Starting phenix.real_space_refine on Thu Feb 5 23:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e5y_47531/02_2026/9e5y_47531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e5y_47531/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9e5y_47531/02_2026/9e5y_47531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e5y_47531/02_2026/9e5y_47531.map" model { file = "/net/cci-nas-00/data/ceres_data/9e5y_47531/02_2026/9e5y_47531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e5y_47531/02_2026/9e5y_47531.cif" } 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-2.0-5952/lib/python3.9/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: 4.29, per 1000 atoms: 0.21 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: 1.56 Conformation dependent library (CDL) restraints added in 894.6 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: 2.35 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: 3.72 Time building geometry restraints manager: 2.03 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=" 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 bond pdb=" N VAL C 245 " pdb=" CA VAL C 245 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.82e+00 ... (remaining 21448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 28163 2.04 - 4.07: 936 4.07 - 6.11: 59 6.11 - 8.15: 19 8.15 - 10.18: 5 Bond angle restraints: 29182 Sorted by residual: 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=" N CYS C 453 " pdb=" CA CYS C 453 " pdb=" C CYS C 453 " ideal model delta sigma weight residual 108.45 113.79 -5.34 1.26e+00 6.30e-01 1.80e+01 angle pdb=" CA GLY C 172 " pdb=" C GLY C 172 " pdb=" O GLY C 172 " ideal model delta sigma weight residual 122.28 118.21 4.07 1.00e+00 1.00e+00 1.66e+01 angle pdb=" C3' DA T 12 " pdb=" O3' DA T 12 " pdb=" P DA T 13 " ideal model delta sigma weight residual 120.20 114.12 6.08 1.50e+00 4.44e-01 1.64e+01 angle pdb=" CA GLY A 753 " pdb=" C GLY A 753 " pdb=" O GLY A 753 " ideal model delta sigma weight residual 122.28 118.30 3.98 1.00e+00 1.00e+00 1.59e+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 - 0.126: 3049 0.126 - 0.252: 99 0.252 - 0.378: 1 0.378 - 0.504: 1 0.504 - 0.630: 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 2.35 2.98 -0.63 2.00e-01 2.50e+01 9.92e+00 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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.94e+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 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.63e+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: 1.040 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.720 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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= 0.358 Angle : 0.763 10.182 29182 Z= 0.481 Chirality : 0.061 0.630 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 covalent geometry : bond 0.00590 (21453) covalent geometry : angle 0.76276 (29182) hydrogen bonds : bond 0.14413 ( 918) hydrogen bonds : angle 6.60948 ( 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 : 1.117 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: 0.1295 time to fit residues: 63.6901 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 : 0.691 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: A 315 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN D 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.180489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127336 restraints weight = 35482.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124725 restraints weight = 24390.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125531 restraints weight = 23755.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125955 restraints weight = 18703.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126425 restraints weight = 16396.417| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21453 Z= 0.238 Angle : 0.642 10.059 29182 Z= 0.345 Chirality : 0.045 0.183 3159 Planarity : 0.005 0.056 3580 Dihedral : 15.056 155.731 3318 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.74 % Allowed : 25.52 % Favored : 69.74 % 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: -1.08 (0.17), residues: 2470 helix: 0.16 (0.17), residues: 917 sheet: -1.37 (0.26), residues: 379 loop : -1.13 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.022 0.002 TYR A 710 PHE 0.022 0.002 PHE C 143 TRP 0.016 0.002 TRP A 69 HIS 0.004 0.001 HIS C 571 Details of bonding type rmsd covalent geometry : bond 0.00557 (21453) covalent geometry : angle 0.64205 (29182) hydrogen bonds : bond 0.04698 ( 918) hydrogen bonds : angle 5.64470 ( 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 374 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 272 time to evaluate : 0.780 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 19 TYR cc_start: 0.8198 (p90) cc_final: 0.7998 (p90) REVERT: A 180 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 218 PHE cc_start: 0.7701 (m-80) cc_final: 0.7469 (t80) REVERT: A 282 LEU cc_start: 0.6614 (tt) cc_final: 0.6403 (tt) REVERT: A 476 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7530 (m-80) REVERT: A 731 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7142 (mp10) REVERT: C 401 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8065 (mmm-85) REVERT: C 768 TYR cc_start: 0.7566 (t80) cc_final: 0.7301 (t80) REVERT: C 808 TYR cc_start: 0.6738 (t80) cc_final: 0.6438 (t80) REVERT: D 49 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7292 (p0) REVERT: D 156 GLU cc_start: 0.7262 (tp30) cc_final: 0.6929 (tp30) REVERT: D 157 ASP cc_start: 0.6313 (OUTLIER) cc_final: 0.6035 (p0) REVERT: E 184 MET cc_start: 0.7853 (mmp) cc_final: 0.6829 (mmp) outliers start: 102 outliers final: 54 residues processed: 345 average time/residue: 0.1409 time to fit residues: 76.4228 Evaluate side-chains 317 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 180 LEU 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 387 SER Chi-restraints excluded: chain A residue 416 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 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 731 GLN 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 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 167 LEU Chi-restraints excluded: chain C residue 15 ILE 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 196 MET Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 369 SER 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 453 CYS 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 738 VAL Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 157 ASP 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 Chi-restraints excluded: chain E residue 216 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 40 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 173 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 0.0870 chunk 190 optimal weight: 0.2980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A 758 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 = 0.4427 r_free = 0.4427 target = 0.183429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131233 restraints weight = 35358.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.128687 restraints weight = 21780.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130519 restraints weight = 18701.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130700 restraints weight = 14589.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130731 restraints weight = 14729.586| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21453 Z= 0.135 Angle : 0.563 9.360 29182 Z= 0.300 Chirality : 0.042 0.158 3159 Planarity : 0.004 0.050 3580 Dihedral : 14.850 155.084 3300 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.91 % Allowed : 26.41 % Favored : 69.69 % 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: -0.78 (0.17), residues: 2470 helix: 0.47 (0.18), residues: 908 sheet: -1.23 (0.27), residues: 379 loop : -0.98 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.023 0.001 TYR C 185 PHE 0.015 0.001 PHE C 218 TRP 0.012 0.001 TRP A 458 HIS 0.006 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00305 (21453) covalent geometry : angle 0.56258 (29182) hydrogen bonds : bond 0.03970 ( 918) hydrogen bonds : angle 5.35233 ( 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 372 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 288 time to evaluate : 0.763 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: 0.8208 (p90) cc_final: 0.7974 (p90) REVERT: A 141 ASP cc_start: 0.7246 (p0) cc_final: 0.6807 (p0) REVERT: A 175 VAL cc_start: 0.7435 (OUTLIER) cc_final: 0.7164 (m) REVERT: A 180 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9107 (mt) REVERT: A 216 GLU cc_start: 0.8532 (pp20) cc_final: 0.7248 (mt-10) REVERT: A 218 PHE cc_start: 0.7722 (m-80) cc_final: 0.7518 (t80) REVERT: A 260 TYR cc_start: 0.6462 (t80) cc_final: 0.5274 (t80) REVERT: A 282 LEU cc_start: 0.6546 (tt) cc_final: 0.6319 (tt) REVERT: A 297 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8160 (mmtt) REVERT: A 476 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7356 (m-80) REVERT: A 649 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.7915 (t0) REVERT: B 124 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7021 (tp-100) REVERT: C 263 ASP cc_start: 0.7502 (m-30) cc_final: 0.7196 (m-30) REVERT: C 768 TYR cc_start: 0.7347 (t80) cc_final: 0.7066 (t80) REVERT: D 49 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7547 (p0) REVERT: D 75 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7731 (tp-100) REVERT: D 157 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.6108 (p0) REVERT: D 177 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7635 (p) REVERT: D 204 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: E 22 MET cc_start: 0.5707 (tpp) cc_final: 0.5352 (tpp) REVERT: E 181 ILE cc_start: 0.5045 (mp) cc_final: 0.4520 (mm) REVERT: E 184 MET cc_start: 0.7742 (mmp) cc_final: 0.6820 (mmp) outliers start: 84 outliers final: 46 residues processed: 346 average time/residue: 0.1309 time to fit residues: 71.3883 Evaluate side-chains 317 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 357 SER 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 570 ILE Chi-restraints excluded: chain A residue 581 THR 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 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 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 99 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 407 PHE 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 709 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 856 SER 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 75 GLN Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 157 ASP 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 E residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 128 optimal weight: 7.9990 chunk 220 optimal weight: 0.1980 chunk 181 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 54 optimal weight: 40.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 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 650 GLN A 758 GLN C 672 ASN D 58 ASN D 186 ASN E 190 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.181860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.128570 restraints weight = 35583.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126363 restraints weight = 20907.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128066 restraints weight = 17860.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.128286 restraints weight = 14194.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128346 restraints weight = 14121.857| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1475 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= 0.172 Angle : 0.576 9.149 29182 Z= 0.308 Chirality : 0.043 0.212 3159 Planarity : 0.004 0.053 3580 Dihedral : 14.795 154.013 3293 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.83 % Allowed : 26.03 % Favored : 69.13 % 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: -0.79 (0.17), residues: 2470 helix: 0.44 (0.17), residues: 913 sheet: -1.24 (0.26), residues: 399 loop : -0.96 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 131 TYR 0.025 0.002 TYR E 165 PHE 0.019 0.001 PHE A 647 TRP 0.013 0.002 TRP A 69 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00402 (21453) covalent geometry : angle 0.57609 (29182) hydrogen bonds : bond 0.03974 ( 918) hydrogen bonds : angle 5.25908 ( 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 375 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 271 time to evaluate : 0.712 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 19 TYR cc_start: 0.8224 (p90) cc_final: 0.7968 (p90) REVERT: A 74 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 141 ASP cc_start: 0.7228 (p0) cc_final: 0.6774 (p0) REVERT: A 175 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7158 (m) REVERT: A 180 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9017 (mt) REVERT: A 218 PHE cc_start: 0.7779 (m-80) cc_final: 0.7533 (t80) REVERT: A 282 LEU cc_start: 0.6484 (tt) cc_final: 0.6279 (tt) REVERT: A 297 LYS cc_start: 0.8339 (mmtm) cc_final: 0.8091 (mmtt) REVERT: A 427 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6400 (mt) REVERT: A 458 TRP cc_start: 0.7316 (m100) cc_final: 0.6934 (m100) REVERT: A 476 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: B 124 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7041 (tp-100) REVERT: C 263 ASP cc_start: 0.7665 (m-30) cc_final: 0.7369 (m-30) REVERT: C 768 TYR cc_start: 0.7457 (t80) cc_final: 0.7078 (t80) REVERT: D 49 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7622 (p0) REVERT: D 75 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7694 (tp-100) REVERT: D 204 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: E 184 MET cc_start: 0.7837 (mmp) cc_final: 0.6942 (mmp) outliers start: 104 outliers final: 62 residues processed: 341 average time/residue: 0.1296 time to fit residues: 70.1987 Evaluate side-chains 335 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 180 LEU 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 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 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 589 VAL 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 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 A residue 893 LEU 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 15 ILE 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 388 PHE Chi-restraints excluded: chain C residue 407 PHE 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 589 VAL Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 636 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 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 75 GLN 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 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: 0.0870 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 236 optimal weight: 40.0000 chunk 172 optimal weight: 0.0770 chunk 87 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN C 672 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 = 0.4430 r_free = 0.4430 target = 0.183510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.130825 restraints weight = 35212.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130009 restraints weight = 22486.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130307 restraints weight = 19699.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130615 restraints weight = 15077.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.130790 restraints weight = 14215.237| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21453 Z= 0.132 Angle : 0.556 9.307 29182 Z= 0.294 Chirality : 0.042 0.161 3159 Planarity : 0.004 0.049 3580 Dihedral : 14.719 153.158 3291 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.14 % Allowed : 27.10 % Favored : 68.76 % 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: -0.67 (0.17), residues: 2470 helix: 0.52 (0.18), residues: 913 sheet: -1.14 (0.26), residues: 399 loop : -0.89 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 131 TYR 0.018 0.001 TYR E 165 PHE 0.017 0.001 PHE A 647 TRP 0.013 0.001 TRP A 458 HIS 0.004 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00303 (21453) covalent geometry : angle 0.55618 (29182) hydrogen bonds : bond 0.03680 ( 918) hydrogen bonds : angle 5.15170 ( 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 368 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 279 time to evaluate : 0.785 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 19 TYR cc_start: 0.8201 (p90) cc_final: 0.7962 (p90) REVERT: A 141 ASP cc_start: 0.7208 (p0) cc_final: 0.6754 (p0) REVERT: A 175 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7167 (m) REVERT: A 180 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9051 (mt) REVERT: A 218 PHE cc_start: 0.7768 (m-80) cc_final: 0.7555 (t80) REVERT: A 297 LYS cc_start: 0.8261 (mmtm) cc_final: 0.8011 (mmtt) REVERT: A 458 TRP cc_start: 0.7280 (m100) cc_final: 0.6871 (m100) REVERT: A 739 GLN cc_start: 0.7652 (mm110) cc_final: 0.7194 (mm110) REVERT: B 124 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7023 (tp40) REVERT: C 202 TRP cc_start: 0.8105 (t60) cc_final: 0.7562 (t60) REVERT: C 263 ASP cc_start: 0.7586 (m-30) cc_final: 0.7293 (m-30) REVERT: C 671 MET cc_start: 0.6637 (mmt) cc_final: 0.6034 (mmm) REVERT: C 768 TYR cc_start: 0.7235 (t80) cc_final: 0.6868 (t80) REVERT: D 1 MET cc_start: 0.7273 (pmm) cc_final: 0.6838 (pmm) REVERT: D 49 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7224 (p0) REVERT: D 75 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7752 (tp-100) REVERT: D 157 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.6408 (p0) REVERT: D 204 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7151 (pm20) REVERT: E 184 MET cc_start: 0.7719 (mmp) cc_final: 0.6934 (mmp) outliers start: 89 outliers final: 61 residues processed: 345 average time/residue: 0.1329 time to fit residues: 73.2016 Evaluate side-chains 333 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 285 PHE 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 453 CYS 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 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 15 ILE 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 140 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 407 PHE 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 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 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 75 GLN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 52 VAL 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: 0.5980 chunk 51 optimal weight: 40.0000 chunk 141 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 85 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 650 GLN C 672 ASN D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.183878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131140 restraints weight = 35227.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128217 restraints weight = 20874.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129934 restraints weight = 18390.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130279 restraints weight = 14468.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130438 restraints weight = 14031.591| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21453 Z= 0.131 Angle : 0.564 9.371 29182 Z= 0.294 Chirality : 0.042 0.183 3159 Planarity : 0.004 0.047 3580 Dihedral : 14.692 152.536 3289 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.00 % Allowed : 27.62 % 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: -0.63 (0.17), residues: 2470 helix: 0.53 (0.17), residues: 920 sheet: -1.13 (0.26), residues: 399 loop : -0.86 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 192 TYR 0.023 0.001 TYR D 165 PHE 0.038 0.001 PHE C 868 TRP 0.011 0.001 TRP A 458 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00302 (21453) covalent geometry : angle 0.56366 (29182) hydrogen bonds : bond 0.03572 ( 918) hydrogen bonds : angle 5.05419 ( 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 365 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 279 time to evaluate : 0.668 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: 0.8156 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 141 ASP cc_start: 0.7146 (p0) cc_final: 0.6684 (p0) REVERT: A 175 VAL cc_start: 0.7285 (OUTLIER) cc_final: 0.6931 (m) REVERT: A 180 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9050 (mt) REVERT: A 218 PHE cc_start: 0.7828 (m-80) cc_final: 0.7560 (t80) REVERT: A 297 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7941 (mmtt) REVERT: A 458 TRP cc_start: 0.7256 (m100) cc_final: 0.6812 (m100) REVERT: A 476 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: A 650 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7739 (pp30) REVERT: A 739 GLN cc_start: 0.7626 (mm110) cc_final: 0.7225 (mm110) REVERT: B 124 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7082 (tp40) REVERT: C 202 TRP cc_start: 0.8147 (t60) cc_final: 0.7567 (t60) REVERT: C 263 ASP cc_start: 0.7612 (m-30) cc_final: 0.7286 (m-30) REVERT: C 656 MET cc_start: 0.7489 (mmm) cc_final: 0.7013 (mmt) REVERT: C 768 TYR cc_start: 0.7449 (t80) cc_final: 0.7170 (t80) REVERT: D 49 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7722 (p0) REVERT: D 75 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7746 (tp-100) REVERT: D 162 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7562 (mpp80) REVERT: D 204 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: E 22 MET cc_start: 0.5764 (tpp) cc_final: 0.5305 (tpp) REVERT: E 184 MET cc_start: 0.8006 (mmp) cc_final: 0.7008 (mmp) outliers start: 86 outliers final: 62 residues processed: 340 average time/residue: 0.1379 time to fit residues: 73.9738 Evaluate side-chains 336 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 265 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 135 HIS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 LEU 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 361 THR Chi-restraints excluded: chain A residue 387 SER 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 589 VAL 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 650 GLN 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 15 ILE 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 140 ASP Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 388 PHE 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 709 VAL Chi-restraints excluded: chain C residue 722 LEU 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 49 ASP Chi-restraints excluded: chain D residue 75 GLN 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 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 199 TRP Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 187 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** 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** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.179311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.126268 restraints weight = 35462.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.122476 restraints weight = 23500.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.124249 restraints weight = 20776.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124578 restraints weight = 17082.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.124631 restraints weight = 16264.944| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21453 Z= 0.276 Angle : 0.671 9.535 29182 Z= 0.355 Chirality : 0.046 0.243 3159 Planarity : 0.004 0.052 3580 Dihedral : 14.877 152.270 3289 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.21 % Allowed : 27.06 % Favored : 67.74 % 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: -0.93 (0.17), residues: 2470 helix: 0.25 (0.17), residues: 918 sheet: -1.28 (0.26), residues: 386 loop : -0.99 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 131 TYR 0.030 0.002 TYR A 710 PHE 0.032 0.002 PHE C 868 TRP 0.017 0.002 TRP A 699 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00649 (21453) covalent geometry : angle 0.67063 (29182) hydrogen bonds : bond 0.04393 ( 918) hydrogen bonds : angle 5.31374 ( 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 372 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 260 time to evaluate : 0.740 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: 0.8245 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 141 ASP cc_start: 0.7284 (p0) cc_final: 0.6813 (p0) REVERT: A 175 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7213 (m) REVERT: A 180 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9067 (mt) REVERT: A 297 LYS cc_start: 0.8311 (mmtm) cc_final: 0.8084 (mmtt) REVERT: A 427 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 476 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: A 649 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7975 (t0) REVERT: A 739 GLN cc_start: 0.7763 (mm110) cc_final: 0.7377 (mm110) REVERT: A 803 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6993 (mtp180) REVERT: B 124 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7142 (tp40) REVERT: C 202 TRP cc_start: 0.8202 (t60) cc_final: 0.7577 (t60) REVERT: C 236 MET cc_start: 0.9205 (tmm) cc_final: 0.8974 (ttt) REVERT: C 671 MET cc_start: 0.7130 (mmt) cc_final: 0.6711 (mmm) REVERT: C 682 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7840 (ptt90) REVERT: C 710 TYR cc_start: 0.8183 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: C 768 TYR cc_start: 0.7467 (t80) cc_final: 0.7171 (t80) REVERT: D 1 MET cc_start: 0.7404 (pmm) cc_final: 0.6822 (pmm) REVERT: D 49 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7254 (p0) REVERT: D 75 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7726 (tp-100) REVERT: D 204 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: E 22 MET cc_start: 0.5762 (tpp) cc_final: 0.5358 (tpp) REVERT: E 184 MET cc_start: 0.7885 (mmp) cc_final: 0.7000 (mmp) outliers start: 112 outliers final: 79 residues processed: 344 average time/residue: 0.1416 time to fit residues: 76.7950 Evaluate side-chains 344 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 252 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 13 ASN 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 135 HIS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 LEU 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 325 VAL 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 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 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 803 ARG 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 867 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 44 ILE 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 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 15 ILE 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 113 ILE Chi-restraints excluded: chain C residue 140 ASP 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 409 LEU 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 682 ARG 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 49 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 75 GLN 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 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 Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 129 optimal weight: 5.9990 chunk 96 optimal weight: 50.0000 chunk 202 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 201 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** 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** A 650 GLN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.182730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.130193 restraints weight = 35030.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127574 restraints weight = 21700.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.129598 restraints weight = 18135.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129680 restraints weight = 14179.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129815 restraints weight = 14033.257| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21453 Z= 0.143 Angle : 0.589 11.410 29182 Z= 0.308 Chirality : 0.043 0.195 3159 Planarity : 0.004 0.050 3580 Dihedral : 14.777 151.146 3289 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.04 % Allowed : 28.17 % Favored : 67.78 % 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: -0.74 (0.17), residues: 2470 helix: 0.44 (0.17), residues: 918 sheet: -1.26 (0.26), residues: 395 loop : -0.87 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 131 TYR 0.024 0.001 TYR D 165 PHE 0.026 0.001 PHE C 868 TRP 0.014 0.001 TRP C 458 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00330 (21453) covalent geometry : angle 0.58924 (29182) hydrogen bonds : bond 0.03686 ( 918) hydrogen bonds : angle 5.14059 ( 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 353 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 266 time to evaluate : 0.741 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: 0.8208 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: A 141 ASP cc_start: 0.7230 (p0) cc_final: 0.6766 (p0) REVERT: A 175 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7108 (m) REVERT: A 180 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9059 (mt) REVERT: A 297 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7986 (mmtt) REVERT: A 476 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 739 GLN cc_start: 0.7623 (mm110) cc_final: 0.7306 (mm110) REVERT: A 803 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.7007 (mtp180) REVERT: B 124 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7065 (tp40) REVERT: C 202 TRP cc_start: 0.8104 (t60) cc_final: 0.7553 (t60) REVERT: C 654 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8443 (mmmt) REVERT: C 671 MET cc_start: 0.6863 (mmt) cc_final: 0.6563 (mmm) REVERT: C 768 TYR cc_start: 0.7354 (t80) cc_final: 0.7141 (t80) REVERT: D 1 MET cc_start: 0.7392 (pmm) cc_final: 0.6895 (pmm) REVERT: D 49 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7237 (p0) REVERT: D 75 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7753 (tp-100) REVERT: D 204 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: E 22 MET cc_start: 0.5772 (tpp) cc_final: 0.5393 (tpp) REVERT: E 184 MET cc_start: 0.7868 (mmp) cc_final: 0.6994 (mmp) outliers start: 87 outliers final: 71 residues processed: 327 average time/residue: 0.1423 time to fit residues: 73.5426 Evaluate side-chains 337 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 256 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 135 HIS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 GLN 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 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 492 ASN 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 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 650 GLN Chi-restraints excluded: chain A residue 803 ARG 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 867 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 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 15 ILE Chi-restraints excluded: chain C residue 17 GLU 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 140 ASP 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 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 668 CYS 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 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 75 GLN 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 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 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: 0.7980 chunk 156 optimal weight: 5.9990 chunk 210 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** 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** ** C 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.182403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.129046 restraints weight = 35182.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126234 restraints weight = 20810.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127860 restraints weight = 18407.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128206 restraints weight = 15006.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128234 restraints weight = 14257.335| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21453 Z= 0.157 Angle : 0.605 10.066 29182 Z= 0.316 Chirality : 0.043 0.203 3159 Planarity : 0.004 0.047 3580 Dihedral : 14.769 151.200 3289 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.60 % Allowed : 28.03 % 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: -0.73 (0.17), residues: 2470 helix: 0.42 (0.17), residues: 920 sheet: -1.27 (0.26), residues: 402 loop : -0.84 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 682 TYR 0.027 0.001 TYR B 216 PHE 0.024 0.001 PHE C 868 TRP 0.012 0.001 TRP A 69 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00368 (21453) covalent geometry : angle 0.60505 (29182) hydrogen bonds : bond 0.03738 ( 918) hydrogen bonds : angle 5.10201 ( 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 359 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 260 time to evaluate : 0.738 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: 0.8230 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: A 141 ASP cc_start: 0.7212 (p0) cc_final: 0.6732 (p0) REVERT: A 175 VAL cc_start: 0.7375 (OUTLIER) cc_final: 0.7019 (m) REVERT: A 180 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9054 (mt) REVERT: A 297 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7963 (mmtt) REVERT: A 476 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: A 649 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7896 (t0) REVERT: A 739 GLN cc_start: 0.7620 (mm110) cc_final: 0.7321 (mm110) REVERT: A 803 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.7058 (mtp180) REVERT: B 124 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7113 (tp40) REVERT: C 202 TRP cc_start: 0.8129 (t60) cc_final: 0.7596 (t60) REVERT: C 236 MET cc_start: 0.9174 (tmm) cc_final: 0.8926 (ttt) REVERT: C 654 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8446 (mmmt) REVERT: C 827 MET cc_start: 0.6436 (ppp) cc_final: 0.5768 (ppp) REVERT: D 49 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7697 (p0) REVERT: D 75 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7740 (tp-100) REVERT: D 204 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: E 22 MET cc_start: 0.5831 (tpp) cc_final: 0.5475 (tpp) REVERT: E 184 MET cc_start: 0.7946 (mmp) cc_final: 0.7037 (mmp) outliers start: 99 outliers final: 75 residues processed: 329 average time/residue: 0.1433 time to fit residues: 74.6061 Evaluate side-chains 338 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 135 HIS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 LEU 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 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 492 ASN 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 589 VAL 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 686 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 803 ARG 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 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 60 PHE 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 15 ILE Chi-restraints excluded: chain C residue 17 GLU 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 140 ASP 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 453 CYS 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 642 ASN Chi-restraints excluded: chain C residue 654 LYS Chi-restraints excluded: chain C residue 668 CYS 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 829 LEU 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 75 GLN 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 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 Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 227 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 184 optimal weight: 0.0010 chunk 76 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 650 GLN C 150 ASN D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.182347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.130247 restraints weight = 35322.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127363 restraints weight = 21612.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129298 restraints weight = 18575.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.129410 restraints weight = 14895.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129502 restraints weight = 14337.495| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21453 Z= 0.158 Angle : 0.608 10.497 29182 Z= 0.317 Chirality : 0.044 0.216 3159 Planarity : 0.004 0.049 3580 Dihedral : 14.753 151.107 3289 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.37 % Allowed : 28.22 % Favored : 67.41 % 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: -0.73 (0.17), residues: 2470 helix: 0.44 (0.17), residues: 919 sheet: -1.25 (0.26), residues: 399 loop : -0.87 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 131 TYR 0.047 0.002 TYR A 90 PHE 0.025 0.001 PHE C 868 TRP 0.015 0.001 TRP C 458 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00369 (21453) covalent geometry : angle 0.60842 (29182) hydrogen bonds : bond 0.03739 ( 918) hydrogen bonds : angle 5.09767 ( 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 353 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 259 time to evaluate : 0.706 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: 0.8231 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: A 141 ASP cc_start: 0.7234 (p0) cc_final: 0.6754 (p0) REVERT: A 175 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7120 (m) REVERT: A 180 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9090 (mt) REVERT: A 218 PHE cc_start: 0.7561 (t80) cc_final: 0.7359 (t80) REVERT: A 297 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7978 (mmtt) REVERT: A 476 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: A 659 MET cc_start: 0.7655 (tmm) cc_final: 0.7452 (tmm) REVERT: A 739 GLN cc_start: 0.7594 (mm110) cc_final: 0.7321 (mm110) REVERT: A 803 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.7006 (mtp180) REVERT: B 124 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7136 (tp40) REVERT: C 17 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: C 202 TRP cc_start: 0.8121 (t60) cc_final: 0.7588 (t60) REVERT: C 236 MET cc_start: 0.9166 (tmm) cc_final: 0.8935 (ttt) REVERT: C 654 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8446 (mmmt) REVERT: C 827 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.5929 (ppp) REVERT: D 49 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7907 (p0) REVERT: D 75 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7732 (tp-100) REVERT: D 162 ARG cc_start: 0.8219 (mpp80) cc_final: 0.7888 (mpp80) REVERT: D 204 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: E 22 MET cc_start: 0.5709 (tpp) cc_final: 0.5341 (tpp) REVERT: E 184 MET cc_start: 0.7902 (mmp) cc_final: 0.7035 (mmp) outliers start: 94 outliers final: 76 residues processed: 327 average time/residue: 0.1386 time to fit residues: 71.7354 Evaluate side-chains 340 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 252 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 135 HIS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 LEU 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 361 THR Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 492 ASN 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 589 VAL 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 650 GLN Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 803 ARG 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 867 LEU Chi-restraints excluded: chain A residue 868 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 60 PHE 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 15 ILE Chi-restraints excluded: chain C residue 17 GLU 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 140 ASP 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 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 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 827 MET 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 75 GLN 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 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 Chi-restraints excluded: chain E residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 226 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A 650 GLN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.182493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.129685 restraints weight = 35391.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126577 restraints weight = 21307.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128520 restraints weight = 18287.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128682 restraints weight = 14823.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.128803 restraints weight = 14484.690| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 21453 Z= 0.193 Angle : 0.769 59.126 29182 Z= 0.429 Chirality : 0.046 0.814 3159 Planarity : 0.004 0.048 3580 Dihedral : 14.753 151.105 3289 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.32 % Allowed : 28.22 % Favored : 67.46 % Cbeta Deviations : 0.04 % 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: -0.74 (0.17), residues: 2470 helix: 0.43 (0.17), residues: 919 sheet: -1.25 (0.26), residues: 399 loop : -0.87 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 131 TYR 0.037 0.002 TYR A 90 PHE 0.024 0.001 PHE C 868 TRP 0.014 0.002 TRP C 458 HIS 0.004 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00425 (21453) covalent geometry : angle 0.76897 (29182) hydrogen bonds : bond 0.03750 ( 918) hydrogen bonds : angle 5.10187 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.73 seconds wall clock time: 64 minutes 27.62 seconds (3867.62 seconds total)