Starting phenix.real_space_refine on Fri Aug 7 11:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea2_47824/08_2026/9ea2_47824.map" } resolution = 3.7 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= 0.003 sd= 0.019 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 13169 2.51 5 N 3492 2.21 5 O 4058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20888 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7277 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 40, 'TRANS': 856} 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: 7277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 897, 7277 Classifications: {'peptide': 897} Link IDs: {'PTRANS': 40, 'TRANS': 856} 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: 4.37, per 1000 atoms: 0.21 Number of scatterers: 20888 At special positions: 0 Unit cell: (110.952, 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 4058 8.00 N 3492 7.00 C 13169 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: 1.54 Conformation dependent library (CDL) restraints added in 796.1 milliseconds 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 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: 75 helices and 29 sheets defined 40.8% alpha, 18.4% beta 20 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.837A pdb=" N ALA A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.711A pdb=" N LYS A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.806A pdb=" N LEU A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 306 through 336 removed outlier: 4.187A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N GLN A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 466 through 502 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 532 through 567 removed outlier: 4.512A pdb=" N TYR A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLY A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 607 Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.717A pdb=" N ILE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 655 removed outlier: 3.596A pdb=" N LEU A 644 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.723A pdb=" N MET A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 removed outlier: 3.762A pdb=" N GLN A 730 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 752 Processing helix chain 'A' and resid 753 through 771 removed outlier: 3.655A pdb=" N VAL A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 770 " --> pdb=" O LYS A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.616A pdb=" N ILE A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 784 through 789 removed outlier: 4.346A pdb=" N TYR A 788 " --> pdb=" O ASP A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 813 Processing helix chain 'A' and resid 851 through 861 removed outlier: 4.065A pdb=" N ASP A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'A' and resid 872 through 883 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 119 through 133 removed outlier: 3.819A pdb=" N ARG B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.544A pdb=" N ILE C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.511A pdb=" N MET C 194 " --> pdb=" O ASN C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 231 removed outlier: 5.527A pdb=" N VAL C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 269 through 277 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 336 removed outlier: 3.746A pdb=" N HIS C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLN C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ARG C 316 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 326 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 411 through 421 removed outlier: 3.684A pdb=" N ARG C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 425 No H-bonds generated for 'chain 'C' and resid 423 through 425' Processing helix chain 'C' and resid 435 through 442 removed outlier: 3.589A pdb=" N TYR C 439 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 503 Processing helix chain 'C' and resid 520 through 529 Processing helix chain 'C' and resid 531 through 568 removed outlier: 4.343A pdb=" N TYR C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLY C 565 " --> pdb=" O ASN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 607 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: 4.134A pdb=" N GLU C 657 " --> pdb=" O LYS C 653 " (cutoff:3.500A) Proline residue: C 658 - end of helix removed outlier: 3.934A pdb=" N GLU C 666 " --> pdb=" O VAL C 662 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 752 Processing helix chain 'C' and resid 753 through 769 removed outlier: 4.160A pdb=" N ARG C 769 " --> pdb=" O GLU C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 799 through 812 Processing helix chain 'C' and resid 851 through 860 removed outlier: 4.286A pdb=" N SER C 856 " --> pdb=" O LYS C 852 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 872 Processing helix chain 'C' and resid 872 through 882 removed outlier: 4.176A pdb=" N LEU C 876 " --> pdb=" O PHE C 872 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 878 " --> pdb=" O LYS C 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 removed outlier: 3.665A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 removed outlier: 3.629A pdb=" N PHE D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.573A pdb=" N LEU D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'E' and resid 4 through 18 removed outlier: 3.607A pdb=" N ILE E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 67 Processing helix chain 'E' and resid 96 through 100 removed outlier: 3.819A pdb=" N VAL E 100 " --> pdb=" O PRO E 97 " (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: 4.101A pdb=" N PHE A 4 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ARG A 18 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE A 8 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 16 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N THR A 10 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ASN A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.550A 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 183 through 188 removed outlier: 6.234A pdb=" N PHE A 143 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N MET A 186 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 145 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE A 188 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP A 147 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS A 111 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 251 Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.878A pdb=" N ARG A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET A 712 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU A 683 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 682 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASP A 408 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 684 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.878A pdb=" N ARG A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASP A 711 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N GLU A 719 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 778 through 782 Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'B' and resid 26 through 32 removed outlier: 5.359A pdb=" N GLN B 27 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.613A pdb=" N PHE B 178 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 142 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 147 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR B 165 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 11 removed outlier: 3.949A pdb=" N PHE C 4 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG C 18 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE C 8 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 16 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR C 10 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB7, first strand: chain 'C' and resid 183 through 188 removed outlier: 6.451A pdb=" N ALA C 109 " --> pdb=" O THR C 211 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 210 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 248 removed outlier: 3.529A pdb=" N SER C 261 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 430 removed outlier: 6.349A pdb=" N MET C 459 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 684 through 686 removed outlier: 4.434A pdb=" N ASP C 711 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA C 706 " --> pdb=" O TRP C 699 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TRP C 699 " --> pdb=" O ALA C 706 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 684 through 686 removed outlier: 4.434A pdb=" N ASP C 711 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP C 711 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 11.847A pdb=" N GLU C 719 " --> pdb=" O ASP C 711 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 778 through 781 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AC6, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AC7, first strand: chain 'D' and resid 166 through 171 removed outlier: 6.619A pdb=" N SER D 166 " --> pdb=" O GLY D 151 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY D 151 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N THR D 168 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 149 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 142 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AC9, first strand: chain 'E' and resid 26 through 32 removed outlier: 5.676A pdb=" N GLN E 27 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 72 through 75 Processing sheet with id=AD2, first strand: chain 'E' and resid 170 through 171 removed outlier: 3.780A pdb=" N GLY E 170 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL E 142 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE E 178 " --> pdb=" O VAL E 142 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2697 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5927 1.34 - 1.46: 4283 1.46 - 1.58: 10927 1.58 - 1.70: 104 1.70 - 1.82: 204 Bond restraints: 21445 Sorted by residual: bond pdb=" N ALA C 615 " pdb=" CA ALA C 615 " ideal model delta sigma weight residual 1.457 1.482 -0.025 6.40e-03 2.44e+04 1.58e+01 bond pdb=" C3' DT T 25 " pdb=" C2' DT T 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT T 22 " pdb=" C2' DT T 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" N ILE C 399 " pdb=" CA ILE C 399 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL C 624 " pdb=" CA VAL C 624 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.02e+01 ... (remaining 21440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 28495 2.36 - 4.71: 587 4.71 - 7.07: 76 7.07 - 9.43: 10 9.43 - 11.78: 4 Bond angle restraints: 29172 Sorted by residual: angle pdb=" N LYS D 164 " pdb=" CA LYS D 164 " pdb=" C LYS D 164 " ideal model delta sigma weight residual 113.43 108.04 5.39 1.26e+00 6.30e-01 1.83e+01 angle pdb=" N ASP C 627 " pdb=" CA ASP C 627 " pdb=" C ASP C 627 " ideal model delta sigma weight residual 114.31 108.86 5.45 1.29e+00 6.01e-01 1.79e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N ASP A 894 " pdb=" CA ASP A 894 " pdb=" C ASP A 894 " ideal model delta sigma weight residual 113.50 108.45 5.05 1.23e+00 6.61e-01 1.69e+01 angle pdb=" N3 DT T 31 " pdb=" C4 DT T 31 " pdb=" O4 DT T 31 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 29167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 12166 35.20 - 70.40: 657 70.40 - 105.59: 31 105.59 - 140.79: 1 140.79 - 175.99: 3 Dihedral angle restraints: 12858 sinusoidal: 5623 harmonic: 7235 Sorted by residual: dihedral pdb=" CA LEU C 249 " pdb=" C LEU C 249 " pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LYS C 248 " pdb=" C LYS C 248 " pdb=" N LEU C 249 " pdb=" CA LEU C 249 " ideal model delta harmonic sigma weight residual -180.00 -156.67 -23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ALA D 206 " pdb=" C ALA D 206 " pdb=" N ALA D 207 " pdb=" CA ALA D 207 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 12855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3068 0.126 - 0.253: 73 0.253 - 0.379: 0 0.379 - 0.506: 1 0.506 - 0.632: 17 Chirality restraints: 3159 Sorted by residual: chirality pdb=" P DG T 3 " pdb=" OP1 DG T 3 " pdb=" OP2 DG T 3 " pdb=" O5' DG T 3 " both_signs ideal model delta sigma weight residual True 2.34 2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P DC T 6 " pdb=" OP1 DC T 6 " pdb=" OP2 DC T 6 " pdb=" O5' DC T 6 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.27e+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 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 3156 not shown) Planarity restraints: 3578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 895 " 0.027 2.00e-02 2.50e+03 2.08e-02 7.56e+00 pdb=" CG PHE C 895 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 895 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 895 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 895 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 895 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE C 895 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 402 " -0.190 9.50e-02 1.11e+02 8.52e-02 4.48e+00 pdb=" NE ARG C 402 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 402 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 402 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 402 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 454 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 455 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 455 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 455 " 0.029 5.00e-02 4.00e+02 ... (remaining 3575 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1291 2.73 - 3.27: 21942 3.27 - 3.81: 36866 3.81 - 4.36: 42536 4.36 - 4.90: 69081 Nonbonded interactions: 171716 Sorted by model distance: nonbonded pdb=" N GLU C 425 " pdb=" OE1 GLU C 425 " model vdw 2.183 3.120 nonbonded pdb=" O LEU D 126 " pdb=" OG SER D 130 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLN C 641 " pdb=" OH TYR C 710 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP C 269 " pdb=" N ASP C 272 " model vdw 2.201 3.120 nonbonded pdb=" O GLY C 878 " pdb=" OG SER C 882 " model vdw 2.216 3.040 ... (remaining 171711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.780 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21445 Z= 0.333 Angle : 0.793 11.782 29172 Z= 0.493 Chirality : 0.066 0.632 3159 Planarity : 0.004 0.085 3578 Dihedral : 19.222 175.990 8208 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.07 % Allowed : 27.20 % Favored : 71.73 % 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: -0.50 (0.17), residues: 2468 helix: 0.69 (0.17), residues: 900 sheet: -0.87 (0.23), residues: 497 loop : -0.84 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 39 TYR 0.031 0.001 TYR E 216 PHE 0.045 0.002 PHE C 895 TRP 0.026 0.002 TRP C 861 HIS 0.008 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.33 (21445) covalent geometry : angle 0.79297 / 0.49 (29172) hydrogen bonds : bond 0.13555 / 9.05 ( 1005) hydrogen bonds : angle 6.48819 / 4.50 ( 2793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 292 time to evaluate : 0.809 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 70 MET cc_start: 0.8715 (tpp) cc_final: 0.8205 (mmm) REVERT: B 1 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5059 (pmm) REVERT: B 121 GLU cc_start: 0.8583 (tt0) cc_final: 0.7850 (tm-30) REVERT: B 184 MET cc_start: 0.8912 (mmm) cc_final: 0.8228 (mmm) REVERT: C 73 MET cc_start: 0.8954 (ttm) cc_final: 0.8660 (ttm) REVERT: C 253 MET cc_start: 0.5674 (ttp) cc_final: 0.5353 (ttt) REVERT: C 699 TRP cc_start: 0.8049 (m100) cc_final: 0.7568 (m100) REVERT: D 22 MET cc_start: 0.5243 (mmm) cc_final: 0.4951 (mmm) REVERT: D 41 GLU cc_start: 0.5868 (pm20) cc_final: 0.5650 (pm20) REVERT: D 144 GLU cc_start: 0.3352 (tm-30) cc_final: 0.2681 (mp0) REVERT: E 10 LEU cc_start: 0.8996 (mt) cc_final: 0.8708 (tt) outliers start: 23 outliers final: 9 residues processed: 305 average time/residue: 0.1572 time to fit residues: 74.5331 Evaluate side-chains 258 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 248 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain E residue 73 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 247 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 292 GLN A 314 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 GLN ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.166034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115688 restraints weight = 45447.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115635 restraints weight = 26495.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116291 restraints weight = 19094.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.116913 restraints weight = 17230.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117069 restraints weight = 15429.985| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21445 Z= 0.143 Angle : 0.620 8.097 29172 Z= 0.336 Chirality : 0.045 0.315 3159 Planarity : 0.004 0.062 3578 Dihedral : 16.143 174.602 3301 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.70 % Allowed : 25.85 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2468 helix: 0.86 (0.17), residues: 919 sheet: -0.80 (0.23), residues: 508 loop : -0.77 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 803 TYR 0.021 0.001 TYR C 575 PHE 0.026 0.002 PHE A 218 TRP 0.013 0.001 TRP C 844 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (21445) covalent geometry : angle 0.62009 / 0.34 (29172) hydrogen bonds : bond 0.04882 / 3.27 ( 1005) hydrogen bonds : angle 5.39809 / 3.75 ( 2793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8624 (tpp) cc_final: 0.8243 (mmm) REVERT: A 83 MET cc_start: 0.8086 (mmm) cc_final: 0.7589 (tpp) REVERT: A 486 MET cc_start: 0.8890 (tmm) cc_final: 0.8607 (tmm) REVERT: A 502 LYS cc_start: 0.4914 (OUTLIER) cc_final: 0.4685 (ptmm) REVERT: A 530 TYR cc_start: 0.3689 (OUTLIER) cc_final: 0.3273 (m-10) REVERT: A 678 MET cc_start: 0.5043 (tmm) cc_final: 0.4725 (tmm) REVERT: A 743 GLU cc_start: 0.8423 (tp30) cc_final: 0.8100 (tp30) REVERT: B 1 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.5170 (pmm) REVERT: B 121 GLU cc_start: 0.8543 (tt0) cc_final: 0.7829 (tm-30) REVERT: B 181 ILE cc_start: 0.8674 (tp) cc_final: 0.8035 (tp) REVERT: C 356 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.5358 (tmt) REVERT: C 600 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: C 699 TRP cc_start: 0.8054 (m100) cc_final: 0.7650 (m100) REVERT: C 872 PHE cc_start: 0.7264 (t80) cc_final: 0.6792 (t80) REVERT: D 51 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7016 (p0) REVERT: E 10 LEU cc_start: 0.9072 (mt) cc_final: 0.8745 (tt) outliers start: 58 outliers final: 20 residues processed: 308 average time/residue: 0.1552 time to fit residues: 74.6462 Evaluate side-chains 267 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 97 optimal weight: 50.0000 chunk 157 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 163 optimal weight: 40.0000 chunk 40 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 213 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.163292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115630 restraints weight = 45645.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113863 restraints weight = 26156.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.114405 restraints weight = 21251.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115060 restraints weight = 18664.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.115137 restraints weight = 16646.233| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21445 Z= 0.214 Angle : 0.639 10.505 29172 Z= 0.345 Chirality : 0.046 0.315 3159 Planarity : 0.004 0.047 3578 Dihedral : 16.081 176.251 3292 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.81 % Allowed : 25.52 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2468 helix: 0.82 (0.17), residues: 916 sheet: -0.89 (0.23), residues: 498 loop : -0.86 (0.19), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 803 TYR 0.026 0.002 TYR C 623 PHE 0.021 0.002 PHE D 152 TRP 0.015 0.002 TRP A 362 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (21445) covalent geometry : angle 0.63925 / 0.35 (29172) hydrogen bonds : bond 0.04747 / 3.15 ( 1005) hydrogen bonds : angle 5.27678 / 3.67 ( 2793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 248 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8095 (mmm) cc_final: 0.7543 (tpp) REVERT: A 486 MET cc_start: 0.8922 (tmm) cc_final: 0.8573 (tmm) REVERT: A 530 TYR cc_start: 0.3599 (OUTLIER) cc_final: 0.3153 (m-10) REVERT: A 577 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7254 (tp) REVERT: A 743 GLU cc_start: 0.8343 (tp30) cc_final: 0.8030 (tp30) REVERT: B 1 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.5027 (pmm) REVERT: B 121 GLU cc_start: 0.8560 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 175 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7455 (tm-30) REVERT: C 356 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.5550 (tmt) REVERT: C 432 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7450 (tmtt) REVERT: C 491 MET cc_start: 0.8222 (ppp) cc_final: 0.7550 (mtm) REVERT: C 600 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: C 671 MET cc_start: 0.8327 (tmm) cc_final: 0.7341 (ppp) REVERT: C 699 TRP cc_start: 0.8358 (m100) cc_final: 0.8014 (m100) REVERT: C 764 PHE cc_start: 0.8354 (t80) cc_final: 0.8114 (t80) REVERT: C 766 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8539 (mmtm) REVERT: C 872 PHE cc_start: 0.7491 (t80) cc_final: 0.7064 (t80) REVERT: D 21 ILE cc_start: 0.6184 (OUTLIER) cc_final: 0.5972 (mm) REVERT: D 51 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7030 (p0) REVERT: D 149 ILE cc_start: 0.7989 (pt) cc_final: 0.7748 (mp) REVERT: E 10 LEU cc_start: 0.9052 (mt) cc_final: 0.8693 (tt) outliers start: 82 outliers final: 36 residues processed: 304 average time/residue: 0.1501 time to fit residues: 72.1154 Evaluate side-chains 277 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 397 LYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 157 optimal weight: 0.3980 chunk 207 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 231 optimal weight: 40.0000 chunk 67 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 56 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.164816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116608 restraints weight = 45453.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115078 restraints weight = 26112.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115859 restraints weight = 19938.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116335 restraints weight = 17959.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116646 restraints weight = 16181.640| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21445 Z= 0.143 Angle : 0.602 12.017 29172 Z= 0.322 Chirality : 0.045 0.313 3159 Planarity : 0.004 0.046 3578 Dihedral : 16.000 175.488 3292 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.11 % Allowed : 26.59 % Favored : 70.29 % 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: -0.36 (0.17), residues: 2468 helix: 0.88 (0.17), residues: 919 sheet: -0.86 (0.23), residues: 498 loop : -0.82 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 803 TYR 0.025 0.001 TYR C 887 PHE 0.016 0.001 PHE D 152 TRP 0.013 0.001 TRP A 362 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21445) covalent geometry : angle 0.60179 / 0.32 (29172) hydrogen bonds : bond 0.04282 / 2.85 ( 1005) hydrogen bonds : angle 5.12521 / 3.57 ( 2793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 GLU cc_start: 0.8870 (pm20) cc_final: 0.8191 (mm-30) REVERT: A 486 MET cc_start: 0.8947 (tmm) cc_final: 0.8543 (tmm) REVERT: A 530 TYR cc_start: 0.3615 (OUTLIER) cc_final: 0.3142 (m-10) REVERT: A 743 GLU cc_start: 0.8407 (tp30) cc_final: 0.8056 (tp30) REVERT: A 840 LYS cc_start: 0.8118 (pttt) cc_final: 0.7730 (tptt) REVERT: B 1 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5115 (pmm) REVERT: B 121 GLU cc_start: 0.8581 (tt0) cc_final: 0.7863 (tm-30) REVERT: B 175 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7548 (tm-30) REVERT: B 203 LYS cc_start: 0.8538 (tptp) cc_final: 0.8317 (mmmt) REVERT: C 432 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7412 (tmtt) REVERT: C 600 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: C 671 MET cc_start: 0.8101 (tmm) cc_final: 0.7525 (ppp) REVERT: C 699 TRP cc_start: 0.8225 (m100) cc_final: 0.7872 (m100) REVERT: C 764 PHE cc_start: 0.8452 (t80) cc_final: 0.8143 (t80) REVERT: C 766 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8509 (mmtm) REVERT: C 872 PHE cc_start: 0.7504 (t80) cc_final: 0.7114 (t80) REVERT: D 22 MET cc_start: 0.4928 (mmm) cc_final: 0.4603 (mmm) REVERT: D 51 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7038 (p0) REVERT: D 149 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7848 (mp) REVERT: E 1 MET cc_start: 0.4652 (tpt) cc_final: 0.4357 (mmm) REVERT: E 10 LEU cc_start: 0.9074 (mt) cc_final: 0.8709 (tt) outliers start: 67 outliers final: 39 residues processed: 305 average time/residue: 0.1484 time to fit residues: 71.6272 Evaluate side-chains 282 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 149 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.159668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108336 restraints weight = 46024.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106473 restraints weight = 25037.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108030 restraints weight = 20592.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108077 restraints weight = 17006.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108242 restraints weight = 17151.724| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 21445 Z= 0.312 Angle : 0.736 10.511 29172 Z= 0.393 Chirality : 0.048 0.324 3159 Planarity : 0.005 0.053 3578 Dihedral : 16.134 174.559 3292 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.70 % Allowed : 25.57 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.17), residues: 2468 helix: 0.64 (0.17), residues: 919 sheet: -1.06 (0.22), residues: 526 loop : -0.97 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 131 TYR 0.029 0.002 TYR C 887 PHE 0.021 0.002 PHE C 638 TRP 0.020 0.002 TRP A 362 HIS 0.009 0.002 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.31 (21445) covalent geometry : angle 0.73629 / 0.39 (29172) hydrogen bonds : bond 0.05141 / 3.39 ( 1005) hydrogen bonds : angle 5.37382 / 3.75 ( 2793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 248 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.8298 (mtm110) cc_final: 0.8027 (mtm180) REVERT: A 297 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7691 (mmmt) REVERT: A 486 MET cc_start: 0.8981 (tmm) cc_final: 0.8575 (tmm) REVERT: A 530 TYR cc_start: 0.3425 (OUTLIER) cc_final: 0.2991 (m-10) REVERT: A 743 GLU cc_start: 0.8449 (tp30) cc_final: 0.8069 (tp30) REVERT: A 840 LYS cc_start: 0.8147 (pttt) cc_final: 0.7771 (tptt) REVERT: B 121 GLU cc_start: 0.8540 (tt0) cc_final: 0.7804 (tm-30) REVERT: B 175 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7485 (tm-30) REVERT: C 180 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8671 (mp) REVERT: C 253 MET cc_start: 0.5711 (ttp) cc_final: 0.5406 (ttt) REVERT: C 356 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.5832 (tmt) REVERT: C 432 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7636 (tmtt) REVERT: C 439 TYR cc_start: 0.7890 (m-80) cc_final: 0.7526 (m-80) REVERT: C 491 MET cc_start: 0.8113 (ppp) cc_final: 0.7614 (mtm) REVERT: C 600 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: C 699 TRP cc_start: 0.8508 (m100) cc_final: 0.8103 (m100) REVERT: C 764 PHE cc_start: 0.8438 (t80) cc_final: 0.8077 (t80) REVERT: C 827 MET cc_start: 0.5986 (mpp) cc_final: 0.5583 (mpp) REVERT: C 872 PHE cc_start: 0.7445 (t80) cc_final: 0.6734 (t80) REVERT: D 21 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6190 (mm) REVERT: D 23 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7692 (tp) REVERT: D 51 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7120 (p0) REVERT: D 149 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7945 (mp) REVERT: E 10 LEU cc_start: 0.9052 (mt) cc_final: 0.8762 (tp) outliers start: 101 outliers final: 63 residues processed: 323 average time/residue: 0.1521 time to fit residues: 77.2970 Evaluate side-chains 307 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 187 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 421 ASN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.161990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110214 restraints weight = 45921.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109474 restraints weight = 28020.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111009 restraints weight = 20062.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111582 restraints weight = 17714.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111633 restraints weight = 15468.786| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21445 Z= 0.178 Angle : 0.637 11.048 29172 Z= 0.340 Chirality : 0.046 0.314 3159 Planarity : 0.004 0.048 3578 Dihedral : 16.060 171.592 3292 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.67 % Allowed : 27.06 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2468 helix: 0.75 (0.17), residues: 920 sheet: -1.08 (0.22), residues: 533 loop : -0.88 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.021 0.002 TYR C 887 PHE 0.015 0.002 PHE C 210 TRP 0.014 0.002 TRP A 362 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (21445) covalent geometry : angle 0.63669 / 0.34 (29172) hydrogen bonds : bond 0.04430 / 2.94 ( 1005) hydrogen bonds : angle 5.16658 / 3.60 ( 2793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8292 (mmm) cc_final: 0.7601 (tpp) REVERT: A 288 GLU cc_start: 0.8888 (pm20) cc_final: 0.8239 (mm-30) REVERT: A 297 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7622 (mmmt) REVERT: A 486 MET cc_start: 0.8993 (tmm) cc_final: 0.8556 (tmm) REVERT: A 678 MET cc_start: 0.5614 (tmm) cc_final: 0.5399 (tmm) REVERT: A 840 LYS cc_start: 0.8202 (pttt) cc_final: 0.7816 (tptt) REVERT: B 121 GLU cc_start: 0.8555 (tt0) cc_final: 0.7822 (tm-30) REVERT: B 175 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7514 (tm-30) REVERT: B 212 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8053 (pm20) REVERT: C 216 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: C 253 MET cc_start: 0.5604 (ttp) cc_final: 0.5310 (ttt) REVERT: C 299 LYS cc_start: 0.6073 (tttt) cc_final: 0.5836 (tttm) REVERT: C 356 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.5642 (tmt) REVERT: C 432 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7512 (tmtt) REVERT: C 439 TYR cc_start: 0.7942 (m-80) cc_final: 0.7474 (m-80) REVERT: C 600 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: C 671 MET cc_start: 0.7992 (tmm) cc_final: 0.7347 (ppp) REVERT: C 699 TRP cc_start: 0.8339 (m100) cc_final: 0.7981 (m100) REVERT: C 764 PHE cc_start: 0.8530 (t80) cc_final: 0.8043 (t80) REVERT: C 827 MET cc_start: 0.5860 (mpp) cc_final: 0.5618 (mpp) REVERT: C 872 PHE cc_start: 0.7437 (t80) cc_final: 0.7038 (t80) REVERT: C 886 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7718 (t0) REVERT: D 22 MET cc_start: 0.5151 (mmm) cc_final: 0.4734 (tpt) REVERT: D 51 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7065 (p0) REVERT: D 126 LEU cc_start: 0.9583 (tp) cc_final: 0.9269 (pp) REVERT: D 149 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7985 (mp) REVERT: E 1 MET cc_start: 0.4555 (tpt) cc_final: 0.4284 (mmm) REVERT: E 10 LEU cc_start: 0.9052 (mt) cc_final: 0.8755 (tp) outliers start: 79 outliers final: 58 residues processed: 296 average time/residue: 0.1442 time to fit residues: 67.2025 Evaluate side-chains 297 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 886 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 142 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 241 optimal weight: 40.0000 chunk 105 optimal weight: 30.0000 chunk 101 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 555 ASN A 569 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.158384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106941 restraints weight = 46124.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105442 restraints weight = 24725.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.106585 restraints weight = 20175.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106723 restraints weight = 16869.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.106840 restraints weight = 16823.383| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 21445 Z= 0.347 Angle : 0.745 9.138 29172 Z= 0.400 Chirality : 0.049 0.327 3159 Planarity : 0.005 0.067 3578 Dihedral : 16.161 169.298 3288 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.83 % Allowed : 26.69 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2468 helix: 0.55 (0.16), residues: 923 sheet: -1.18 (0.22), residues: 532 loop : -1.09 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 674 TYR 0.029 0.002 TYR C 623 PHE 0.021 0.002 PHE A 388 TRP 0.017 0.002 TRP A 362 HIS 0.009 0.002 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00806 / 0.35 (21445) covalent geometry : angle 0.74492 / 0.40 (29172) hydrogen bonds : bond 0.05187 / 3.42 ( 1005) hydrogen bonds : angle 5.42694 / 3.79 ( 2793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 239 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8332 (mmt) cc_final: 0.7893 (mtm) REVERT: A 329 GLN cc_start: 0.9000 (tp40) cc_final: 0.8755 (tp40) REVERT: A 486 MET cc_start: 0.9014 (tmm) cc_final: 0.8576 (tmm) REVERT: A 530 TYR cc_start: 0.3206 (OUTLIER) cc_final: 0.2555 (m-10) REVERT: A 613 PHE cc_start: 0.8092 (m-80) cc_final: 0.7766 (m-10) REVERT: A 678 MET cc_start: 0.5798 (tmm) cc_final: 0.4729 (mtt) REVERT: A 840 LYS cc_start: 0.8273 (pttt) cc_final: 0.7895 (tptt) REVERT: B 121 GLU cc_start: 0.8513 (tt0) cc_final: 0.7773 (tm-30) REVERT: B 175 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7480 (tm-30) REVERT: B 212 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8019 (pm20) REVERT: C 253 MET cc_start: 0.5724 (ttp) cc_final: 0.5426 (ttt) REVERT: C 356 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.5815 (tmt) REVERT: C 432 LYS cc_start: 0.7951 (tmtt) cc_final: 0.7495 (tmtt) REVERT: C 439 TYR cc_start: 0.7948 (m-80) cc_final: 0.7351 (m-80) REVERT: C 600 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8578 (tm-30) REVERT: C 671 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7710 (ppp) REVERT: C 699 TRP cc_start: 0.8570 (m100) cc_final: 0.8184 (m100) REVERT: C 764 PHE cc_start: 0.8455 (t80) cc_final: 0.7913 (t80) REVERT: C 827 MET cc_start: 0.6584 (mpp) cc_final: 0.6307 (mpp) REVERT: C 872 PHE cc_start: 0.7631 (t80) cc_final: 0.7093 (t80) REVERT: D 51 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7048 (p0) REVERT: D 149 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8014 (mp) REVERT: D 186 ASN cc_start: 0.8804 (t0) cc_final: 0.8471 (m-40) REVERT: E 10 LEU cc_start: 0.9023 (mt) cc_final: 0.8746 (tp) outliers start: 104 outliers final: 80 residues processed: 310 average time/residue: 0.1424 time to fit residues: 70.0087 Evaluate side-chains 315 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 229 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 254 TYR Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 886 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 0.7980 chunk 163 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 236 optimal weight: 50.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN C 478 GLN C 864 HIS ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.161438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112248 restraints weight = 45619.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110776 restraints weight = 25534.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.110758 restraints weight = 21084.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.111191 restraints weight = 20525.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111844 restraints weight = 17489.671| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21445 Z= 0.173 Angle : 0.651 9.862 29172 Z= 0.348 Chirality : 0.046 0.314 3159 Planarity : 0.005 0.057 3578 Dihedral : 16.065 166.798 3288 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.67 % Allowed : 28.22 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2468 helix: 0.65 (0.17), residues: 922 sheet: -1.14 (0.22), residues: 535 loop : -0.95 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 674 TYR 0.028 0.002 TYR D 39 PHE 0.019 0.002 PHE E 28 TRP 0.016 0.002 TRP A 213 HIS 0.012 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (21445) covalent geometry : angle 0.65116 / 0.35 (29172) hydrogen bonds : bond 0.04508 / 2.97 ( 1005) hydrogen bonds : angle 5.21429 / 3.64 ( 2793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 245 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6984 (pt0) cc_final: 0.6364 (mp0) REVERT: A 288 GLU cc_start: 0.8887 (pm20) cc_final: 0.8217 (mm-30) REVERT: A 297 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7545 (mmmt) REVERT: A 329 GLN cc_start: 0.8991 (tp40) cc_final: 0.8711 (tp40) REVERT: A 486 MET cc_start: 0.8976 (tmm) cc_final: 0.8536 (tmm) REVERT: A 530 TYR cc_start: 0.3669 (OUTLIER) cc_final: 0.2950 (m-10) REVERT: A 678 MET cc_start: 0.5607 (tmm) cc_final: 0.4545 (mtt) REVERT: A 840 LYS cc_start: 0.8285 (pttt) cc_final: 0.7902 (tptt) REVERT: A 894 ASP cc_start: 0.8864 (t0) cc_final: 0.8472 (p0) REVERT: B 1 MET cc_start: 0.5402 (OUTLIER) cc_final: 0.4594 (pmm) REVERT: B 175 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7580 (tm-30) REVERT: B 212 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8121 (pm20) REVERT: C 63 MET cc_start: 0.8610 (mmt) cc_final: 0.8312 (mmt) REVERT: C 253 MET cc_start: 0.5585 (ttp) cc_final: 0.5274 (ttt) REVERT: C 356 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.5745 (tmt) REVERT: C 432 LYS cc_start: 0.7935 (tmtt) cc_final: 0.7435 (tmtt) REVERT: C 439 TYR cc_start: 0.8065 (m-80) cc_final: 0.7392 (m-80) REVERT: C 491 MET cc_start: 0.8077 (ppp) cc_final: 0.7821 (mtm) REVERT: C 575 TYR cc_start: 0.8273 (t80) cc_final: 0.8037 (t80) REVERT: C 600 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: C 671 MET cc_start: 0.7957 (tmm) cc_final: 0.7338 (ppp) REVERT: C 699 TRP cc_start: 0.8415 (m100) cc_final: 0.8061 (m100) REVERT: C 764 PHE cc_start: 0.8651 (t80) cc_final: 0.7989 (t80) REVERT: C 872 PHE cc_start: 0.7447 (t80) cc_final: 0.7152 (t80) REVERT: D 22 MET cc_start: 0.5230 (mmm) cc_final: 0.4844 (tpt) REVERT: D 23 LEU cc_start: 0.8005 (tp) cc_final: 0.7624 (tp) REVERT: D 126 LEU cc_start: 0.9609 (tp) cc_final: 0.9351 (pp) REVERT: E 1 MET cc_start: 0.4511 (tpt) cc_final: 0.4233 (mmm) REVERT: E 10 LEU cc_start: 0.9080 (mt) cc_final: 0.8788 (tp) outliers start: 79 outliers final: 60 residues processed: 298 average time/residue: 0.1425 time to fit residues: 67.3535 Evaluate side-chains 293 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 247 optimal weight: 50.0000 chunk 206 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.161519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.112234 restraints weight = 45504.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111738 restraints weight = 24211.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111940 restraints weight = 20859.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.112449 restraints weight = 19182.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.113168 restraints weight = 16522.731| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21445 Z= 0.166 Angle : 0.651 10.187 29172 Z= 0.344 Chirality : 0.046 0.311 3159 Planarity : 0.004 0.054 3578 Dihedral : 16.006 166.737 3288 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.49 % Allowed : 28.27 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2468 helix: 0.70 (0.17), residues: 923 sheet: -1.00 (0.22), residues: 524 loop : -0.93 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 128 TYR 0.024 0.002 TYR D 39 PHE 0.017 0.001 PHE E 28 TRP 0.016 0.002 TRP C 213 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (21445) covalent geometry : angle 0.65146 / 0.34 (29172) hydrogen bonds : bond 0.04349 / 2.87 ( 1005) hydrogen bonds : angle 5.14529 / 3.59 ( 2793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 242 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6839 (pt0) cc_final: 0.6325 (mp0) REVERT: A 182 ARG cc_start: 0.8183 (mtm110) cc_final: 0.7940 (mtm110) REVERT: A 288 GLU cc_start: 0.8806 (pm20) cc_final: 0.8140 (mm-30) REVERT: A 297 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7591 (mmmt) REVERT: A 329 GLN cc_start: 0.9001 (tp40) cc_final: 0.8725 (tp40) REVERT: A 486 MET cc_start: 0.8981 (tmm) cc_final: 0.8525 (tmm) REVERT: A 530 TYR cc_start: 0.3909 (OUTLIER) cc_final: 0.3230 (m-10) REVERT: A 678 MET cc_start: 0.5354 (tmm) cc_final: 0.4872 (mtt) REVERT: A 840 LYS cc_start: 0.8307 (pttt) cc_final: 0.7932 (tptt) REVERT: A 859 LEU cc_start: 0.7062 (pp) cc_final: 0.6810 (mm) REVERT: B 1 MET cc_start: 0.5311 (OUTLIER) cc_final: 0.4441 (pmm) REVERT: B 175 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7566 (tm-30) REVERT: B 212 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8094 (pm20) REVERT: C 63 MET cc_start: 0.8607 (mmt) cc_final: 0.8310 (mmt) REVERT: C 216 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: C 253 MET cc_start: 0.5537 (ttp) cc_final: 0.5277 (ttt) REVERT: C 356 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.5738 (tmt) REVERT: C 575 TYR cc_start: 0.8212 (t80) cc_final: 0.7982 (t80) REVERT: C 600 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (tm-30) REVERT: C 671 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7344 (ppp) REVERT: C 699 TRP cc_start: 0.8451 (m100) cc_final: 0.8103 (m100) REVERT: C 764 PHE cc_start: 0.8576 (t80) cc_final: 0.7946 (t80) REVERT: C 872 PHE cc_start: 0.7568 (t80) cc_final: 0.7311 (t80) REVERT: D 22 MET cc_start: 0.5240 (mmm) cc_final: 0.4837 (tpt) REVERT: D 126 LEU cc_start: 0.9591 (tp) cc_final: 0.9333 (pp) REVERT: E 1 MET cc_start: 0.4527 (tpt) cc_final: 0.4204 (mmm) REVERT: E 10 LEU cc_start: 0.9060 (mt) cc_final: 0.8774 (tp) outliers start: 75 outliers final: 59 residues processed: 294 average time/residue: 0.1382 time to fit residues: 65.2541 Evaluate side-chains 302 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 437 HIS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 671 MET Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 203 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 236 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 220 optimal weight: 20.0000 chunk 207 optimal weight: 40.0000 chunk 138 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.160169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109632 restraints weight = 45835.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.108926 restraints weight = 26103.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109543 restraints weight = 19426.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.109950 restraints weight = 19283.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110047 restraints weight = 16333.710| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21445 Z= 0.241 Angle : 0.687 10.582 29172 Z= 0.366 Chirality : 0.047 0.317 3159 Planarity : 0.005 0.062 3578 Dihedral : 16.037 165.981 3288 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.58 % Allowed : 27.80 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.17), residues: 2468 helix: 0.65 (0.17), residues: 923 sheet: -1.14 (0.22), residues: 536 loop : -0.98 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 128 TYR 0.028 0.002 TYR A 664 PHE 0.021 0.002 PHE A 367 TRP 0.015 0.002 TRP A 362 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (21445) covalent geometry : angle 0.68738 / 0.37 (29172) hydrogen bonds : bond 0.04603 / 3.05 ( 1005) hydrogen bonds : angle 5.22622 / 3.65 ( 2793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4936 Ramachandran restraints generated. 2468 Oldfield, 0 Emsley, 2468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 243 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7890 (mtm) REVERT: A 129 GLU cc_start: 0.6930 (pt0) cc_final: 0.6461 (mp0) REVERT: A 182 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7998 (mtm110) REVERT: A 288 GLU cc_start: 0.8829 (pm20) cc_final: 0.8184 (mm-30) REVERT: A 297 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7589 (mmmt) REVERT: A 329 GLN cc_start: 0.9017 (tp40) cc_final: 0.8719 (tp40) REVERT: A 486 MET cc_start: 0.8987 (tmm) cc_final: 0.8509 (tmm) REVERT: A 530 TYR cc_start: 0.3861 (OUTLIER) cc_final: 0.3137 (m-10) REVERT: A 613 PHE cc_start: 0.8006 (m-80) cc_final: 0.7724 (m-10) REVERT: A 678 MET cc_start: 0.5386 (tmm) cc_final: 0.4817 (mtt) REVERT: A 680 MET cc_start: 0.7398 (mmm) cc_final: 0.6809 (mmm) REVERT: B 1 MET cc_start: 0.5393 (OUTLIER) cc_final: 0.4467 (pmm) REVERT: B 72 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7800 (tp30) REVERT: B 175 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7605 (tm-30) REVERT: B 212 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8109 (pm20) REVERT: C 63 MET cc_start: 0.8594 (mmt) cc_final: 0.8287 (mmt) REVERT: C 253 MET cc_start: 0.5646 (ttp) cc_final: 0.5315 (ttt) REVERT: C 356 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.5854 (tmt) REVERT: C 600 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8618 (tm-30) REVERT: C 699 TRP cc_start: 0.8501 (m100) cc_final: 0.8115 (m100) REVERT: C 764 PHE cc_start: 0.8591 (t80) cc_final: 0.7928 (t80) REVERT: C 872 PHE cc_start: 0.7540 (t80) cc_final: 0.7271 (t80) REVERT: D 22 MET cc_start: 0.5331 (mmm) cc_final: 0.4941 (tpt) REVERT: D 126 LEU cc_start: 0.9576 (tp) cc_final: 0.9338 (pp) REVERT: D 180 PHE cc_start: 0.8802 (m-80) cc_final: 0.8516 (m-80) REVERT: E 1 MET cc_start: 0.4171 (tpt) cc_final: 0.3785 (mmm) REVERT: E 10 LEU cc_start: 0.9052 (mt) cc_final: 0.8769 (tp) REVERT: E 55 TYR cc_start: 0.5537 (OUTLIER) cc_final: 0.5031 (m-80) outliers start: 77 outliers final: 64 residues processed: 294 average time/residue: 0.1266 time to fit residues: 60.1468 Evaluate side-chains 311 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 111 CYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 476 PHE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 612 ASP Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 388 PHE Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 600 GLU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 TYR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 171 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 40.0000 chunk 247 optimal weight: 50.0000 chunk 240 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 206 optimal weight: 0.0470 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 234 optimal weight: 6.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.159836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110122 restraints weight = 45624.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109000 restraints weight = 26045.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.108943 restraints weight = 20260.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109515 restraints weight = 18932.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.109751 restraints weight = 17169.002| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21445 Z= 0.240 Angle : 0.696 11.592 29172 Z= 0.369 Chirality : 0.047 0.318 3159 Planarity : 0.005 0.066 3578 Dihedral : 16.057 163.948 3288 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.67 % Allowed : 27.71 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.17), residues: 2468 helix: 0.64 (0.17), residues: 922 sheet: -1.12 (0.22), residues: 536 loop : -1.00 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 674 TYR 0.023 0.002 TYR C 222 PHE 0.023 0.002 PHE A 367 TRP 0.016 0.002 TRP A 362 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (21445) covalent geometry : angle 0.69646 / 0.37 (29172) hydrogen bonds : bond 0.04628 / 3.06 ( 1005) hydrogen bonds : angle 5.25163 / 3.67 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.65 seconds wall clock time: 65 minutes 40.23 seconds (3940.23 seconds total)