Starting phenix.real_space_refine on Fri Aug 7 11:13:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5y_47531/08_2026/9e5y_47531.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.021 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 P 53 5.49 5 S 116 5.16 5 C 13173 2.51 5 N 3494 2.21 5 O 4060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 20896 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7281 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 40, 'TRANS': 857} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "C" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7281 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 40, 'TRANS': 857} Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "P" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 657 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 4.64, per 1000 atoms: 0.22 Number of scatterers: 20896 At special positions: 0 Unit cell: (113.436, 152.352, 141.588, 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) S 116 16.00 P 53 15.00 O 4060 8.00 N 3494 7.00 C 13173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 537.7 milliseconds 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4650 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 30 sheets defined 40.7% alpha, 17.3% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.879A pdb=" N LYS A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.511A pdb=" N ASP A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.223A pdb=" N MET A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 232 through 237' Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.660A pdb=" N LEU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.967A pdb=" N GLU A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 336 removed outlier: 3.636A pdb=" N VAL A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 removed outlier: 3.541A pdb=" N TYR A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.550A pdb=" N THR A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 435 through 441 removed outlier: 4.162A pdb=" N TYR A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 501 removed outlier: 3.880A pdb=" N GLN A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.743A pdb=" N LEU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 568 removed outlier: 3.534A pdb=" N LEU A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TYR A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 584 through 607 removed outlier: 3.625A pdb=" N LYS A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 634 Processing helix chain 'A' and resid 640 through 655 removed outlier: 3.826A pdb=" N GLY A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 653 " --> pdb=" O ASN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.604A pdb=" N MET A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 751 Processing helix chain 'A' and resid 753 through 769 removed outlier: 3.531A pdb=" N LYS A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.603A pdb=" N ILE A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 789 removed outlier: 4.160A pdb=" N ASP A 789 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 812 Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 854 through 861 removed outlier: 3.592A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 870 Processing helix chain 'A' and resid 872 through 883 removed outlier: 3.865A pdb=" N SER A 882 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 898 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 119 through 133 removed outlier: 4.077A pdb=" N ARG B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 62 through 75 removed outlier: 3.806A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 removed outlier: 4.058A pdb=" N ALA C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 190 through 205 removed outlier: 4.139A pdb=" N MET C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.570A pdb=" N ALA C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.622A pdb=" N ASN C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 237 removed outlier: 4.343A pdb=" N SER C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 237' Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 269 through 278 removed outlier: 4.023A pdb=" N LYS C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 313 through 336 removed outlier: 3.761A pdb=" N SER C 319 " --> pdb=" O GLN C 315 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.609A pdb=" N LEU C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.518A pdb=" N MET C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.531A pdb=" N THR C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 421 Processing helix chain 'C' and resid 435 through 441 removed outlier: 3.585A pdb=" N TYR C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 441 " --> pdb=" O HIS C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 503 Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 531 through 562 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 576 through 607 removed outlier: 3.913A pdb=" N THR C 584 " --> pdb=" O ALA C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 634 Processing helix chain 'C' and resid 635 through 638 Processing helix chain 'C' and resid 640 through 672 removed outlier: 4.054A pdb=" N GLU C 657 " --> pdb=" O LYS C 653 " (cutoff:3.500A) Proline residue: C 658 - end of helix removed outlier: 4.103A pdb=" N VAL C 662 " --> pdb=" O PRO C 658 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 751 Processing helix chain 'C' and resid 753 through 771 removed outlier: 3.830A pdb=" N VAL C 757 " --> pdb=" O GLY C 753 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 758 " --> pdb=" O GLU C 754 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 769 " --> pdb=" O GLU C 765 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN C 770 " --> pdb=" O LYS C 766 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 771 " --> pdb=" O GLU C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 799 through 812 removed outlier: 3.723A pdb=" N GLY C 804 " --> pdb=" O PHE C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 862 removed outlier: 4.220A pdb=" N SER C 856 " --> pdb=" O LYS C 852 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 872 Processing helix chain 'C' and resid 872 through 882 Processing helix chain 'C' and resid 893 through 898 removed outlier: 3.745A pdb=" N GLY C 898 " --> pdb=" O ASP C 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 18 removed outlier: 3.683A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 66 removed outlier: 3.735A pdb=" N LEU D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.833A pdb=" N LEU D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 56 through 67 removed outlier: 3.544A pdb=" N PHE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 6.517A pdb=" N ARG A 18 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE A 8 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 16 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR A 10 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.704A pdb=" N LYS A 48 " --> pdb=" O VAL A 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 removed outlier: 5.657A pdb=" N ALA A 109 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.286A pdb=" N GLU A 129 " --> pdb=" O THR A 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.500A pdb=" N GLY A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 removed outlier: 3.633A pdb=" N LYS A 257 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 614 through 617 removed outlier: 5.672A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 684 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP A 408 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 682 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 683 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 712 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 614 through 617 removed outlier: 5.672A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 684 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASP A 408 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A 682 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU A 683 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A 712 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP A 711 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 11.439A pdb=" N GLU A 719 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 778 through 781 removed outlier: 3.559A pdb=" N GLU A 778 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.964A pdb=" N ALA B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.855A pdb=" N THR B 89 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 166 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR E 165 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE E 147 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 142 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE E 178 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 182 through 183 removed outlier: 6.703A pdb=" N ILE B 147 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR B 165 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 11 removed outlier: 3.986A pdb=" N PHE C 4 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C 18 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE C 8 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 16 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR C 10 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 36 through 40 removed outlier: 4.058A pdb=" N TYR C 47 " --> pdb=" O CYS C 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 183 through 188 removed outlier: 6.230A pdb=" N PHE C 143 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N MET C 186 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 145 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE C 188 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP C 147 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 211 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS C 111 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 210 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 removed outlier: 7.482A pdb=" N THR C 116 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 130 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 247 through 248 Processing sheet with id=AC3, first strand: chain 'C' and resid 614 through 615 removed outlier: 3.991A pdb=" N TYR C 623 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 404 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP C 408 " --> pdb=" O ARG C 682 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG C 682 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 427 through 430 removed outlier: 6.505A pdb=" N MET C 459 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 699 through 701 removed outlier: 7.080A pdb=" N ARG C 704 " --> pdb=" O LYS C 700 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.604A pdb=" N VAL C 709 " --> pdb=" O HIS C 721 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP C 711 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N GLU C 719 " --> pdb=" O ASP C 711 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 778 through 780 removed outlier: 3.925A pdb=" N GLU C 778 " --> pdb=" O VAL C 828 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 826 " --> pdb=" O LYS C 780 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP C 844 " --> pdb=" O MET C 827 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AC9, first strand: chain 'D' and resid 26 through 32 removed outlier: 6.077A pdb=" N GLN D 27 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 44 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.267A pdb=" N PHE D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 142 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 147 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AD3, first strand: chain 'E' and resid 26 through 32 removed outlier: 6.848A pdb=" N PHE E 28 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 11.062A pdb=" N ASP E 46 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N MET E 30 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 10.946A pdb=" N ILE E 44 " --> pdb=" O MET E 30 " (cutoff:3.500A) removed outlier: 11.621A pdb=" N ARG E 32 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N ALA E 42 " --> pdb=" O ARG E 32 " (cutoff:3.500A) 883 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5128 1.33 - 1.45: 4352 1.45 - 1.57: 11665 1.57 - 1.69: 104 1.69 - 1.81: 204 Bond restraints: 21453 Sorted by residual: bond pdb=" N MET A 350 " pdb=" CA MET A 350 " ideal model delta sigma weight residual 1.456 1.488 -0.033 8.70e-03 1.32e+04 1.41e+01 bond pdb=" N ILE C 230 " pdb=" CA ILE C 230 " ideal model delta sigma weight residual 1.452 1.496 -0.043 1.18e-02 7.18e+03 1.35e+01 bond pdb=" N LYS C 874 " pdb=" CA LYS C 874 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.32e+01 bond pdb=" C3' DT T 22 " pdb=" C2' DT T 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" N LYS A 166 " pdb=" CA LYS A 166 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.09e-02 8.42e+03 9.87e+00 ... (remaining 21448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 28111 2.04 - 4.07: 987 4.07 - 6.11: 60 6.11 - 8.15: 19 8.15 - 10.18: 5 Bond angle restraints: 29182 Sorted by residual: angle pdb=" C3' DA T 12 " pdb=" O3' DA T 12 " pdb=" P DA T 13 " ideal model delta sigma weight residual 119.70 114.12 5.58 1.20e+00 6.94e-01 2.16e+01 angle pdb=" CA GLY A 232 " pdb=" C GLY A 232 " pdb=" O GLY A 232 " ideal model delta sigma weight residual 122.25 117.75 4.50 9.90e-01 1.02e+00 2.07e+01 angle pdb=" N3 DT P 12 " pdb=" C4 DT P 12 " pdb=" O4 DT P 12 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT T 18 " pdb=" C4 DT T 18 " pdb=" O4 DT T 18 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT T 19 " pdb=" C4 DT T 19 " pdb=" O4 DT T 19 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 29177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 12065 31.79 - 63.57: 765 63.57 - 95.36: 28 95.36 - 127.14: 0 127.14 - 158.93: 2 Dihedral angle restraints: 12860 sinusoidal: 5623 harmonic: 7237 Sorted by residual: dihedral pdb=" CA VAL A 245 " pdb=" C VAL A 245 " pdb=" N LYS A 246 " pdb=" CA LYS A 246 " ideal model delta harmonic sigma weight residual -180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DC T 4 " pdb=" C3' DC T 4 " pdb=" O3' DC T 4 " pdb=" P DA T 5 " ideal model delta sinusoidal sigma weight residual 220.00 61.07 158.93 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CA ALA C 615 " pdb=" C ALA C 615 " pdb=" N ALA C 616 " pdb=" CA ALA C 616 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 12857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 3057 0.128 - 0.256: 91 0.256 - 0.384: 1 0.384 - 0.512: 1 0.512 - 0.640: 9 Chirality restraints: 3159 Sorted by residual: chirality pdb=" P DG T 3 " pdb=" OP1 DG T 3 " pdb=" OP2 DG T 3 " pdb=" O5' DG T 3 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DA T 5 " pdb=" OP1 DA T 5 " pdb=" OP2 DA T 5 " pdb=" O5' DA T 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" P DA T 8 " pdb=" OP1 DA T 8 " pdb=" OP2 DA T 8 " pdb=" O5' DA T 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.93e+00 ... (remaining 3156 not shown) Planarity restraints: 3580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 162 " -0.237 9.50e-02 1.11e+02 1.06e-01 6.90e+00 pdb=" NE ARG D 162 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 162 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 162 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 162 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 866 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" C THR A 866 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 866 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 867 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 423 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 424 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 424 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 424 " -0.030 5.00e-02 4.00e+02 ... (remaining 3577 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1913 2.74 - 3.28: 22117 3.28 - 3.82: 36267 3.82 - 4.36: 41937 4.36 - 4.90: 68808 Nonbonded interactions: 171042 Sorted by model distance: nonbonded pdb=" O GLY A 505 " pdb=" OG1 THR A 531 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR C 460 " pdb=" OD1 ASN C 579 " model vdw 2.199 3.040 nonbonded pdb=" ND2 ASN A 599 " pdb=" OD1 ASP A 612 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN A 110 " pdb=" NE2 GLN A 329 " model vdw 2.213 3.120 nonbonded pdb=" ND2 ASN C 783 " pdb=" OP1 DG P 24 " model vdw 2.214 3.120 ... (remaining 171037 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.006 0.062 21453 Z= 0.392 Angle : 0.777 10.182 29182 Z= 0.516 Chirality : 0.062 0.640 3159 Planarity : 0.005 0.106 3580 Dihedral : 18.162 158.930 8210 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.58 % Allowed : 27.48 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2470 helix: 0.06 (0.17), residues: 897 sheet: -1.40 (0.26), residues: 379 loop : -1.09 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 131 TYR 0.026 0.002 TYR C 768 PHE 0.034 0.002 PHE C 647 TRP 0.022 0.002 TRP A 202 HIS 0.005 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.39 (21453) covalent geometry : angle 0.77666 / 0.52 (29182) hydrogen bonds : bond 0.14413 / 9.37 ( 918) hydrogen bonds : angle 6.60948 / 4.79 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 MET cc_start: 0.6402 (tpp) cc_final: 0.6195 (tpp) REVERT: C 118 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: C 202 TRP cc_start: 0.8141 (t60) cc_final: 0.7510 (t-100) REVERT: C 885 MET cc_start: 0.7746 (ttm) cc_final: 0.7544 (ttm) REVERT: D 157 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5973 (p0) REVERT: E 22 MET cc_start: 0.5485 (tpp) cc_final: 0.5093 (tpp) REVERT: E 184 MET cc_start: 0.7047 (mmp) cc_final: 0.6182 (mmp) outliers start: 34 outliers final: 16 residues processed: 316 average time/residue: 0.1379 time to fit residues: 68.6106 Evaluate side-chains 282 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASN Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 157 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 50.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS E 190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.180854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.127401 restraints weight = 35480.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124521 restraints weight = 22116.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126091 restraints weight = 19636.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126466 restraints weight = 15922.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126545 restraints weight = 15674.635| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21453 Z= 0.244 Angle : 0.655 9.087 29182 Z= 0.357 Chirality : 0.046 0.265 3159 Planarity : 0.005 0.057 3580 Dihedral : 15.206 154.993 3318 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.32 % Allowed : 26.27 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2470 helix: 0.09 (0.17), residues: 914 sheet: -1.43 (0.26), residues: 384 loop : -1.15 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 131 TYR 0.024 0.002 TYR C 153 PHE 0.023 0.002 PHE A 218 TRP 0.016 0.002 TRP A 69 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (21453) covalent geometry : angle 0.65476 / 0.36 (29182) hydrogen bonds : bond 0.04924 / 3.24 ( 918) hydrogen bonds : angle 5.73190 / 4.16 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 270 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: B 124 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7107 (tp-100) REVERT: C 152 MET cc_start: 0.8103 (ptt) cc_final: 0.7892 (ptp) REVERT: C 471 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7950 (mt-10) REVERT: C 768 TYR cc_start: 0.7513 (t80) cc_final: 0.7284 (t80) REVERT: C 808 TYR cc_start: 0.6716 (t80) cc_final: 0.6470 (t80) REVERT: D 49 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7271 (p0) REVERT: D 156 GLU cc_start: 0.7299 (tp30) cc_final: 0.6908 (tp30) REVERT: E 184 MET cc_start: 0.7722 (mmp) cc_final: 0.6725 (mmp) outliers start: 93 outliers final: 48 residues processed: 336 average time/residue: 0.1276 time to fit residues: 68.6378 Evaluate side-chains 303 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 40 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 0.0570 chunk 190 optimal weight: 3.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.181273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128196 restraints weight = 35288.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125279 restraints weight = 21867.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127020 restraints weight = 19036.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127274 restraints weight = 15337.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127298 restraints weight = 15177.932| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21453 Z= 0.193 Angle : 0.604 9.136 29182 Z= 0.328 Chirality : 0.045 0.280 3159 Planarity : 0.004 0.053 3580 Dihedral : 15.100 155.253 3298 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.32 % Allowed : 26.22 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.17), residues: 2470 helix: 0.24 (0.17), residues: 915 sheet: -1.36 (0.26), residues: 384 loop : -1.09 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 682 TYR 0.017 0.002 TYR C 623 PHE 0.017 0.001 PHE C 143 TRP 0.014 0.002 TRP A 69 HIS 0.017 0.001 HIS D 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (21453) covalent geometry : angle 0.60407 / 0.33 (29182) hydrogen bonds : bond 0.04467 / 2.96 ( 918) hydrogen bonds : angle 5.55472 / 4.02 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 276 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7362 (m-80) REVERT: A 649 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 657 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7691 (tp30) REVERT: C 768 TYR cc_start: 0.7469 (t80) cc_final: 0.7154 (t80) REVERT: D 49 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7575 (p0) REVERT: D 156 GLU cc_start: 0.7257 (tp30) cc_final: 0.6941 (tp30) REVERT: D 177 THR cc_start: 0.7849 (OUTLIER) cc_final: 0.7634 (p) REVERT: E 22 MET cc_start: 0.5851 (tpp) cc_final: 0.4951 (tpp) REVERT: E 181 ILE cc_start: 0.5074 (mp) cc_final: 0.4515 (mm) REVERT: E 184 MET cc_start: 0.7779 (mmp) cc_final: 0.6831 (mmp) outliers start: 93 outliers final: 61 residues processed: 342 average time/residue: 0.1325 time to fit residues: 71.8610 Evaluate side-chains 327 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 181 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 156 optimal weight: 0.0000 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 3.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN D 58 ASN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.180898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127545 restraints weight = 35645.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.125299 restraints weight = 21861.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126946 restraints weight = 18604.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127030 restraints weight = 14861.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.127155 restraints weight = 14909.447| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21453 Z= 0.201 Angle : 0.603 9.092 29182 Z= 0.325 Chirality : 0.045 0.295 3159 Planarity : 0.004 0.054 3580 Dihedral : 15.090 154.106 3296 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.39 % Allowed : 26.13 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.17), residues: 2470 helix: 0.27 (0.17), residues: 916 sheet: -1.36 (0.26), residues: 386 loop : -1.08 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.025 0.002 TYR E 165 PHE 0.021 0.002 PHE C 143 TRP 0.016 0.002 TRP A 458 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (21453) covalent geometry : angle 0.60279 / 0.33 (29182) hydrogen bonds : bond 0.04299 / 2.84 ( 918) hydrogen bonds : angle 5.44775 / 3.95 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 269 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLU cc_start: 0.8568 (pp20) cc_final: 0.7279 (mt-10) REVERT: A 224 MET cc_start: 0.5288 (ptm) cc_final: 0.5015 (ptm) REVERT: A 297 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8284 (mmtt) REVERT: A 427 ILE cc_start: 0.6720 (OUTLIER) cc_final: 0.6494 (mt) REVERT: A 458 TRP cc_start: 0.7363 (m100) cc_final: 0.7046 (m100) REVERT: A 476 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7432 (m-80) REVERT: A 649 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7935 (t0) REVERT: A 657 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: A 731 GLN cc_start: 0.7280 (mp10) cc_final: 0.6989 (mp10) REVERT: B 124 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7209 (tp40) REVERT: C 401 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7939 (mmm-85) REVERT: C 768 TYR cc_start: 0.7501 (t80) cc_final: 0.7106 (t80) REVERT: D 49 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7552 (p0) REVERT: E 184 MET cc_start: 0.7828 (mmp) cc_final: 0.6869 (mmp) outliers start: 116 outliers final: 77 residues processed: 352 average time/residue: 0.1255 time to fit residues: 70.2022 Evaluate side-chains 343 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 259 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 196 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 236 optimal weight: 40.0000 chunk 172 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.181637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128003 restraints weight = 35401.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125261 restraints weight = 20880.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126885 restraints weight = 18453.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127275 restraints weight = 14657.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127287 restraints weight = 14420.015| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21453 Z= 0.168 Angle : 0.585 9.178 29182 Z= 0.315 Chirality : 0.044 0.296 3159 Planarity : 0.004 0.052 3580 Dihedral : 15.047 153.145 3296 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.07 % Allowed : 26.73 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2470 helix: 0.37 (0.17), residues: 911 sheet: -1.30 (0.26), residues: 384 loop : -1.02 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.029 0.002 TYR E 165 PHE 0.017 0.001 PHE A 647 TRP 0.015 0.002 TRP A 458 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (21453) covalent geometry : angle 0.58518 / 0.31 (29182) hydrogen bonds : bond 0.04096 / 2.71 ( 918) hydrogen bonds : angle 5.36011 / 3.88 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 274 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 141 ASP cc_start: 0.7217 (p0) cc_final: 0.6787 (p0) REVERT: A 216 GLU cc_start: 0.8564 (pp20) cc_final: 0.7282 (mt-10) REVERT: A 258 GLU cc_start: 0.6915 (tt0) cc_final: 0.6591 (tm-30) REVERT: A 297 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8169 (mmtt) REVERT: A 427 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6402 (mt) REVERT: A 458 TRP cc_start: 0.7357 (m100) cc_final: 0.7034 (m100) REVERT: A 476 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: A 657 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: B 124 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7115 (tp-100) REVERT: C 401 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7920 (mmm-85) REVERT: C 768 TYR cc_start: 0.7494 (t80) cc_final: 0.7076 (t80) REVERT: D 49 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7670 (p0) REVERT: D 75 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7871 (tp-100) REVERT: D 204 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: E 22 MET cc_start: 0.5815 (tpp) cc_final: 0.5511 (tpp) REVERT: E 184 MET cc_start: 0.7892 (mmp) cc_final: 0.6958 (mmp) outliers start: 109 outliers final: 77 residues processed: 351 average time/residue: 0.1342 time to fit residues: 75.0791 Evaluate side-chains 348 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 263 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 661 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 145 optimal weight: 1.9990 chunk 51 optimal weight: 40.0000 chunk 141 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 96 optimal weight: 0.0170 chunk 85 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.182205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129441 restraints weight = 35346.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126652 restraints weight = 21412.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128399 restraints weight = 18629.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128750 restraints weight = 14789.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128745 restraints weight = 14620.229| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21453 Z= 0.151 Angle : 0.587 9.268 29182 Z= 0.312 Chirality : 0.044 0.297 3159 Planarity : 0.004 0.050 3580 Dihedral : 14.985 152.307 3291 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.97 % Allowed : 26.64 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2470 helix: 0.40 (0.17), residues: 914 sheet: -1.22 (0.26), residues: 381 loop : -1.00 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 131 TYR 0.021 0.002 TYR E 165 PHE 0.019 0.001 PHE C 407 TRP 0.016 0.001 TRP A 458 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (21453) covalent geometry : angle 0.58720 / 0.31 (29182) hydrogen bonds : bond 0.03938 / 2.61 ( 918) hydrogen bonds : angle 5.26459 / 3.81 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 278 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: A 141 ASP cc_start: 0.7235 (p0) cc_final: 0.6800 (p0) REVERT: A 258 GLU cc_start: 0.6902 (tt0) cc_final: 0.6087 (tm-30) REVERT: A 260 TYR cc_start: 0.6651 (t80) cc_final: 0.5001 (t80) REVERT: A 297 LYS cc_start: 0.8320 (mmtm) cc_final: 0.8097 (mmtt) REVERT: A 427 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6422 (mt) REVERT: A 476 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: A 512 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7381 (pp20) REVERT: B 124 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7107 (tp40) REVERT: C 202 TRP cc_start: 0.8125 (t60) cc_final: 0.7577 (t60) REVERT: C 401 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7922 (mmm-85) REVERT: C 672 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7932 (t0) REVERT: D 1 MET cc_start: 0.7358 (pmm) cc_final: 0.6887 (pmm) REVERT: D 49 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7229 (p0) REVERT: D 75 GLN cc_start: 0.8453 (mm-40) cc_final: 0.7891 (tp-100) REVERT: D 204 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: E 22 MET cc_start: 0.5794 (tpp) cc_final: 0.5564 (tpp) REVERT: E 184 MET cc_start: 0.7820 (mmp) cc_final: 0.6963 (mmp) outliers start: 107 outliers final: 76 residues processed: 354 average time/residue: 0.1308 time to fit residues: 73.5549 Evaluate side-chains 352 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 187 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 226 optimal weight: 40.0000 chunk 98 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.180575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127199 restraints weight = 35437.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124459 restraints weight = 21528.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126115 restraints weight = 18870.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126374 restraints weight = 14907.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126550 restraints weight = 14533.465| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21453 Z= 0.220 Angle : 0.626 9.640 29182 Z= 0.333 Chirality : 0.045 0.310 3159 Planarity : 0.004 0.051 3580 Dihedral : 15.012 151.889 3291 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 5.35 % Allowed : 26.78 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2470 helix: 0.27 (0.17), residues: 915 sheet: -1.30 (0.26), residues: 384 loop : -1.05 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.020 0.002 TYR A 670 PHE 0.036 0.002 PHE C 868 TRP 0.022 0.002 TRP A 458 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 (21453) covalent geometry : angle 0.62614 / 0.33 (29182) hydrogen bonds : bond 0.04195 / 2.78 ( 918) hydrogen bonds : angle 5.33123 / 3.86 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 263 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 141 ASP cc_start: 0.7251 (p0) cc_final: 0.6815 (p0) REVERT: A 258 GLU cc_start: 0.6972 (tt0) cc_final: 0.5957 (tm-30) REVERT: A 297 LYS cc_start: 0.8323 (mmtm) cc_final: 0.8099 (mmtt) REVERT: A 427 ILE cc_start: 0.6738 (OUTLIER) cc_final: 0.6506 (mt) REVERT: A 458 TRP cc_start: 0.7352 (m100) cc_final: 0.7075 (m100) REVERT: A 476 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 657 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7730 (tp30) REVERT: A 739 GLN cc_start: 0.7616 (mm110) cc_final: 0.7105 (mm110) REVERT: B 30 MET cc_start: 0.7853 (ptt) cc_final: 0.7423 (ptm) REVERT: B 124 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: C 202 TRP cc_start: 0.8209 (t60) cc_final: 0.7633 (t60) REVERT: C 401 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7960 (mmm-85) REVERT: C 654 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8406 (mmmt) REVERT: C 672 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7913 (t0) REVERT: C 710 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: D 49 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7713 (p0) REVERT: D 75 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7867 (tp-100) REVERT: D 177 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7712 (p) REVERT: D 204 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7158 (pm20) REVERT: E 184 MET cc_start: 0.7812 (mmp) cc_final: 0.6961 (mmp) outliers start: 115 outliers final: 87 residues processed: 347 average time/residue: 0.1319 time to fit residues: 73.8009 Evaluate side-chains 353 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 254 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 91 PHE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 710 TYR Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 129 optimal weight: 0.4980 chunk 96 optimal weight: 20.0000 chunk 202 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 245 optimal weight: 50.0000 chunk 13 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 175 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.184624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.140589 restraints weight = 35218.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139550 restraints weight = 28138.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.141221 restraints weight = 25313.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141552 restraints weight = 15650.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.143133 restraints weight = 14410.212| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21453 Z= 0.118 Angle : 0.594 9.553 29182 Z= 0.311 Chirality : 0.044 0.290 3159 Planarity : 0.004 0.051 3580 Dihedral : 14.912 151.258 3291 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.72 % Allowed : 28.45 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2470 helix: 0.51 (0.17), residues: 904 sheet: -1.17 (0.27), residues: 381 loop : -0.92 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 131 TYR 0.026 0.001 TYR D 165 PHE 0.028 0.001 PHE C 868 TRP 0.021 0.001 TRP A 458 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (21453) covalent geometry : angle 0.59397 / 0.31 (29182) hydrogen bonds : bond 0.03721 / 2.49 ( 918) hydrogen bonds : angle 5.19136 / 3.75 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 283 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.8142 (p90) cc_final: 0.7902 (p90) REVERT: A 141 ASP cc_start: 0.7266 (p0) cc_final: 0.6825 (p0) REVERT: A 258 GLU cc_start: 0.6985 (tt0) cc_final: 0.6712 (tm-30) REVERT: A 297 LYS cc_start: 0.8229 (mmtm) cc_final: 0.8004 (mmtt) REVERT: A 427 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.6179 (mt) REVERT: A 458 TRP cc_start: 0.7101 (m100) cc_final: 0.6828 (m100) REVERT: A 476 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: A 659 MET cc_start: 0.7834 (tmm) cc_final: 0.7598 (tmm) REVERT: A 739 GLN cc_start: 0.7730 (mm110) cc_final: 0.7282 (mm110) REVERT: B 30 MET cc_start: 0.7621 (ptt) cc_final: 0.7242 (ptm) REVERT: B 124 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7050 (tp40) REVERT: C 253 MET cc_start: 0.4590 (OUTLIER) cc_final: 0.3214 (mtm) REVERT: C 654 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8458 (mmmt) REVERT: C 656 MET cc_start: 0.7079 (mmm) cc_final: 0.6749 (mmt) REVERT: C 671 MET cc_start: 0.6313 (mmt) cc_final: 0.5868 (mmm) REVERT: C 672 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7953 (t0) REVERT: D 1 MET cc_start: 0.7083 (pmm) cc_final: 0.6751 (pmm) REVERT: D 49 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7582 (p0) REVERT: D 75 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7801 (tp-100) REVERT: D 204 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: E 22 MET cc_start: 0.5511 (tpp) cc_final: 0.5074 (tpp) REVERT: E 90 ILE cc_start: 0.9265 (mp) cc_final: 0.9017 (tt) REVERT: E 181 ILE cc_start: 0.4713 (mp) cc_final: 0.4136 (mm) REVERT: E 184 MET cc_start: 0.7609 (mmp) cc_final: 0.6919 (mmp) outliers start: 80 outliers final: 62 residues processed: 335 average time/residue: 0.1330 time to fit residues: 71.5487 Evaluate side-chains 342 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 162 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 210 optimal weight: 0.0060 chunk 72 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 242 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.183310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.130753 restraints weight = 35366.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.128624 restraints weight = 20610.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130324 restraints weight = 17442.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130565 restraints weight = 13793.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130589 restraints weight = 13664.725| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21453 Z= 0.144 Angle : 0.598 10.578 29182 Z= 0.313 Chirality : 0.044 0.298 3159 Planarity : 0.004 0.059 3580 Dihedral : 14.872 151.056 3291 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.81 % Allowed : 28.50 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.17), residues: 2470 helix: 0.51 (0.17), residues: 915 sheet: -1.15 (0.27), residues: 381 loop : -0.98 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.022 0.001 TYR A 710 PHE 0.031 0.001 PHE A 218 TRP 0.019 0.001 TRP A 458 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (21453) covalent geometry : angle 0.59774 / 0.31 (29182) hydrogen bonds : bond 0.03796 / 2.53 ( 918) hydrogen bonds : angle 5.15551 / 3.73 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 272 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7214 (p0) cc_final: 0.6776 (p0) REVERT: A 260 TYR cc_start: 0.6458 (t80) cc_final: 0.6198 (t80) REVERT: A 297 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7958 (mmtt) REVERT: A 427 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6448 (mt) REVERT: A 458 TRP cc_start: 0.7278 (m100) cc_final: 0.6981 (m100) REVERT: A 476 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: A 739 GLN cc_start: 0.7700 (mm110) cc_final: 0.7273 (mm110) REVERT: B 30 MET cc_start: 0.7844 (ptt) cc_final: 0.7407 (ptm) REVERT: B 124 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7114 (tp40) REVERT: C 202 TRP cc_start: 0.8151 (t60) cc_final: 0.7613 (t60) REVERT: C 550 ASN cc_start: 0.8999 (t0) cc_final: 0.8719 (t0) REVERT: C 654 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8428 (mmmt) REVERT: C 656 MET cc_start: 0.7435 (mmm) cc_final: 0.7004 (mmt) REVERT: C 671 MET cc_start: 0.6530 (mmt) cc_final: 0.5978 (mmm) REVERT: C 672 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 1 MET cc_start: 0.7307 (pmm) cc_final: 0.6840 (pmm) REVERT: D 49 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.7564 (p0) REVERT: D 75 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7864 (tp-100) REVERT: D 204 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: E 22 MET cc_start: 0.5776 (tpp) cc_final: 0.5387 (tpp) REVERT: E 181 ILE cc_start: 0.4954 (mp) cc_final: 0.4411 (mm) REVERT: E 184 MET cc_start: 0.7923 (mmp) cc_final: 0.7045 (mmp) outliers start: 82 outliers final: 65 residues processed: 329 average time/residue: 0.1382 time to fit residues: 72.6548 Evaluate side-chains 334 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 262 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 227 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129361 restraints weight = 35489.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126387 restraints weight = 20702.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.128092 restraints weight = 18108.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128469 restraints weight = 14562.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128480 restraints weight = 14243.135| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21453 Z= 0.168 Angle : 0.625 11.747 29182 Z= 0.326 Chirality : 0.045 0.302 3159 Planarity : 0.004 0.057 3580 Dihedral : 14.880 150.957 3291 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.67 % Allowed : 28.96 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2470 helix: 0.53 (0.17), residues: 908 sheet: -1.20 (0.26), residues: 386 loop : -0.97 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 131 TYR 0.027 0.002 TYR A 710 PHE 0.021 0.001 PHE C 868 TRP 0.015 0.002 TRP A 202 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (21453) covalent geometry : angle 0.62544 / 0.33 (29182) hydrogen bonds : bond 0.03897 / 2.59 ( 918) hydrogen bonds : angle 5.19666 / 3.76 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 268 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: A 141 ASP cc_start: 0.7208 (p0) cc_final: 0.6780 (p0) REVERT: A 260 TYR cc_start: 0.6725 (t80) cc_final: 0.6057 (t80) REVERT: A 297 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7979 (mmtt) REVERT: A 427 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6471 (mt) REVERT: A 458 TRP cc_start: 0.7290 (m100) cc_final: 0.7031 (m100) REVERT: A 476 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: A 739 GLN cc_start: 0.7711 (mm110) cc_final: 0.7339 (mm110) REVERT: B 30 MET cc_start: 0.7863 (ptt) cc_final: 0.7457 (ptm) REVERT: B 124 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7119 (tp40) REVERT: C 186 MET cc_start: 0.7728 (ptp) cc_final: 0.7526 (ptp) REVERT: C 202 TRP cc_start: 0.8139 (t60) cc_final: 0.7618 (t60) REVERT: C 236 MET cc_start: 0.9149 (tmm) cc_final: 0.8909 (ttt) REVERT: C 550 ASN cc_start: 0.9000 (t0) cc_final: 0.8740 (t0) REVERT: C 654 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8430 (mmmt) REVERT: C 656 MET cc_start: 0.7412 (mmm) cc_final: 0.6973 (mmt) REVERT: C 671 MET cc_start: 0.6554 (mmt) cc_final: 0.6023 (mmm) REVERT: C 672 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 1 MET cc_start: 0.7327 (pmm) cc_final: 0.6859 (pmm) REVERT: D 49 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7509 (p0) REVERT: D 75 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7877 (tp-100) REVERT: D 204 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: E 22 MET cc_start: 0.5787 (tpp) cc_final: 0.5407 (tpp) REVERT: E 181 ILE cc_start: 0.4961 (mp) cc_final: 0.4419 (mm) REVERT: E 184 MET cc_start: 0.7968 (mmp) cc_final: 0.7064 (mmp) outliers start: 79 outliers final: 69 residues processed: 324 average time/residue: 0.1307 time to fit residues: 68.1732 Evaluate side-chains 339 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 262 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 TYR Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 846 SER Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 453 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 ASP Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 672 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 893 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 199 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 118 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.185109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.132984 restraints weight = 35429.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.130966 restraints weight = 20926.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132732 restraints weight = 17589.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132831 restraints weight = 14145.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133128 restraints weight = 14043.276| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21453 Z= 0.118 Angle : 0.601 11.058 29182 Z= 0.311 Chirality : 0.044 0.295 3159 Planarity : 0.004 0.056 3580 Dihedral : 14.809 150.595 3291 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.35 % Allowed : 29.15 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.63 (0.17), residues: 2470 helix: 0.59 (0.17), residues: 909 sheet: -1.21 (0.26), residues: 397 loop : -0.86 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 578 TYR 0.021 0.001 TYR A 710 PHE 0.022 0.001 PHE C 868 TRP 0.018 0.001 TRP A 458 HIS 0.004 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (21453) covalent geometry : angle 0.60123 / 0.31 (29182) hydrogen bonds : bond 0.03609 / 2.40 ( 918) hydrogen bonds : angle 5.11154 / 3.69 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3532.76 seconds wall clock time: 62 minutes 3.52 seconds (3723.52 seconds total)