Starting phenix.real_space_refine on Fri Aug 7 16:28:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.cif Found real_map, /net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13es_77025/08_2026/13es_77025.map" } resolution = 3.23 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.038 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: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 109 5.16 5 C 14252 2.51 5 N 3789 2.21 5 O 4290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22447 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7344 Classifications: {'peptide': 916} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 860} Chain breaks: 1 Chain: "B" Number of atoms: 7344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7344 Classifications: {'peptide': 916} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 860} Chain breaks: 1 Chain: "C" Number of atoms: 7344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7344 Classifications: {'peptide': 916} Link IDs: {'PCIS': 4, 'PTRANS': 51, 'TRANS': 860} Chain breaks: 1 Chain: "G" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 408 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Planarities with less than four sites: {'CGU:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CA': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.10, per 1000 atoms: 0.23 Number of scatterers: 22447 At special positions: 0 Unit cell: (116.6, 116.6, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 109 16.00 O 4290 8.00 N 3789 7.00 C 14252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 22 " distance=2.54 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: 1.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5222 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 18.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.653A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 478 through 481 removed outlier: 3.736A pdb=" N LEU A 481 " --> pdb=" O ALA A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.904A pdb=" N ASN A 531 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 532 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 removed outlier: 3.719A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 593 removed outlier: 3.562A pdb=" N LEU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.738A pdb=" N ASP A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 762 through 775 Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.833A pdb=" N PHE A 798 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 removed outlier: 3.504A pdb=" N GLN A 822 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 891 through 896 Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.648A pdb=" N TYR B 23 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 24' Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.836A pdb=" N ALA B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 274' Processing helix chain 'B' and resid 331 through 334 Processing helix chain 'B' and resid 365 through 377 Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.724A pdb=" N ILE B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.618A pdb=" N ASN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 removed outlier: 3.731A pdb=" N LEU B 481 " --> pdb=" O ALA B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 478 through 481' Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 510 through 514 Processing helix chain 'B' and resid 526 through 530 Processing helix chain 'B' and resid 540 through 551 removed outlier: 3.817A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 635 removed outlier: 3.527A pdb=" N ARG B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.728A pdb=" N ASP B 640 " --> pdb=" O ASP B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 710 Processing helix chain 'B' and resid 762 through 775 Processing helix chain 'B' and resid 785 through 789 Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.797A pdb=" N PHE B 798 " --> pdb=" O PHE B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 896 removed outlier: 3.919A pdb=" N ASN B 896 " --> pdb=" O LEU B 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.764A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.512A pdb=" N ALA C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.653A pdb=" N MET C 315 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY C 316 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 378 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 464 through 477 Processing helix chain 'C' and resid 478 through 481 Processing helix chain 'C' and resid 482 through 486 Processing helix chain 'C' and resid 500 through 507 removed outlier: 3.554A pdb=" N LYS C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 507 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.711A pdb=" N ASP C 530 " --> pdb=" O ASP C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 551 removed outlier: 3.557A pdb=" N LEU C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 570 removed outlier: 4.010A pdb=" N LYS C 570 " --> pdb=" O PHE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 593 Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.536A pdb=" N ASP C 604 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 600 through 605' Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 705 through 710 Processing helix chain 'C' and resid 714 through 716 No H-bonds generated for 'chain 'C' and resid 714 through 716' Processing helix chain 'C' and resid 763 through 775 Processing helix chain 'C' and resid 794 through 798 removed outlier: 3.871A pdb=" N PHE C 798 " --> pdb=" O PHE C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 822 removed outlier: 3.543A pdb=" N GLN C 822 " --> pdb=" O ILE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 25 through 32 removed outlier: 3.657A pdb=" N VAL G 30 " --> pdb=" O CGU G 26 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.506A pdb=" N SER A 607 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG A 104 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 613 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP A 102 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU A 615 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR A 100 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 removed outlier: 3.534A pdb=" N TRP A 583 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.826A pdb=" N LEU A 94 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.528A pdb=" N ARG C 453 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.831A pdb=" N ALA A 219 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N TYR A 287 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY A 221 " --> pdb=" O TYR A 287 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N GLU A 289 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 223 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 284 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 13.217A pdb=" N MET A 264 " --> pdb=" O PRO C 431 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE A 266 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 188 Processing sheet with id=AA7, first strand: chain 'A' and resid 251 through 253 removed outlier: 3.527A pdb=" N VAL A 251 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 259 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 253 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 302 removed outlier: 6.075A pdb=" N GLN A 318 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 401 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 412 through 416 removed outlier: 4.030A pdb=" N ASN A 412 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 412 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 412 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 426 through 429 removed outlier: 4.471A pdb=" N PHE B 266 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 284 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 219 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR B 287 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY B 221 " --> pdb=" O TYR B 287 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU B 289 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 223 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 220 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 removed outlier: 6.570A pdb=" N ARG A 453 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 137 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 133 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 641 through 644 Processing sheet with id=AB6, first strand: chain 'A' and resid 649 through 656 removed outlier: 4.351A pdb=" N GLY A 677 " --> pdb=" O GLU A 921 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP A 871 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 662 through 670 removed outlier: 3.681A pdb=" N VAL A 663 " --> pdb=" O PHE A 905 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 669 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS A 899 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 900 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE A 725 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP A 902 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 723 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 904 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 721 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU A 906 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 662 through 670 removed outlier: 3.681A pdb=" N VAL A 663 " --> pdb=" O PHE A 905 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER A 669 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS A 899 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 900 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE A 725 " --> pdb=" O ALA A 900 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASP A 902 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 723 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR A 904 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 721 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLU A 906 " --> pdb=" O LYS A 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 799 through 806 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 68 removed outlier: 7.037A pdb=" N ARG B 104 " --> pdb=" O ASP B 611 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 613 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 102 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU B 615 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR B 100 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 105 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.842A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.842A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AC5, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.785A pdb=" N THR B 192 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AC7, first strand: chain 'B' and resid 298 through 302 removed outlier: 6.080A pdb=" N GLN B 318 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AC9, first strand: chain 'B' and resid 401 through 402 Processing sheet with id=AD1, first strand: chain 'B' and resid 440 through 441 removed outlier: 3.512A pdb=" N LEU B 426 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 450 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU B 451 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ALA C 172 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B 453 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP C 135 " --> pdb=" O HIS C 167 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 440 through 441 removed outlier: 4.587A pdb=" N PHE C 266 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 220 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.665A pdb=" N GLN B 641 " --> pdb=" O VAL B 928 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 643 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 649 through 656 removed outlier: 4.251A pdb=" N GLY B 677 " --> pdb=" O GLU B 921 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP B 871 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 662 through 670 removed outlier: 3.512A pdb=" N LEU B 901 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 669 " --> pdb=" O HIS B 899 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS B 899 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 720 " --> pdb=" O GLU B 906 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 662 through 670 removed outlier: 3.512A pdb=" N LEU B 901 " --> pdb=" O ILE B 667 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER B 669 " --> pdb=" O HIS B 899 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS B 899 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS B 720 " --> pdb=" O GLU B 906 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 721 " --> pdb=" O PHE B 743 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 799 through 806 Processing sheet with id=AD8, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.757A pdb=" N LEU C 615 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 104 " --> pdb=" O ASP C 611 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 613 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP C 102 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU C 615 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR C 100 " --> pdb=" O LEU C 615 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 105 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 79 through 88 removed outlier: 3.680A pdb=" N VAL C 347 " --> pdb=" O GLU C 582 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 94 through 95 removed outlier: 3.508A pdb=" N LEU C 94 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 185 through 188 removed outlier: 6.994A pdb=" N LYS C 194 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 250 through 252 removed outlier: 3.518A pdb=" N VAL C 251 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 259 " --> pdb=" O VAL C 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 298 through 302 removed outlier: 6.437A pdb=" N GLN C 318 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AE6, first strand: chain 'C' and resid 401 through 402 Processing sheet with id=AE7, first strand: chain 'C' and resid 641 through 644 removed outlier: 3.564A pdb=" N GLN C 641 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 926 " --> pdb=" O PHE C 643 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 925 " --> pdb=" O LEU C 941 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 941 " --> pdb=" O VAL C 925 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 649 through 656 removed outlier: 4.354A pdb=" N GLY C 677 " --> pdb=" O GLU C 921 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 662 through 670 removed outlier: 4.408A pdb=" N SER C 669 " --> pdb=" O HIS C 899 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS C 899 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 720 " --> pdb=" O GLU C 906 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 662 through 670 removed outlier: 4.408A pdb=" N SER C 669 " --> pdb=" O HIS C 899 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS C 899 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 720 " --> pdb=" O GLU C 906 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 755 through 756 removed outlier: 4.528A pdb=" N MET C 761 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 799 through 806 587 hydrogen bonds defined for protein. 1506 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: 5.50 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3753 1.31 - 1.43: 6474 1.43 - 1.56: 12618 1.56 - 1.68: 1 1.68 - 1.81: 195 Bond restraints: 23041 Sorted by residual: bond pdb=" C LYS C 165 " pdb=" O LYS C 165 " ideal model delta sigma weight residual 1.235 1.183 0.053 1.28e-02 6.10e+03 1.69e+01 bond pdb=" C THR C 166 " pdb=" O THR C 166 " ideal model delta sigma weight residual 1.234 1.185 0.049 1.23e-02 6.61e+03 1.62e+01 bond pdb=" C HIS A 167 " pdb=" O HIS A 167 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.22e-02 6.72e+03 9.35e+00 bond pdb=" C LYS B 165 " pdb=" O LYS B 165 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.38e-02 5.25e+03 9.31e+00 bond pdb=" CA LYS B 165 " pdb=" C LYS B 165 " ideal model delta sigma weight residual 1.528 1.567 -0.039 1.45e-02 4.76e+03 7.22e+00 ... (remaining 23036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 31009 1.90 - 3.79: 286 3.79 - 5.69: 26 5.69 - 7.58: 7 7.58 - 9.48: 4 Bond angle restraints: 31332 Sorted by residual: angle pdb=" CA LYS C 165 " pdb=" C LYS C 165 " pdb=" O LYS C 165 " ideal model delta sigma weight residual 120.70 114.59 6.11 1.08e+00 8.57e-01 3.20e+01 angle pdb=" CA HIS A 167 " pdb=" CB HIS A 167 " pdb=" CG HIS A 167 " ideal model delta sigma weight residual 113.80 118.70 -4.90 1.00e+00 1.00e+00 2.40e+01 angle pdb=" C GLN B 164 " pdb=" CA GLN B 164 " pdb=" CB GLN B 164 " ideal model delta sigma weight residual 110.10 119.14 -9.04 1.90e+00 2.77e-01 2.27e+01 angle pdb=" N LYS B 165 " pdb=" CA LYS B 165 " pdb=" CB LYS B 165 " ideal model delta sigma weight residual 110.07 101.69 8.38 1.81e+00 3.05e-01 2.15e+01 angle pdb=" N HIS A 167 " pdb=" CA HIS A 167 " pdb=" C HIS A 167 " ideal model delta sigma weight residual 108.75 100.89 7.86 1.71e+00 3.42e-01 2.11e+01 ... (remaining 31327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 13102 15.69 - 31.39: 470 31.39 - 47.08: 72 47.08 - 62.77: 20 62.77 - 78.47: 2 Dihedral angle restraints: 13666 sinusoidal: 5489 harmonic: 8177 Sorted by residual: dihedral pdb=" CA LYS B 194 " pdb=" C LYS B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 150.07 29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ALA C 352 " pdb=" C ALA C 352 " pdb=" N SER C 353 " pdb=" CA SER C 353 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLN C 354 " pdb=" C GLN C 354 " pdb=" N LEU C 355 " pdb=" CA LEU C 355 " ideal model delta harmonic sigma weight residual 180.00 155.19 24.81 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 13663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2987 0.074 - 0.149: 305 0.149 - 0.223: 3 0.223 - 0.297: 1 0.297 - 0.372: 1 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CA GLN B 164 " pdb=" N GLN B 164 " pdb=" C GLN B 164 " pdb=" CB GLN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA LYS B 165 " pdb=" N LYS B 165 " pdb=" C LYS B 165 " pdb=" CB LYS B 165 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA GLN A 164 " pdb=" N GLN A 164 " pdb=" C GLN A 164 " pdb=" CB GLN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3294 not shown) Planarity restraints: 4132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 167 " 0.013 2.00e-02 2.50e+03 1.39e-02 2.89e+00 pdb=" CG HIS A 167 " -0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS A 167 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS A 167 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 167 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS A 167 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 165 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C LYS C 165 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS C 165 " 0.009 2.00e-02 2.50e+03 pdb=" N THR C 166 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 203 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO C 204 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 204 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 204 " 0.018 5.00e-02 4.00e+02 ... (remaining 4129 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 83 2.46 - 3.07: 14161 3.07 - 3.68: 30850 3.68 - 4.29: 46246 4.29 - 4.90: 81180 Nonbonded interactions: 172520 Sorted by model distance: nonbonded pdb="CA CA G 503 " pdb="CA CA G 504 " model vdw 1.852 1.980 nonbonded pdb=" OG1 THR B 76 " pdb=" OG SER B 79 " model vdw 2.213 3.040 nonbonded pdb=" O GLU A 137 " pdb=" N GLN A 164 " model vdw 2.220 3.120 nonbonded pdb=" O ASP C 645 " pdb=" OG SER C 648 " model vdw 2.238 3.040 nonbonded pdb=" O PHE A 31 " pdb=" OG1 THR A 35 " model vdw 2.257 3.040 ... (remaining 172515 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.290 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 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 : 0.004 0.507 23042 Z= 0.203 Angle : 0.490 17.845 31334 Z= 0.284 Chirality : 0.043 0.372 3297 Planarity : 0.003 0.033 4132 Dihedral : 8.346 78.465 8441 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.61 % Allowed : 4.00 % Favored : 94.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -0.78 (0.16), residues: 2752 helix: 1.29 (0.34), residues: 281 sheet: 0.48 (0.24), residues: 492 loop : -1.13 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 544 TYR 0.012 0.001 TYR B 195 PHE 0.007 0.001 PHE B 875 TRP 0.005 0.001 TRP A 765 HIS 0.016 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.12 (23041) covalent geometry : angle 0.47932 / 0.28 (31332) SS BOND : bond 0.50705 / 26.69 ( 1) SS BOND : angle 12.62556 / 6.65 ( 2) hydrogen bonds : bond 0.27981 / 17.98 ( 551) hydrogen bonds : angle 9.59809 / 6.87 ( 1506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 684 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7108 (mmt) cc_final: 0.6684 (mmt) REVERT: A 14 HIS cc_start: 0.6647 (m-70) cc_final: 0.6404 (m90) REVERT: A 63 ARG cc_start: 0.7583 (mtp85) cc_final: 0.6927 (mtp85) REVERT: A 65 THR cc_start: 0.7585 (m) cc_final: 0.7252 (p) REVERT: A 83 ARG cc_start: 0.6348 (ttm170) cc_final: 0.5965 (ttp80) REVERT: A 92 ARG cc_start: 0.6653 (mtt90) cc_final: 0.6363 (mtp180) REVERT: A 94 LEU cc_start: 0.7111 (tp) cc_final: 0.6830 (tt) REVERT: A 104 ARG cc_start: 0.7386 (mtp180) cc_final: 0.6919 (mtm180) REVERT: A 137 GLU cc_start: 0.5518 (tt0) cc_final: 0.5264 (tt0) REVERT: A 203 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6754 (mt-10) REVERT: A 231 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7541 (mttp) REVERT: A 280 LEU cc_start: 0.6809 (tp) cc_final: 0.6554 (tp) REVERT: A 294 GLU cc_start: 0.8008 (pt0) cc_final: 0.7699 (pt0) REVERT: A 303 MET cc_start: 0.7795 (tpt) cc_final: 0.7547 (tpp) REVERT: A 414 CYS cc_start: 0.6804 (m) cc_final: 0.6434 (m) REVERT: A 445 GLU cc_start: 0.5865 (tp30) cc_final: 0.5608 (tp30) REVERT: A 476 ASN cc_start: 0.7368 (m-40) cc_final: 0.6910 (m110) REVERT: A 500 THR cc_start: 0.6166 (m) cc_final: 0.5706 (p) REVERT: A 502 ASP cc_start: 0.6473 (t70) cc_final: 0.6181 (t0) REVERT: A 504 MET cc_start: 0.7813 (mtt) cc_final: 0.7528 (mtp) REVERT: A 532 VAL cc_start: 0.7762 (t) cc_final: 0.7340 (m) REVERT: A 544 ARG cc_start: 0.6698 (mtm180) cc_final: 0.6260 (mtp85) REVERT: A 631 GLU cc_start: 0.6380 (tt0) cc_final: 0.6141 (tt0) REVERT: A 635 ARG cc_start: 0.6981 (mtt-85) cc_final: 0.6764 (mtp85) REVERT: A 652 MET cc_start: 0.7105 (mmm) cc_final: 0.6897 (mmm) REVERT: A 719 LYS cc_start: 0.7324 (tppp) cc_final: 0.7037 (mttt) REVERT: A 743 PHE cc_start: 0.6560 (m-80) cc_final: 0.6288 (m-80) REVERT: A 815 GLN cc_start: 0.6464 (mm-40) cc_final: 0.6187 (mm-40) REVERT: A 838 GLU cc_start: 0.8170 (pt0) cc_final: 0.7775 (pt0) REVERT: A 903 MET cc_start: 0.7079 (mtp) cc_final: 0.6522 (mtm) REVERT: A 936 ILE cc_start: 0.7506 (mt) cc_final: 0.7302 (tt) REVERT: B 69 ILE cc_start: 0.8289 (mt) cc_final: 0.7972 (mm) REVERT: B 72 ASP cc_start: 0.7852 (t0) cc_final: 0.7224 (t0) REVERT: B 96 MET cc_start: 0.7458 (tpp) cc_final: 0.7156 (mmm) REVERT: B 104 ARG cc_start: 0.6937 (mtp180) cc_final: 0.6548 (mtm180) REVERT: B 106 VAL cc_start: 0.7659 (t) cc_final: 0.7376 (p) REVERT: B 117 SER cc_start: 0.7715 (m) cc_final: 0.6886 (p) REVERT: B 210 GLN cc_start: 0.7301 (tt0) cc_final: 0.5824 (tp40) REVERT: B 317 GLN cc_start: 0.7646 (pt0) cc_final: 0.7374 (pt0) REVERT: B 337 MET cc_start: 0.7726 (mtm) cc_final: 0.7471 (mtt) REVERT: B 426 LEU cc_start: 0.7002 (mt) cc_final: 0.6743 (mp) REVERT: B 445 GLU cc_start: 0.6904 (tt0) cc_final: 0.6305 (tm-30) REVERT: B 450 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5532 (m-40) REVERT: B 461 GLU cc_start: 0.7161 (tt0) cc_final: 0.6825 (mt-10) REVERT: B 495 SER cc_start: 0.7381 (t) cc_final: 0.7080 (p) REVERT: B 556 VAL cc_start: 0.7656 (t) cc_final: 0.7410 (m) REVERT: B 582 GLU cc_start: 0.7097 (tt0) cc_final: 0.6688 (tt0) REVERT: B 612 SER cc_start: 0.8007 (m) cc_final: 0.7618 (p) REVERT: B 622 MET cc_start: 0.5310 (ttm) cc_final: 0.4985 (ttm) REVERT: B 645 ASP cc_start: 0.7706 (t0) cc_final: 0.7212 (t0) REVERT: B 680 PHE cc_start: 0.8228 (p90) cc_final: 0.7413 (p90) REVERT: B 686 LYS cc_start: 0.6145 (ttpm) cc_final: 0.5896 (ttpp) REVERT: B 738 LEU cc_start: 0.6436 (mt) cc_final: 0.6174 (mp) REVERT: B 742 GLU cc_start: 0.6724 (pt0) cc_final: 0.6203 (pm20) REVERT: B 786 SER cc_start: 0.7470 (m) cc_final: 0.7173 (t) REVERT: B 795 PHE cc_start: 0.7070 (t80) cc_final: 0.6675 (t80) REVERT: B 809 THR cc_start: 0.7428 (m) cc_final: 0.7054 (p) REVERT: B 816 GLN cc_start: 0.6887 (tt0) cc_final: 0.6543 (tp40) REVERT: B 836 MET cc_start: 0.7401 (ttm) cc_final: 0.6840 (ttp) REVERT: B 853 LYS cc_start: 0.7129 (mttp) cc_final: 0.6915 (mttp) REVERT: B 872 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6610 (mtt-85) REVERT: C 63 ARG cc_start: 0.7097 (mmt90) cc_final: 0.6614 (mmm160) REVERT: C 112 THR cc_start: 0.8184 (p) cc_final: 0.7838 (t) REVERT: C 164 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6423 (mt0) REVERT: C 197 ASP cc_start: 0.6713 (t0) cc_final: 0.6436 (t70) REVERT: C 264 MET cc_start: 0.7642 (mtm) cc_final: 0.7361 (mtm) REVERT: C 290 ASP cc_start: 0.7317 (t0) cc_final: 0.7075 (t0) REVERT: C 292 ASP cc_start: 0.7608 (t0) cc_final: 0.7181 (t0) REVERT: C 303 MET cc_start: 0.7790 (tpt) cc_final: 0.7511 (tpp) REVERT: C 311 SER cc_start: 0.7240 (t) cc_final: 0.6838 (p) REVERT: C 413 TYR cc_start: 0.7770 (m-80) cc_final: 0.7478 (m-10) REVERT: C 432 LYS cc_start: 0.6867 (mtmt) cc_final: 0.6611 (mtmm) REVERT: C 484 LYS cc_start: 0.7637 (ptmt) cc_final: 0.7415 (ptpp) REVERT: C 495 SER cc_start: 0.8136 (t) cc_final: 0.7933 (t) REVERT: C 499 ASN cc_start: 0.6606 (m-40) cc_final: 0.6406 (m110) REVERT: C 504 MET cc_start: 0.7474 (mtp) cc_final: 0.7215 (mtm) REVERT: C 508 VAL cc_start: 0.7382 (m) cc_final: 0.7168 (p) REVERT: C 514 VAL cc_start: 0.7386 (t) cc_final: 0.7132 (p) REVERT: C 591 MET cc_start: 0.7399 (mmm) cc_final: 0.7152 (mmt) REVERT: C 628 SER cc_start: 0.6013 (t) cc_final: 0.5500 (m) REVERT: C 681 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7525 (t) REVERT: C 752 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 754 TYR cc_start: 0.7680 (m-10) cc_final: 0.7214 (m-10) REVERT: C 785 GLU cc_start: 0.7306 (mp0) cc_final: 0.6770 (mp0) REVERT: C 807 ASP cc_start: 0.6671 (t0) cc_final: 0.6310 (t0) REVERT: C 816 GLN cc_start: 0.7935 (tt0) cc_final: 0.4779 (tt0) REVERT: C 817 VAL cc_start: 0.7446 (t) cc_final: 0.7120 (t) REVERT: C 829 VAL cc_start: 0.7331 (t) cc_final: 0.7013 (m) REVERT: C 876 SER cc_start: 0.7847 (t) cc_final: 0.7373 (p) REVERT: C 921 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6258 (mm-30) REVERT: C 925 VAL cc_start: 0.7658 (t) cc_final: 0.7450 (t) REVERT: C 929 HIS cc_start: 0.6733 (t70) cc_final: 0.6508 (t70) REVERT: C 931 PRO cc_start: 0.8031 (Cg_endo) cc_final: 0.7802 (Cg_exo) REVERT: C 945 PHE cc_start: 0.8102 (m-80) cc_final: 0.7802 (m-80) outliers start: 39 outliers final: 14 residues processed: 711 average time/residue: 0.1632 time to fit residues: 177.1594 Evaluate side-chains 589 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 572 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 681 THR Chi-restraints excluded: chain G residue 36 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 261 GLN A 362 GLN A 644 ASN A 799 GLN A 822 GLN A 929 HIS B 14 HIS B 171 GLN B 351 GLN B 362 GLN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 499 ASN B 599 ASN B 644 ASN C 310 ASN C 318 GLN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN C 899 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096925 restraints weight = 31856.448| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.86 r_work: 0.3063 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23042 Z= 0.207 Angle : 0.582 8.784 31334 Z= 0.314 Chirality : 0.047 0.174 3297 Planarity : 0.005 0.057 4132 Dihedral : 6.280 83.223 3158 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 2.88 % Allowed : 9.15 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -1.06 (0.16), residues: 2752 helix: 0.27 (0.30), residues: 341 sheet: 0.33 (0.22), residues: 582 loop : -1.31 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 33 TYR 0.034 0.002 TYR C 23 PHE 0.026 0.002 PHE A 680 TRP 0.013 0.002 TRP A 765 HIS 0.007 0.002 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (23041) covalent geometry : angle 0.58211 / 0.31 (31332) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 1.47148 / 0.83 ( 2) hydrogen bonds : bond 0.05296 / 3.45 ( 551) hydrogen bonds : angle 6.33499 / 4.56 ( 1506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 596 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7155 (pt0) cc_final: 0.6873 (pt0) REVERT: A 38 TYR cc_start: 0.7126 (p90) cc_final: 0.6515 (p90) REVERT: A 63 ARG cc_start: 0.8428 (mtp85) cc_final: 0.7905 (mtp85) REVERT: A 65 THR cc_start: 0.7722 (m) cc_final: 0.7501 (p) REVERT: A 94 LEU cc_start: 0.8645 (tp) cc_final: 0.8389 (tt) REVERT: A 137 GLU cc_start: 0.7329 (tt0) cc_final: 0.7044 (tt0) REVERT: A 268 SER cc_start: 0.8771 (t) cc_final: 0.8539 (p) REVERT: A 409 GLU cc_start: 0.7301 (mp0) cc_final: 0.7057 (mp0) REVERT: A 413 TYR cc_start: 0.8064 (m-80) cc_final: 0.7862 (m-80) REVERT: A 432 LYS cc_start: 0.7957 (tttm) cc_final: 0.7693 (tttp) REVERT: A 500 THR cc_start: 0.8207 (m) cc_final: 0.7945 (m) REVERT: A 502 ASP cc_start: 0.7907 (t70) cc_final: 0.7512 (t0) REVERT: A 504 MET cc_start: 0.8598 (mtt) cc_final: 0.8398 (mtp) REVERT: A 532 VAL cc_start: 0.8702 (t) cc_final: 0.8492 (m) REVERT: A 544 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7772 (mtp85) REVERT: A 583 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.8032 (t-100) REVERT: A 788 LYS cc_start: 0.8267 (mttm) cc_final: 0.8026 (mttt) REVERT: A 835 THR cc_start: 0.7593 (p) cc_final: 0.7272 (p) REVERT: A 903 MET cc_start: 0.8112 (mtp) cc_final: 0.7900 (mtm) REVERT: A 929 HIS cc_start: 0.8261 (t70) cc_final: 0.7851 (t-90) REVERT: A 936 ILE cc_start: 0.8632 (mt) cc_final: 0.8297 (tt) REVERT: B 11 SER cc_start: 0.8770 (t) cc_final: 0.8303 (p) REVERT: B 12 TYR cc_start: 0.8390 (t80) cc_final: 0.7920 (t80) REVERT: B 69 ILE cc_start: 0.8948 (mt) cc_final: 0.8736 (mm) REVERT: B 96 MET cc_start: 0.8807 (tpp) cc_final: 0.8255 (mmm) REVERT: B 117 SER cc_start: 0.8537 (m) cc_final: 0.8238 (p) REVERT: B 292 ASP cc_start: 0.8023 (t0) cc_final: 0.7753 (t0) REVERT: B 426 LEU cc_start: 0.8791 (mt) cc_final: 0.8588 (mp) REVERT: B 451 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6487 (mm-30) REVERT: B 495 SER cc_start: 0.8323 (t) cc_final: 0.8022 (p) REVERT: B 502 ASP cc_start: 0.8157 (t0) cc_final: 0.7938 (t70) REVERT: B 612 SER cc_start: 0.8491 (m) cc_final: 0.8254 (p) REVERT: B 786 SER cc_start: 0.8524 (m) cc_final: 0.8272 (t) REVERT: B 791 MET cc_start: 0.8063 (ttm) cc_final: 0.7765 (ttm) REVERT: B 795 PHE cc_start: 0.8340 (t80) cc_final: 0.8027 (t80) REVERT: B 872 ARG cc_start: 0.7318 (ttm-80) cc_final: 0.7039 (mtt90) REVERT: B 930 ARG cc_start: 0.7939 (mtm-85) cc_final: 0.7709 (mtm-85) REVERT: C 69 ILE cc_start: 0.8411 (mm) cc_final: 0.8208 (mm) REVERT: C 109 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7914 (mtm-85) REVERT: C 166 THR cc_start: 0.8400 (p) cc_final: 0.8199 (m) REVERT: C 194 LYS cc_start: 0.8496 (tttt) cc_final: 0.8281 (tttp) REVERT: C 264 MET cc_start: 0.8303 (mtm) cc_final: 0.8001 (mtm) REVERT: C 271 GLU cc_start: 0.8044 (tt0) cc_final: 0.7826 (tt0) REVERT: C 290 ASP cc_start: 0.7690 (t0) cc_final: 0.7456 (t0) REVERT: C 311 SER cc_start: 0.8532 (t) cc_final: 0.8204 (p) REVERT: C 413 TYR cc_start: 0.8469 (m-80) cc_final: 0.8211 (m-80) REVERT: C 452 ILE cc_start: 0.8437 (mm) cc_final: 0.8233 (mt) REVERT: C 544 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7981 (mtp180) REVERT: C 591 MET cc_start: 0.8689 (mmm) cc_final: 0.8471 (mmm) REVERT: C 628 SER cc_start: 0.8045 (t) cc_final: 0.7420 (m) REVERT: C 646 TYR cc_start: 0.7681 (t80) cc_final: 0.7268 (t80) REVERT: C 709 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7516 (p0) REVERT: C 785 GLU cc_start: 0.7980 (mp0) cc_final: 0.7694 (mp0) REVERT: C 817 VAL cc_start: 0.8797 (t) cc_final: 0.8459 (m) REVERT: C 876 SER cc_start: 0.8202 (t) cc_final: 0.7973 (p) REVERT: C 927 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7826 (ttt-90) outliers start: 70 outliers final: 50 residues processed: 632 average time/residue: 0.1489 time to fit residues: 143.5196 Evaluate side-chains 612 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 559 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 906 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 164 GLN Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 608 ILE Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 720 LYS Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 170 optimal weight: 0.0000 chunk 57 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS B 171 GLN B 351 GLN B 362 GLN B 422 ASN C 310 ASN C 499 ASN C 537 HIS C 758 GLN C 775 ASN C 899 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098448 restraints weight = 31969.794| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.91 r_work: 0.3077 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23042 Z= 0.119 Angle : 0.513 8.294 31334 Z= 0.276 Chirality : 0.044 0.167 3297 Planarity : 0.004 0.047 4132 Dihedral : 5.841 84.074 3148 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 2.76 % Allowed : 11.70 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -1.00 (0.16), residues: 2752 helix: 0.30 (0.30), residues: 341 sheet: 0.35 (0.22), residues: 582 loop : -1.27 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 930 TYR 0.031 0.001 TYR C 23 PHE 0.017 0.001 PHE A 169 TRP 0.011 0.001 TRP A 678 HIS 0.006 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (23041) covalent geometry : angle 0.51288 / 0.28 (31332) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.99241 / 0.56 ( 2) hydrogen bonds : bond 0.04152 / 2.74 ( 551) hydrogen bonds : angle 5.92658 / 4.26 ( 1506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 567 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.7163 (pt0) cc_final: 0.6812 (pp20) REVERT: A 38 TYR cc_start: 0.7149 (p90) cc_final: 0.6484 (p90) REVERT: A 63 ARG cc_start: 0.8384 (mtp85) cc_final: 0.7844 (mtp85) REVERT: A 94 LEU cc_start: 0.8677 (tp) cc_final: 0.8400 (tt) REVERT: A 409 GLU cc_start: 0.7377 (mp0) cc_final: 0.7071 (mp0) REVERT: A 487 TYR cc_start: 0.8596 (p90) cc_final: 0.8365 (p90) REVERT: A 500 THR cc_start: 0.8159 (m) cc_final: 0.7926 (m) REVERT: A 502 ASP cc_start: 0.7922 (t70) cc_final: 0.7536 (t0) REVERT: A 504 MET cc_start: 0.8564 (mtt) cc_final: 0.8354 (mtp) REVERT: A 544 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7808 (mtp85) REVERT: A 583 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.8007 (t-100) REVERT: A 788 LYS cc_start: 0.8316 (mttm) cc_final: 0.8100 (mttt) REVERT: A 835 THR cc_start: 0.7635 (p) cc_final: 0.7324 (p) REVERT: A 903 MET cc_start: 0.8162 (mtp) cc_final: 0.7923 (mtm) REVERT: A 936 ILE cc_start: 0.8641 (mt) cc_final: 0.8300 (tt) REVERT: B 11 SER cc_start: 0.8722 (t) cc_final: 0.8248 (p) REVERT: B 96 MET cc_start: 0.8751 (tpp) cc_final: 0.8278 (mmm) REVERT: B 117 SER cc_start: 0.8508 (m) cc_final: 0.8228 (p) REVERT: B 292 ASP cc_start: 0.7998 (t0) cc_final: 0.7755 (t0) REVERT: B 426 LEU cc_start: 0.8783 (mt) cc_final: 0.8565 (mp) REVERT: B 451 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6281 (mm-30) REVERT: B 495 SER cc_start: 0.8260 (t) cc_final: 0.7979 (p) REVERT: B 502 ASP cc_start: 0.8189 (t0) cc_final: 0.7967 (t70) REVERT: B 612 SER cc_start: 0.8498 (m) cc_final: 0.8218 (p) REVERT: B 652 MET cc_start: 0.8283 (mmm) cc_final: 0.7825 (mmm) REVERT: B 742 GLU cc_start: 0.7705 (pm20) cc_final: 0.7267 (pp20) REVERT: B 786 SER cc_start: 0.8430 (m) cc_final: 0.8170 (t) REVERT: B 795 PHE cc_start: 0.8369 (t80) cc_final: 0.8024 (t80) REVERT: B 872 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6901 (mtt90) REVERT: B 930 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: C 83 ARG cc_start: 0.6697 (mtp180) cc_final: 0.6488 (mtp180) REVERT: C 109 ARG cc_start: 0.8271 (mtt180) cc_final: 0.7898 (mtm-85) REVERT: C 264 MET cc_start: 0.8254 (mtm) cc_final: 0.8014 (mtm) REVERT: C 290 ASP cc_start: 0.7680 (t0) cc_final: 0.7417 (t0) REVERT: C 311 SER cc_start: 0.8523 (t) cc_final: 0.8138 (p) REVERT: C 413 TYR cc_start: 0.8487 (m-80) cc_final: 0.8255 (m-10) REVERT: C 544 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8122 (mtp180) REVERT: C 628 SER cc_start: 0.8038 (t) cc_final: 0.7425 (m) REVERT: C 646 TYR cc_start: 0.7624 (t80) cc_final: 0.7125 (t80) REVERT: C 659 ASN cc_start: 0.8268 (m110) cc_final: 0.8003 (m110) REVERT: C 785 GLU cc_start: 0.7921 (mp0) cc_final: 0.7591 (mp0) REVERT: C 817 VAL cc_start: 0.8833 (t) cc_final: 0.8470 (m) REVERT: C 876 SER cc_start: 0.8196 (t) cc_final: 0.7918 (p) REVERT: C 927 ARG cc_start: 0.8047 (mtp85) cc_final: 0.7816 (ttt90) outliers start: 67 outliers final: 45 residues processed: 595 average time/residue: 0.1486 time to fit residues: 135.1929 Evaluate side-chains 600 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 553 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 810 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 84 optimal weight: 0.4980 chunk 252 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN A 644 ASN A 929 HIS B 210 GLN B 422 ASN C 499 ASN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097395 restraints weight = 31940.979| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.99 r_work: 0.3056 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23042 Z= 0.143 Angle : 0.527 8.565 31334 Z= 0.283 Chirality : 0.045 0.181 3297 Planarity : 0.005 0.046 4132 Dihedral : 5.808 85.053 3141 Min Nonbonded Distance : 1.696 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.04 % Rotamer: Outliers : 2.93 % Allowed : 12.07 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.98 (0.16), residues: 2752 helix: 0.57 (0.31), residues: 323 sheet: 0.34 (0.22), residues: 582 loop : -1.28 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.028 0.001 TYR C 23 PHE 0.019 0.002 PHE A 680 TRP 0.013 0.001 TRP B 211 HIS 0.008 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (23041) covalent geometry : angle 0.52652 / 0.28 (31332) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 0.91760 / 0.52 ( 2) hydrogen bonds : bond 0.04119 / 2.71 ( 551) hydrogen bonds : angle 5.68580 / 4.09 ( 1506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 549 time to evaluate : 0.635 Fit side-chains REVERT: A 38 TYR cc_start: 0.7213 (p90) cc_final: 0.6561 (p90) REVERT: A 63 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7772 (mtp85) REVERT: A 94 LEU cc_start: 0.8648 (tp) cc_final: 0.8357 (tt) REVERT: A 137 GLU cc_start: 0.7464 (tt0) cc_final: 0.7232 (tt0) REVERT: A 285 VAL cc_start: 0.8394 (t) cc_final: 0.8085 (p) REVERT: A 331 ASP cc_start: 0.7985 (t0) cc_final: 0.7711 (t0) REVERT: A 409 GLU cc_start: 0.7432 (mp0) cc_final: 0.7052 (mp0) REVERT: A 487 TYR cc_start: 0.8575 (p90) cc_final: 0.8363 (p90) REVERT: A 502 ASP cc_start: 0.7930 (t70) cc_final: 0.7611 (t0) REVERT: A 504 MET cc_start: 0.8585 (mtt) cc_final: 0.8331 (mtp) REVERT: A 544 ARG cc_start: 0.8150 (mtm180) cc_final: 0.7750 (mtp85) REVERT: A 583 TRP cc_start: 0.8218 (OUTLIER) cc_final: 0.7939 (t-100) REVERT: A 686 LYS cc_start: 0.8632 (ttpp) cc_final: 0.8224 (mtpp) REVERT: A 788 LYS cc_start: 0.8287 (mttm) cc_final: 0.8057 (mttt) REVERT: A 846 PHE cc_start: 0.8422 (t80) cc_final: 0.8175 (t80) REVERT: A 903 MET cc_start: 0.8126 (mtp) cc_final: 0.7864 (mtm) REVERT: A 906 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 912 GLU cc_start: 0.7974 (pt0) cc_final: 0.7744 (pt0) REVERT: A 930 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8307 (ttm-80) REVERT: A 936 ILE cc_start: 0.8605 (mt) cc_final: 0.8232 (tt) REVERT: B 11 SER cc_start: 0.8643 (t) cc_final: 0.8124 (p) REVERT: B 96 MET cc_start: 0.8731 (tpp) cc_final: 0.8299 (mmm) REVERT: B 117 SER cc_start: 0.8595 (m) cc_final: 0.8216 (p) REVERT: B 292 ASP cc_start: 0.8050 (t0) cc_final: 0.7744 (t0) REVERT: B 426 LEU cc_start: 0.8750 (mt) cc_final: 0.8540 (mp) REVERT: B 495 SER cc_start: 0.8265 (t) cc_final: 0.7960 (p) REVERT: B 502 ASP cc_start: 0.8238 (t0) cc_final: 0.8026 (t70) REVERT: B 612 SER cc_start: 0.8499 (m) cc_final: 0.8226 (p) REVERT: B 742 GLU cc_start: 0.7780 (pm20) cc_final: 0.7469 (pm20) REVERT: B 786 SER cc_start: 0.8339 (m) cc_final: 0.8061 (t) REVERT: B 795 PHE cc_start: 0.8309 (t80) cc_final: 0.7966 (t80) REVERT: B 872 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6867 (mtt90) REVERT: C 83 ARG cc_start: 0.6603 (mtp180) cc_final: 0.6353 (mtp180) REVERT: C 109 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7963 (mtm-85) REVERT: C 136 ASP cc_start: 0.7675 (t0) cc_final: 0.7465 (m-30) REVERT: C 264 MET cc_start: 0.8249 (mtm) cc_final: 0.7986 (mtm) REVERT: C 290 ASP cc_start: 0.7833 (t0) cc_final: 0.7565 (t0) REVERT: C 311 SER cc_start: 0.8563 (t) cc_final: 0.8221 (p) REVERT: C 356 ASN cc_start: 0.7834 (t0) cc_final: 0.7488 (t0) REVERT: C 413 TYR cc_start: 0.8504 (m-80) cc_final: 0.8285 (m-10) REVERT: C 544 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8036 (mtp180) REVERT: C 628 SER cc_start: 0.7866 (t) cc_final: 0.7258 (m) REVERT: C 646 TYR cc_start: 0.7582 (t80) cc_final: 0.7056 (t80) REVERT: C 659 ASN cc_start: 0.8296 (m110) cc_final: 0.8021 (m110) REVERT: C 709 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7460 (p0) REVERT: C 785 GLU cc_start: 0.7983 (mp0) cc_final: 0.7615 (mp0) REVERT: C 817 VAL cc_start: 0.8754 (t) cc_final: 0.8449 (m) REVERT: C 876 SER cc_start: 0.8301 (t) cc_final: 0.7876 (p) REVERT: C 878 ASN cc_start: 0.8241 (p0) cc_final: 0.7953 (p0) REVERT: C 945 PHE cc_start: 0.8932 (m-80) cc_final: 0.8448 (m-80) REVERT: G 18 MET cc_start: 0.8179 (mmm) cc_final: 0.7956 (mmm) outliers start: 71 outliers final: 57 residues processed: 580 average time/residue: 0.1467 time to fit residues: 130.5883 Evaluate side-chains 599 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 539 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 207 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 222 optimal weight: 0.0970 chunk 199 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN A 644 ASN A 929 HIS B 210 GLN B 362 GLN B 422 ASN C 499 ASN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.097830 restraints weight = 31671.257| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.98 r_work: 0.3068 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23042 Z= 0.121 Angle : 0.506 9.136 31334 Z= 0.272 Chirality : 0.044 0.163 3297 Planarity : 0.004 0.058 4132 Dihedral : 5.758 85.952 3141 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.87 % Favored : 95.09 % Rotamer: Outliers : 3.21 % Allowed : 12.28 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.93 (0.16), residues: 2752 helix: 0.61 (0.31), residues: 323 sheet: 0.43 (0.22), residues: 576 loop : -1.26 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.025 0.001 TYR C 23 PHE 0.018 0.001 PHE A 169 TRP 0.014 0.001 TRP B 211 HIS 0.008 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (23041) covalent geometry : angle 0.50603 / 0.27 (31332) SS BOND : bond 0.00168 / 0.09 ( 1) SS BOND : angle 0.77952 / 0.45 ( 2) hydrogen bonds : bond 0.03754 / 2.48 ( 551) hydrogen bonds : angle 5.54218 / 3.97 ( 1506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 554 time to evaluate : 0.582 Fit side-chains REVERT: A 38 TYR cc_start: 0.7170 (p90) cc_final: 0.6563 (p90) REVERT: A 63 ARG cc_start: 0.8380 (mtp85) cc_final: 0.7925 (mtp85) REVERT: A 94 LEU cc_start: 0.8676 (tp) cc_final: 0.8389 (tt) REVERT: A 137 GLU cc_start: 0.7438 (tt0) cc_final: 0.7100 (tt0) REVERT: A 285 VAL cc_start: 0.8382 (t) cc_final: 0.8095 (p) REVERT: A 331 ASP cc_start: 0.7958 (t0) cc_final: 0.7724 (t0) REVERT: A 409 GLU cc_start: 0.7423 (mp0) cc_final: 0.7123 (mp0) REVERT: A 413 TYR cc_start: 0.8080 (m-80) cc_final: 0.7725 (m-80) REVERT: A 451 GLU cc_start: 0.7503 (mp0) cc_final: 0.7271 (mt-10) REVERT: A 487 TYR cc_start: 0.8556 (p90) cc_final: 0.8326 (p90) REVERT: A 502 ASP cc_start: 0.7955 (t70) cc_final: 0.7638 (t0) REVERT: A 504 MET cc_start: 0.8560 (mtt) cc_final: 0.8247 (mtp) REVERT: A 544 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7781 (mtp85) REVERT: A 583 TRP cc_start: 0.8199 (OUTLIER) cc_final: 0.7960 (t-100) REVERT: A 686 LYS cc_start: 0.8638 (ttpp) cc_final: 0.8249 (mtpp) REVERT: A 788 LYS cc_start: 0.8310 (mttm) cc_final: 0.8081 (mttt) REVERT: A 846 PHE cc_start: 0.8413 (t80) cc_final: 0.8164 (t80) REVERT: A 903 MET cc_start: 0.8145 (mtp) cc_final: 0.7890 (mtm) REVERT: A 906 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 930 ARG cc_start: 0.8490 (ttm110) cc_final: 0.8271 (ttm-80) REVERT: A 936 ILE cc_start: 0.8599 (mt) cc_final: 0.8226 (tt) REVERT: B 11 SER cc_start: 0.8671 (t) cc_final: 0.8158 (p) REVERT: B 92 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7803 (mtt90) REVERT: B 96 MET cc_start: 0.8722 (tpp) cc_final: 0.8060 (mmt) REVERT: B 117 SER cc_start: 0.8614 (m) cc_final: 0.8261 (p) REVERT: B 292 ASP cc_start: 0.8049 (t0) cc_final: 0.7754 (t0) REVERT: B 426 LEU cc_start: 0.8755 (mt) cc_final: 0.8549 (mp) REVERT: B 495 SER cc_start: 0.8275 (t) cc_final: 0.7990 (p) REVERT: B 652 MET cc_start: 0.8267 (mmm) cc_final: 0.7736 (mmm) REVERT: B 742 GLU cc_start: 0.7803 (pm20) cc_final: 0.7348 (pp20) REVERT: B 786 SER cc_start: 0.8372 (m) cc_final: 0.8106 (t) REVERT: B 795 PHE cc_start: 0.8322 (t80) cc_final: 0.7985 (t80) REVERT: B 872 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.7019 (mtp85) REVERT: C 7 MET cc_start: 0.5205 (mtm) cc_final: 0.4937 (ttm) REVERT: C 83 ARG cc_start: 0.6606 (mtp180) cc_final: 0.6345 (mtp180) REVERT: C 109 ARG cc_start: 0.8282 (mtt180) cc_final: 0.7955 (mtm-85) REVERT: C 264 MET cc_start: 0.8274 (mtm) cc_final: 0.8046 (mtm) REVERT: C 290 ASP cc_start: 0.7780 (t0) cc_final: 0.7526 (t0) REVERT: C 292 ASP cc_start: 0.7776 (t0) cc_final: 0.7538 (t70) REVERT: C 311 SER cc_start: 0.8559 (t) cc_final: 0.8205 (p) REVERT: C 336 LEU cc_start: 0.8615 (mt) cc_final: 0.8223 (mp) REVERT: C 356 ASN cc_start: 0.7759 (t0) cc_final: 0.7392 (t0) REVERT: C 413 TYR cc_start: 0.8490 (m-80) cc_final: 0.8274 (m-10) REVERT: C 544 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8010 (mtp180) REVERT: C 628 SER cc_start: 0.7918 (t) cc_final: 0.7300 (m) REVERT: C 646 TYR cc_start: 0.7595 (t80) cc_final: 0.7117 (t80) REVERT: C 659 ASN cc_start: 0.8307 (m110) cc_final: 0.8038 (m110) REVERT: C 785 GLU cc_start: 0.7978 (mp0) cc_final: 0.7611 (mp0) REVERT: C 876 SER cc_start: 0.8272 (t) cc_final: 0.7830 (p) REVERT: C 945 PHE cc_start: 0.8936 (m-80) cc_final: 0.8434 (m-80) outliers start: 78 outliers final: 61 residues processed: 585 average time/residue: 0.1538 time to fit residues: 138.5376 Evaluate side-chains 606 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 543 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 414 CYS Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 49 optimal weight: 3.9990 chunk 99 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 ASN A 775 ASN A 929 HIS B 210 GLN B 244 ASN B 261 GLN B 362 GLN B 422 ASN B 641 GLN C 499 ASN C 537 HIS C 758 GLN C 821 HIS ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100217 restraints weight = 31432.913| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.83 r_work: 0.3113 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23042 Z= 0.102 Angle : 0.492 9.310 31334 Z= 0.264 Chirality : 0.044 0.162 3297 Planarity : 0.004 0.046 4132 Dihedral : 5.663 86.292 3141 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 3.09 % Allowed : 12.94 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.87 (0.16), residues: 2752 helix: 0.69 (0.31), residues: 323 sheet: 0.38 (0.22), residues: 582 loop : -1.20 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 33 TYR 0.020 0.001 TYR C 23 PHE 0.017 0.001 PHE A 169 TRP 0.015 0.001 TRP B 211 HIS 0.009 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (23041) covalent geometry : angle 0.49209 / 0.26 (31332) SS BOND : bond 0.00104 / 0.05 ( 1) SS BOND : angle 0.65860 / 0.38 ( 2) hydrogen bonds : bond 0.03458 / 2.30 ( 551) hydrogen bonds : angle 5.42393 / 3.88 ( 1506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 548 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8429 (mtp85) cc_final: 0.8024 (mtp85) REVERT: A 94 LEU cc_start: 0.8668 (tp) cc_final: 0.8407 (tt) REVERT: A 137 GLU cc_start: 0.7344 (tt0) cc_final: 0.7002 (tt0) REVERT: A 315 MET cc_start: 0.6544 (mmt) cc_final: 0.5123 (mmm) REVERT: A 409 GLU cc_start: 0.7357 (mp0) cc_final: 0.7109 (mp0) REVERT: A 413 TYR cc_start: 0.8081 (m-80) cc_final: 0.7822 (m-80) REVERT: A 451 GLU cc_start: 0.7470 (mp0) cc_final: 0.7268 (mt-10) REVERT: A 487 TYR cc_start: 0.8492 (p90) cc_final: 0.8255 (p90) REVERT: A 502 ASP cc_start: 0.7978 (t70) cc_final: 0.7681 (t0) REVERT: A 504 MET cc_start: 0.8479 (mtt) cc_final: 0.8176 (mtp) REVERT: A 544 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7768 (mtp85) REVERT: A 583 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7964 (t-100) REVERT: A 686 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8218 (mtpp) REVERT: A 788 LYS cc_start: 0.8361 (mttm) cc_final: 0.8149 (mttt) REVERT: A 846 PHE cc_start: 0.8312 (t80) cc_final: 0.8057 (t80) REVERT: A 903 MET cc_start: 0.8160 (mtp) cc_final: 0.7941 (mtm) REVERT: A 906 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 936 ILE cc_start: 0.8649 (mt) cc_final: 0.8322 (tt) REVERT: B 11 SER cc_start: 0.8756 (t) cc_final: 0.8288 (p) REVERT: B 92 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7852 (mtt90) REVERT: B 96 MET cc_start: 0.8695 (tpp) cc_final: 0.8050 (mmt) REVERT: B 117 SER cc_start: 0.8533 (m) cc_final: 0.8300 (p) REVERT: B 292 ASP cc_start: 0.7945 (t0) cc_final: 0.7690 (t0) REVERT: B 426 LEU cc_start: 0.8767 (mt) cc_final: 0.8566 (mp) REVERT: B 495 SER cc_start: 0.8294 (t) cc_final: 0.8006 (p) REVERT: B 652 MET cc_start: 0.8277 (mmm) cc_final: 0.7845 (mmm) REVERT: B 786 SER cc_start: 0.8417 (m) cc_final: 0.8180 (t) REVERT: B 795 PHE cc_start: 0.8321 (t80) cc_final: 0.8015 (t80) REVERT: B 872 ARG cc_start: 0.7261 (ttm-80) cc_final: 0.7025 (mtp85) REVERT: C 7 MET cc_start: 0.5395 (mtm) cc_final: 0.4993 (ttm) REVERT: C 109 ARG cc_start: 0.8225 (mtt180) cc_final: 0.7938 (mtm-85) REVERT: C 290 ASP cc_start: 0.7729 (t0) cc_final: 0.7515 (t0) REVERT: C 292 ASP cc_start: 0.7708 (t0) cc_final: 0.7487 (t70) REVERT: C 311 SER cc_start: 0.8545 (t) cc_final: 0.8222 (p) REVERT: C 336 LEU cc_start: 0.8659 (mt) cc_final: 0.8240 (mp) REVERT: C 544 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (mtp180) REVERT: C 628 SER cc_start: 0.8090 (t) cc_final: 0.7455 (m) REVERT: C 646 TYR cc_start: 0.7608 (t80) cc_final: 0.7095 (t80) REVERT: C 659 ASN cc_start: 0.8286 (m110) cc_final: 0.8013 (m110) REVERT: C 687 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7112 (pt0) REVERT: C 785 GLU cc_start: 0.7944 (mp0) cc_final: 0.7640 (mp0) REVERT: C 876 SER cc_start: 0.8166 (t) cc_final: 0.7859 (p) REVERT: C 878 ASN cc_start: 0.8245 (p0) cc_final: 0.8023 (p0) REVERT: C 945 PHE cc_start: 0.8988 (m-80) cc_final: 0.8500 (m-80) outliers start: 75 outliers final: 64 residues processed: 580 average time/residue: 0.1471 time to fit residues: 132.2434 Evaluate side-chains 606 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 540 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 583 TRP Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 530 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 853 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 167 optimal weight: 2.9990 chunk 94 optimal weight: 0.0470 chunk 111 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 276 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 644 ASN A 775 ASN A 929 HIS B 210 GLN B 261 GLN B 590 ASN C 499 ASN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100892 restraints weight = 31396.340| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.82 r_work: 0.3126 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 23042 Z= 0.095 Angle : 0.487 9.404 31334 Z= 0.260 Chirality : 0.043 0.161 3297 Planarity : 0.004 0.045 4132 Dihedral : 5.604 86.637 3141 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 3.01 % Allowed : 13.60 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.80 (0.16), residues: 2752 helix: 0.91 (0.31), residues: 323 sheet: 0.40 (0.22), residues: 582 loop : -1.17 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 33 TYR 0.017 0.001 TYR B 503 PHE 0.019 0.001 PHE A 169 TRP 0.016 0.001 TRP B 211 HIS 0.008 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 (23041) covalent geometry : angle 0.48708 / 0.26 (31332) SS BOND : bond 0.00109 / 0.06 ( 1) SS BOND : angle 0.60860 / 0.35 ( 2) hydrogen bonds : bond 0.03281 / 2.18 ( 551) hydrogen bonds : angle 5.36538 / 3.83 ( 1506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 547 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7997 (mtp85) REVERT: A 88 VAL cc_start: 0.8125 (t) cc_final: 0.7738 (m) REVERT: A 94 LEU cc_start: 0.8671 (tp) cc_final: 0.8401 (tt) REVERT: A 137 GLU cc_start: 0.7278 (tt0) cc_final: 0.6947 (tt0) REVERT: A 285 VAL cc_start: 0.8355 (t) cc_final: 0.8086 (p) REVERT: A 409 GLU cc_start: 0.7326 (mp0) cc_final: 0.7088 (mp0) REVERT: A 412 ASN cc_start: 0.7626 (m-40) cc_final: 0.7296 (m-40) REVERT: A 413 TYR cc_start: 0.8051 (m-80) cc_final: 0.7808 (m-80) REVERT: A 451 GLU cc_start: 0.7437 (mp0) cc_final: 0.7191 (mt-10) REVERT: A 487 TYR cc_start: 0.8470 (p90) cc_final: 0.8221 (p90) REVERT: A 502 ASP cc_start: 0.7995 (t70) cc_final: 0.7681 (t0) REVERT: A 504 MET cc_start: 0.8470 (mtt) cc_final: 0.8167 (mtp) REVERT: A 544 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7757 (mtp85) REVERT: A 686 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8185 (mtpp) REVERT: A 788 LYS cc_start: 0.8365 (mttm) cc_final: 0.8144 (mttt) REVERT: A 846 PHE cc_start: 0.8315 (t80) cc_final: 0.8057 (t80) REVERT: A 903 MET cc_start: 0.8160 (mtp) cc_final: 0.7947 (mtm) REVERT: A 906 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7600 (mm-30) REVERT: A 936 ILE cc_start: 0.8645 (mt) cc_final: 0.8325 (tt) REVERT: B 11 SER cc_start: 0.8748 (t) cc_final: 0.8292 (p) REVERT: B 92 ARG cc_start: 0.8087 (mtt90) cc_final: 0.7849 (mtt90) REVERT: B 96 MET cc_start: 0.8672 (tpp) cc_final: 0.8005 (mmt) REVERT: B 117 SER cc_start: 0.8560 (m) cc_final: 0.8290 (p) REVERT: B 182 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7254 (mt-10) REVERT: B 292 ASP cc_start: 0.7901 (t0) cc_final: 0.7641 (t0) REVERT: B 495 SER cc_start: 0.8271 (t) cc_final: 0.8004 (p) REVERT: B 742 GLU cc_start: 0.7673 (pm20) cc_final: 0.7450 (pm20) REVERT: B 760 ASN cc_start: 0.7896 (p0) cc_final: 0.7622 (p0) REVERT: B 786 SER cc_start: 0.8420 (m) cc_final: 0.8177 (t) REVERT: B 795 PHE cc_start: 0.8325 (t80) cc_final: 0.8031 (t80) REVERT: C 109 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7912 (mtm-85) REVERT: C 290 ASP cc_start: 0.7722 (t0) cc_final: 0.7513 (t0) REVERT: C 311 SER cc_start: 0.8535 (t) cc_final: 0.8206 (p) REVERT: C 336 LEU cc_start: 0.8651 (mt) cc_final: 0.8242 (mp) REVERT: C 544 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7930 (mtp180) REVERT: C 628 SER cc_start: 0.8080 (t) cc_final: 0.7440 (m) REVERT: C 646 TYR cc_start: 0.7606 (t80) cc_final: 0.7113 (t80) REVERT: C 659 ASN cc_start: 0.8294 (m110) cc_final: 0.8073 (m110) REVERT: C 687 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7106 (pt0) REVERT: C 785 GLU cc_start: 0.7936 (mp0) cc_final: 0.7640 (mp0) REVERT: C 801 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7538 (mtm) REVERT: C 876 SER cc_start: 0.8134 (t) cc_final: 0.7801 (p) REVERT: C 878 ASN cc_start: 0.8223 (p0) cc_final: 0.8010 (p0) REVERT: C 945 PHE cc_start: 0.8993 (m-80) cc_final: 0.8498 (m-80) outliers start: 73 outliers final: 58 residues processed: 576 average time/residue: 0.1485 time to fit residues: 131.4812 Evaluate side-chains 598 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 538 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 493 LYS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 530 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 122 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 223 optimal weight: 0.0000 chunk 219 optimal weight: 4.9990 chunk 185 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 239 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 GLN A 471 ASN A 644 ASN A 775 ASN A 929 HIS B 210 GLN B 261 GLN B 310 ASN B 371 GLN C 499 ASN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.101102 restraints weight = 30914.662| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.81 r_work: 0.3133 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23042 Z= 0.089 Angle : 0.478 9.399 31334 Z= 0.255 Chirality : 0.043 0.163 3297 Planarity : 0.004 0.041 4132 Dihedral : 5.522 86.963 3141 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.55 % Allowed : 14.22 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -0.75 (0.16), residues: 2752 helix: 0.94 (0.31), residues: 326 sheet: 0.42 (0.22), residues: 582 loop : -1.13 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 33 TYR 0.017 0.001 TYR B 503 PHE 0.019 0.001 PHE A 169 TRP 0.019 0.001 TRP B 211 HIS 0.006 0.001 HIS C 929 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (23041) covalent geometry : angle 0.47784 / 0.26 (31332) SS BOND : bond 0.00066 / 0.03 ( 1) SS BOND : angle 0.57030 / 0.33 ( 2) hydrogen bonds : bond 0.03148 / 2.10 ( 551) hydrogen bonds : angle 5.27826 / 3.77 ( 1506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 554 time to evaluate : 0.869 Fit side-chains REVERT: A 38 TYR cc_start: 0.7014 (p90) cc_final: 0.6453 (p90) REVERT: A 63 ARG cc_start: 0.8415 (mtp85) cc_final: 0.7982 (mtp85) REVERT: A 88 VAL cc_start: 0.8104 (t) cc_final: 0.7714 (m) REVERT: A 94 LEU cc_start: 0.8681 (tp) cc_final: 0.8410 (tt) REVERT: A 137 GLU cc_start: 0.7249 (tt0) cc_final: 0.6886 (tt0) REVERT: A 285 VAL cc_start: 0.8365 (t) cc_final: 0.8075 (p) REVERT: A 409 GLU cc_start: 0.7289 (mp0) cc_final: 0.7080 (mp0) REVERT: A 413 TYR cc_start: 0.8042 (m-80) cc_final: 0.7832 (m-80) REVERT: A 451 GLU cc_start: 0.7394 (mp0) cc_final: 0.7090 (mt-10) REVERT: A 502 ASP cc_start: 0.8070 (t70) cc_final: 0.7754 (t0) REVERT: A 544 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7767 (mtp85) REVERT: A 578 SER cc_start: 0.8408 (m) cc_final: 0.8201 (t) REVERT: A 686 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8188 (mtpp) REVERT: A 788 LYS cc_start: 0.8363 (mttm) cc_final: 0.8145 (mttt) REVERT: A 846 PHE cc_start: 0.8315 (t80) cc_final: 0.8076 (t80) REVERT: A 903 MET cc_start: 0.8164 (mtp) cc_final: 0.7944 (mtm) REVERT: A 906 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 936 ILE cc_start: 0.8630 (mt) cc_final: 0.8314 (tt) REVERT: B 11 SER cc_start: 0.8728 (t) cc_final: 0.8272 (p) REVERT: B 63 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7580 (mmt90) REVERT: B 92 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7810 (mtt90) REVERT: B 96 MET cc_start: 0.8652 (tpp) cc_final: 0.7977 (mmt) REVERT: B 117 SER cc_start: 0.8571 (m) cc_final: 0.8299 (p) REVERT: B 182 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7235 (mt-10) REVERT: B 188 VAL cc_start: 0.8224 (t) cc_final: 0.7945 (p) REVERT: B 292 ASP cc_start: 0.7842 (t0) cc_final: 0.7588 (t0) REVERT: B 476 ASN cc_start: 0.8267 (m-40) cc_final: 0.7924 (m110) REVERT: B 495 SER cc_start: 0.8261 (t) cc_final: 0.8000 (p) REVERT: B 760 ASN cc_start: 0.7855 (p0) cc_final: 0.7575 (p0) REVERT: B 786 SER cc_start: 0.8414 (m) cc_final: 0.8174 (t) REVERT: C 109 ARG cc_start: 0.8193 (mtt180) cc_final: 0.7891 (mtm-85) REVERT: C 290 ASP cc_start: 0.7709 (t0) cc_final: 0.7499 (t0) REVERT: C 311 SER cc_start: 0.8492 (t) cc_final: 0.8186 (p) REVERT: C 336 LEU cc_start: 0.8666 (mt) cc_final: 0.8247 (mp) REVERT: C 470 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7715 (mtm180) REVERT: C 544 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7910 (mtp180) REVERT: C 628 SER cc_start: 0.8077 (t) cc_final: 0.7455 (m) REVERT: C 646 TYR cc_start: 0.7632 (t80) cc_final: 0.7087 (t80) REVERT: C 659 ASN cc_start: 0.8312 (m110) cc_final: 0.8061 (m110) REVERT: C 687 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7050 (pt0) REVERT: C 785 GLU cc_start: 0.7922 (mp0) cc_final: 0.7639 (mp0) REVERT: C 801 MET cc_start: 0.7730 (mtp) cc_final: 0.7484 (mtm) REVERT: C 945 PHE cc_start: 0.9001 (m-80) cc_final: 0.8502 (m-80) outliers start: 62 outliers final: 52 residues processed: 581 average time/residue: 0.1490 time to fit residues: 132.3602 Evaluate side-chains 589 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 536 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 530 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 79 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 233 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 chunk 94 optimal weight: 0.3980 chunk 206 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 ASN A 644 ASN A 775 ASN A 929 HIS ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN C 499 ASN C 537 HIS C 758 GLN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101024 restraints weight = 31298.468| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.84 r_work: 0.3126 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23042 Z= 0.099 Angle : 0.492 9.758 31334 Z= 0.262 Chirality : 0.044 0.183 3297 Planarity : 0.004 0.042 4132 Dihedral : 5.476 86.987 3139 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.51 % Allowed : 14.96 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -0.75 (0.16), residues: 2752 helix: 0.93 (0.31), residues: 326 sheet: 0.41 (0.22), residues: 582 loop : -1.13 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 930 TYR 0.017 0.001 TYR B 503 PHE 0.020 0.001 PHE A 169 TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (23041) covalent geometry : angle 0.49217 / 0.26 (31332) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.55584 / 0.32 ( 2) hydrogen bonds : bond 0.03267 / 2.18 ( 551) hydrogen bonds : angle 5.25902 / 3.76 ( 1506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 545 time to evaluate : 0.580 Fit side-chains REVERT: A 38 TYR cc_start: 0.7020 (p90) cc_final: 0.6450 (p90) REVERT: A 63 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7980 (mtp85) REVERT: A 94 LEU cc_start: 0.8677 (tp) cc_final: 0.8418 (tt) REVERT: A 285 VAL cc_start: 0.8381 (t) cc_final: 0.8095 (p) REVERT: A 409 GLU cc_start: 0.7277 (mp0) cc_final: 0.7075 (mp0) REVERT: A 412 ASN cc_start: 0.7679 (m-40) cc_final: 0.7433 (m-40) REVERT: A 451 GLU cc_start: 0.7392 (mp0) cc_final: 0.7097 (mt-10) REVERT: A 502 ASP cc_start: 0.8075 (t70) cc_final: 0.7748 (t0) REVERT: A 544 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7764 (mtp85) REVERT: A 578 SER cc_start: 0.8426 (m) cc_final: 0.8205 (t) REVERT: A 686 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8179 (mtpp) REVERT: A 846 PHE cc_start: 0.8328 (t80) cc_final: 0.8086 (t80) REVERT: A 903 MET cc_start: 0.8178 (mtp) cc_final: 0.7963 (mtm) REVERT: A 906 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 936 ILE cc_start: 0.8637 (mt) cc_final: 0.8317 (tt) REVERT: B 11 SER cc_start: 0.8721 (t) cc_final: 0.8258 (p) REVERT: B 92 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7834 (mtt90) REVERT: B 96 MET cc_start: 0.8659 (tpp) cc_final: 0.7993 (mmt) REVERT: B 117 SER cc_start: 0.8574 (m) cc_final: 0.8299 (p) REVERT: B 182 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7255 (mt-10) REVERT: B 188 VAL cc_start: 0.8232 (t) cc_final: 0.7967 (p) REVERT: B 292 ASP cc_start: 0.7844 (t0) cc_final: 0.7584 (t0) REVERT: B 446 PHE cc_start: 0.8024 (m-80) cc_final: 0.7820 (m-80) REVERT: B 476 ASN cc_start: 0.8288 (m-40) cc_final: 0.7886 (m110) REVERT: B 495 SER cc_start: 0.8262 (t) cc_final: 0.7995 (p) REVERT: B 742 GLU cc_start: 0.7621 (pm20) cc_final: 0.7395 (pm20) REVERT: B 760 ASN cc_start: 0.7881 (p0) cc_final: 0.7606 (p0) REVERT: B 786 SER cc_start: 0.8429 (m) cc_final: 0.8177 (t) REVERT: C 290 ASP cc_start: 0.7729 (t0) cc_final: 0.7511 (t0) REVERT: C 311 SER cc_start: 0.8492 (t) cc_final: 0.8201 (p) REVERT: C 336 LEU cc_start: 0.8652 (mt) cc_final: 0.8221 (mp) REVERT: C 470 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7748 (mtm180) REVERT: C 544 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7928 (mtp180) REVERT: C 628 SER cc_start: 0.8078 (t) cc_final: 0.7436 (m) REVERT: C 646 TYR cc_start: 0.7646 (t80) cc_final: 0.7110 (t80) REVERT: C 659 ASN cc_start: 0.8309 (m110) cc_final: 0.8073 (m110) REVERT: C 687 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7130 (pt0) REVERT: C 715 ASN cc_start: 0.8381 (m-40) cc_final: 0.8166 (m-40) REVERT: C 785 GLU cc_start: 0.7920 (mp0) cc_final: 0.7650 (mp0) REVERT: C 801 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7541 (mtm) REVERT: C 945 PHE cc_start: 0.8990 (m-80) cc_final: 0.8495 (m-80) REVERT: G 18 MET cc_start: 0.8152 (mmm) cc_final: 0.7834 (tpp) outliers start: 61 outliers final: 56 residues processed: 571 average time/residue: 0.1448 time to fit residues: 127.3511 Evaluate side-chains 599 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 541 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 644 ASN Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 775 ASN Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 644 ASN Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 307 LYS Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 882 MET Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 185 optimal weight: 0.2980 chunk 27 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 191 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 GLN A 471 ASN A 775 ASN A 929 HIS B 261 GLN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 537 HIS C 758 GLN C 775 ASN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 825 ASN ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.101386 restraints weight = 31343.517| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.84 r_work: 0.3136 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23042 Z= 0.091 Angle : 0.487 10.102 31334 Z= 0.259 Chirality : 0.043 0.183 3297 Planarity : 0.004 0.043 4132 Dihedral : 5.442 86.977 3139 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.47 % Allowed : 14.92 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -0.73 (0.16), residues: 2752 helix: 0.97 (0.31), residues: 326 sheet: 0.41 (0.22), residues: 582 loop : -1.11 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.017 0.001 TYR B 503 PHE 0.028 0.001 PHE B 446 TRP 0.020 0.001 TRP B 211 HIS 0.004 0.001 HIS A 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (23041) covalent geometry : angle 0.48749 / 0.26 (31332) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 0.50921 / 0.29 ( 2) hydrogen bonds : bond 0.03148 / 2.11 ( 551) hydrogen bonds : angle 5.23997 / 3.74 ( 1506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 543 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 38 TYR cc_start: 0.7009 (p90) cc_final: 0.6465 (p90) REVERT: A 63 ARG cc_start: 0.8417 (mtp85) cc_final: 0.7976 (mtp85) REVERT: A 94 LEU cc_start: 0.8680 (tp) cc_final: 0.8419 (tt) REVERT: A 285 VAL cc_start: 0.8379 (t) cc_final: 0.8092 (p) REVERT: A 412 ASN cc_start: 0.7673 (m-40) cc_final: 0.7461 (m-40) REVERT: A 451 GLU cc_start: 0.7371 (mp0) cc_final: 0.7081 (mt-10) REVERT: A 502 ASP cc_start: 0.8093 (t70) cc_final: 0.7782 (t0) REVERT: A 544 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7783 (mtp85) REVERT: A 578 SER cc_start: 0.8412 (m) cc_final: 0.8206 (t) REVERT: A 646 TYR cc_start: 0.8082 (t80) cc_final: 0.7449 (t80) REVERT: A 686 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8179 (mtpp) REVERT: A 846 PHE cc_start: 0.8321 (t80) cc_final: 0.8082 (t80) REVERT: A 903 MET cc_start: 0.8183 (mtp) cc_final: 0.7975 (mtm) REVERT: A 906 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 936 ILE cc_start: 0.8629 (mt) cc_final: 0.8314 (tt) REVERT: B 11 SER cc_start: 0.8708 (t) cc_final: 0.8256 (p) REVERT: B 92 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7835 (mtt90) REVERT: B 96 MET cc_start: 0.8649 (tpp) cc_final: 0.7981 (mmt) REVERT: B 117 SER cc_start: 0.8576 (m) cc_final: 0.8305 (p) REVERT: B 182 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7276 (mt-10) REVERT: B 188 VAL cc_start: 0.8206 (t) cc_final: 0.7945 (p) REVERT: B 292 ASP cc_start: 0.7805 (t0) cc_final: 0.7548 (t0) REVERT: B 476 ASN cc_start: 0.8281 (m-40) cc_final: 0.7904 (m110) REVERT: B 495 SER cc_start: 0.8267 (t) cc_final: 0.8005 (p) REVERT: B 755 ASN cc_start: 0.8011 (m-40) cc_final: 0.7800 (m-40) REVERT: B 760 ASN cc_start: 0.7859 (p0) cc_final: 0.7518 (p0) REVERT: B 786 SER cc_start: 0.8432 (m) cc_final: 0.8182 (t) REVERT: C 290 ASP cc_start: 0.7727 (t0) cc_final: 0.7507 (t0) REVERT: C 311 SER cc_start: 0.8477 (t) cc_final: 0.8179 (p) REVERT: C 336 LEU cc_start: 0.8633 (mt) cc_final: 0.8212 (mp) REVERT: C 544 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7956 (mtp180) REVERT: C 628 SER cc_start: 0.8068 (t) cc_final: 0.7427 (m) REVERT: C 646 TYR cc_start: 0.7648 (t80) cc_final: 0.7129 (t80) REVERT: C 659 ASN cc_start: 0.8352 (m110) cc_final: 0.8109 (m110) REVERT: C 687 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7127 (pt0) REVERT: C 785 GLU cc_start: 0.7944 (mp0) cc_final: 0.7671 (mp0) REVERT: C 801 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7504 (mtm) REVERT: C 945 PHE cc_start: 0.8993 (m-80) cc_final: 0.8505 (m-80) REVERT: G 18 MET cc_start: 0.8142 (mmm) cc_final: 0.7819 (tpp) outliers start: 60 outliers final: 50 residues processed: 568 average time/residue: 0.1594 time to fit residues: 138.9941 Evaluate side-chains 591 residues out of total 2427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 539 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 687 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 435 GLN Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 527 ASP Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 652 MET Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 836 MET Chi-restraints excluded: chain C residue 846 PHE Chi-restraints excluded: chain C residue 912 GLU Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 184 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 256 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 404 HIS A 471 ASN A 644 ASN A 775 ASN A 929 HIS ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN C 537 HIS C 758 GLN C 775 ASN ** C 823 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100710 restraints weight = 31469.790| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.83 r_work: 0.3109 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23042 Z= 0.113 Angle : 0.510 9.688 31334 Z= 0.271 Chirality : 0.044 0.188 3297 Planarity : 0.004 0.043 4132 Dihedral : 5.482 86.664 3139 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.39 % Allowed : 15.08 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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 are not related in a simple way. whole: -0.79 (0.16), residues: 2752 helix: 0.90 (0.31), residues: 323 sheet: 0.38 (0.22), residues: 582 loop : -1.15 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.017 0.001 TYR B 503 PHE 0.023 0.001 PHE B 446 TRP 0.020 0.001 TRP B 211 HIS 0.005 0.001 HIS B 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (23041) covalent geometry : angle 0.51013 / 0.27 (31332) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 0.59209 / 0.34 ( 2) hydrogen bonds : bond 0.03437 / 2.28 ( 551) hydrogen bonds : angle 5.26417 / 3.77 ( 1506) =============================================================================== Job complete usr+sys time: 4946.43 seconds wall clock time: 85 minutes 26.91 seconds (5126.91 seconds total)