen bonds : angle 4.87349 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10283.15 seconds wall clock time: 175 minutes 58.81 seconds (10558.81 seconds total)