Starting phenix.real_space_refine on Thu Feb 5 23:51:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea2_47824/02_2026/9ea2_47824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea2_47824/02_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_47824/02_2026/9ea2_47824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea2_47824/02_2026/9ea2_47824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ea2_47824/02_2026/9ea2_47824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea2_47824/02_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-2.0-5952/lib/python3.9/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: 3.95, per 1000 atoms: 0.19 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: 1.65 Conformation dependent library (CDL) restraints added in 917.9 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: 2.54 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: 4.33 Time building geometry restraints manager: 2.19 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=" 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 bond pdb=" N ILE D 182 " pdb=" CA ILE D 182 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 9.91e+00 bond pdb=" N TYR C 413 " pdb=" CA TYR C 413 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.49e+00 ... (remaining 21440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 28534 2.36 - 4.71: 548 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=" 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=" CB MET A 229 " pdb=" CG MET A 229 " pdb=" SD MET A 229 " ideal model delta sigma weight residual 112.70 124.48 -11.78 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C ALA C 615 " pdb=" CA ALA C 615 " pdb=" CB ALA C 615 " ideal model delta sigma weight residual 117.07 111.49 5.58 1.44e+00 4.82e-01 1.50e+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 - 0.124: 3066 0.124 - 0.249: 75 0.249 - 0.373: 0 0.373 - 0.498: 1 0.498 - 0.622: 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 2.35 2.97 -0.62 2.00e-01 2.50e+01 9.68e+00 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 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" P DA T 5 " pdb=" OP1 DA T 5 " pdb=" OP2 DA T 5 " pdb=" O5' DA T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.93e+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: 0.010 Normalize map: mean=0, sd=1: 0.970 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.130 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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= 0.292 Angle : 0.780 11.782 29172 Z= 0.461 Chirality : 0.064 0.622 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 covalent geometry : bond 0.00464 (21445) covalent geometry : angle 0.78046 (29172) hydrogen bonds : bond 0.13555 ( 1005) hydrogen bonds : angle 6.48819 ( 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 : 0.710 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: 0.1457 time to fit residues: 68.8948 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 : 0.705 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 314 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** A 676 HIS ** 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 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.166349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.115676 restraints weight = 45503.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.115819 restraints weight = 27897.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116836 restraints weight = 19004.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117637 restraints weight = 17648.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.117657 restraints weight = 15318.142| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21445 Z= 0.136 Angle : 0.597 7.273 29172 Z= 0.321 Chirality : 0.043 0.161 3159 Planarity : 0.004 0.053 3578 Dihedral : 15.938 173.718 3301 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.74 % Allowed : 25.85 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2468 helix: 0.94 (0.17), residues: 918 sheet: -0.80 (0.23), residues: 502 loop : -0.78 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 803 TYR 0.023 0.001 TYR C 887 PHE 0.024 0.002 PHE C 872 TRP 0.013 0.001 TRP C 844 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00302 (21445) covalent geometry : angle 0.59667 (29172) hydrogen bonds : bond 0.04532 ( 1005) hydrogen bonds : angle 5.23856 ( 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 334 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8086 (mmm) cc_final: 0.7620 (tpp) REVERT: A 486 MET cc_start: 0.8891 (tmm) cc_final: 0.8603 (tmm) REVERT: A 530 TYR cc_start: 0.3635 (OUTLIER) cc_final: 0.3256 (m-10) REVERT: A 743 GLU cc_start: 0.8426 (tp30) cc_final: 0.8118 (tp30) REVERT: B 1 MET cc_start: 0.5794 (OUTLIER) cc_final: 0.5239 (pmm) REVERT: B 121 GLU cc_start: 0.8557 (tt0) cc_final: 0.7836 (tm-30) REVERT: B 175 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7536 (tm-30) REVERT: B 181 ILE cc_start: 0.8596 (tp) cc_final: 0.7883 (tp) REVERT: C 224 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7438 (mtt) REVERT: C 253 MET cc_start: 0.5745 (ttp) cc_final: 0.5436 (ttt) REVERT: C 286 SER cc_start: 0.9189 (p) cc_final: 0.8980 (m) REVERT: C 356 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.5160 (tmt) REVERT: C 439 TYR cc_start: 0.7875 (m-80) cc_final: 0.7562 (m-80) REVERT: C 459 MET cc_start: 0.7167 (ttm) cc_final: 0.6762 (ttp) REVERT: C 600 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: C 699 TRP cc_start: 0.8112 (m100) cc_final: 0.7681 (m100) REVERT: C 764 PHE cc_start: 0.8469 (t80) cc_final: 0.8204 (t80) REVERT: C 872 PHE cc_start: 0.7423 (t80) cc_final: 0.7030 (t80) REVERT: D 51 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7033 (p0) REVERT: E 10 LEU cc_start: 0.9048 (mt) cc_final: 0.8707 (tt) outliers start: 59 outliers final: 17 residues processed: 316 average time/residue: 0.1337 time to fit residues: 66.3083 Evaluate side-chains 263 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 530 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 1 MET 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 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 6 ASP 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: 9.9990 chunk 48 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 139 optimal weight: 0.0470 chunk 77 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 163 optimal weight: 40.0000 chunk 40 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 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 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.166401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.115545 restraints weight = 45711.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115221 restraints weight = 27669.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.115730 restraints weight = 21024.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116478 restraints weight = 19443.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.116817 restraints weight = 16322.152| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21445 Z= 0.129 Angle : 0.578 14.404 29172 Z= 0.307 Chirality : 0.043 0.161 3159 Planarity : 0.004 0.043 3578 Dihedral : 15.733 175.984 3292 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.84 % Allowed : 25.48 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2468 helix: 0.99 (0.17), residues: 919 sheet: -0.79 (0.23), residues: 506 loop : -0.76 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 131 TYR 0.020 0.001 TYR C 575 PHE 0.019 0.001 PHE A 868 TRP 0.012 0.001 TRP A 362 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00288 (21445) covalent geometry : angle 0.57792 (29172) hydrogen bonds : bond 0.04039 ( 1005) hydrogen bonds : angle 4.99504 ( 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 332 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 MET cc_start: 0.8628 (mmm) cc_final: 0.8417 (mmm) REVERT: A 288 GLU cc_start: 0.8890 (pm20) cc_final: 0.8299 (mm-30) REVERT: A 486 MET cc_start: 0.8935 (tmm) cc_final: 0.8558 (tmm) REVERT: A 489 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 530 TYR cc_start: 0.3433 (OUTLIER) cc_final: 0.3011 (m-10) REVERT: A 667 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5235 (mt) REVERT: A 743 GLU cc_start: 0.8394 (tp30) cc_final: 0.8058 (tp30) REVERT: A 840 LYS cc_start: 0.8111 (pttt) cc_final: 0.7724 (tptt) REVERT: B 1 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5135 (pmm) REVERT: B 121 GLU cc_start: 0.8579 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 175 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7493 (tm-30) REVERT: C 253 MET cc_start: 0.5597 (ttp) cc_final: 0.5331 (ttt) REVERT: C 432 LYS cc_start: 0.7841 (tmtt) cc_final: 0.7376 (tmtt) REVERT: C 486 MET cc_start: 0.8677 (tpp) cc_final: 0.8322 (tpp) REVERT: C 489 GLU cc_start: 0.8125 (tp30) cc_final: 0.7502 (pt0) REVERT: C 600 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: C 671 MET cc_start: 0.8254 (tmm) cc_final: 0.7771 (ppp) REVERT: C 678 MET cc_start: 0.7809 (tpp) cc_final: 0.7601 (ttm) REVERT: C 699 TRP cc_start: 0.8126 (m100) cc_final: 0.7764 (m100) REVERT: C 764 PHE cc_start: 0.8465 (t80) cc_final: 0.8086 (t80) REVERT: C 766 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8567 (mmtm) REVERT: C 872 PHE cc_start: 0.7485 (t80) cc_final: 0.7058 (t80) REVERT: D 51 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7025 (p0) REVERT: D 149 ILE cc_start: 0.7955 (pt) cc_final: 0.7689 (mp) REVERT: E 1 MET cc_start: 0.3987 (mmm) cc_final: 0.3586 (mmm) REVERT: E 12 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7978 (mmtt) outliers start: 61 outliers final: 33 residues processed: 314 average time/residue: 0.1348 time to fit residues: 65.6985 Evaluate side-chains 277 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 294 GLU Chi-restraints excluded: chain A residue 357 SER 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 667 LEU 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 249 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 476 PHE 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 23 LEU 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 184 MET 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: 9.9990 chunk 207 optimal weight: 40.0000 chunk 103 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 191 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 HIS ** C 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.163511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114027 restraints weight = 45904.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.112114 restraints weight = 27673.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113208 restraints weight = 23201.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.113573 restraints weight = 17583.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.113807 restraints weight = 16746.332| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21445 Z= 0.184 Angle : 0.608 11.755 29172 Z= 0.325 Chirality : 0.044 0.219 3159 Planarity : 0.004 0.039 3578 Dihedral : 15.685 174.276 3292 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.95 % Allowed : 25.38 % 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: -0.29 (0.17), residues: 2468 helix: 0.96 (0.17), residues: 919 sheet: -0.79 (0.22), residues: 508 loop : -0.82 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.026 0.002 TYR C 887 PHE 0.030 0.002 PHE C 895 TRP 0.016 0.002 TRP A 362 HIS 0.011 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00424 (21445) covalent geometry : angle 0.60818 (29172) hydrogen bonds : bond 0.04211 ( 1005) hydrogen bonds : angle 4.99772 ( 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 342 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 257 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.8345 (mtm110) cc_final: 0.7988 (mtm180) REVERT: A 486 MET cc_start: 0.8983 (tmm) cc_final: 0.8545 (tmm) REVERT: A 667 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5283 (mp) REVERT: A 840 LYS cc_start: 0.8163 (pttt) cc_final: 0.7761 (tptt) REVERT: B 1 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5444 (pmm) REVERT: B 121 GLU cc_start: 0.8557 (tt0) cc_final: 0.7833 (tm-30) REVERT: B 175 GLU cc_start: 0.8526 (mm-30) cc_final: 0.7563 (tm-30) REVERT: C 112 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7537 (m-30) REVERT: C 253 MET cc_start: 0.5703 (ttp) cc_final: 0.5414 (ttt) REVERT: C 432 LYS cc_start: 0.7917 (tmtt) cc_final: 0.7486 (tmtt) REVERT: C 439 TYR cc_start: 0.7959 (m-80) cc_final: 0.7469 (m-80) REVERT: C 600 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: C 671 MET cc_start: 0.8265 (tmm) cc_final: 0.7847 (ppp) REVERT: C 699 TRP cc_start: 0.8349 (m100) cc_final: 0.7939 (m100) REVERT: C 764 PHE cc_start: 0.8427 (t80) cc_final: 0.7939 (t80) REVERT: C 827 MET cc_start: 0.6051 (mpp) cc_final: 0.5655 (mpp) REVERT: C 872 PHE cc_start: 0.7475 (t80) cc_final: 0.7119 (t80) REVERT: D 22 MET cc_start: 0.4944 (mmm) cc_final: 0.4618 (mmm) REVERT: D 51 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7027 (p0) REVERT: D 149 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (mp) outliers start: 85 outliers final: 47 residues processed: 318 average time/residue: 0.1369 time to fit residues: 68.3849 Evaluate side-chains 295 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 399 ILE 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 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 729 THR 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 112 ASP 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 408 ASP Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 476 PHE 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 600 GLU Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 676 HIS Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 38 THR 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 183 ASN Chi-restraints excluded: chain D residue 184 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 149 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 HIS ** 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 = 0.4333 r_free = 0.4333 target = 0.162322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110455 restraints weight = 45765.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.109768 restraints weight = 28011.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111501 restraints weight = 19509.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111995 restraints weight = 17687.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111909 restraints weight = 15476.888| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21445 Z= 0.208 Angle : 0.631 11.923 29172 Z= 0.335 Chirality : 0.044 0.168 3159 Planarity : 0.004 0.041 3578 Dihedral : 15.705 172.507 3291 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.18 % Allowed : 25.52 % 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: 0.92 (0.17), residues: 921 sheet: -0.89 (0.22), residues: 510 loop : -0.85 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 674 TYR 0.025 0.002 TYR C 887 PHE 0.016 0.002 PHE A 764 TRP 0.015 0.002 TRP A 362 HIS 0.009 0.002 HIS C 676 Details of bonding type rmsd covalent geometry : bond 0.00489 (21445) covalent geometry : angle 0.63132 (29172) hydrogen bonds : bond 0.04291 ( 1005) hydrogen bonds : angle 5.04420 ( 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 347 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 257 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8225 (mmm) cc_final: 0.7439 (tpp) REVERT: A 224 MET cc_start: 0.8947 (mmm) cc_final: 0.8508 (mmm) REVERT: A 288 GLU cc_start: 0.8902 (pm20) cc_final: 0.8333 (mm-30) REVERT: A 486 MET cc_start: 0.8987 (tmm) cc_final: 0.8549 (tmm) REVERT: A 530 TYR cc_start: 0.3336 (OUTLIER) cc_final: 0.2636 (m-10) REVERT: A 667 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5690 (mp) REVERT: A 840 LYS cc_start: 0.8258 (pttt) cc_final: 0.7847 (tptt) REVERT: A 890 LYS cc_start: 0.9250 (tmtt) cc_final: 0.9001 (tptp) REVERT: B 121 GLU cc_start: 0.8564 (tt0) cc_final: 0.7833 (tm-30) REVERT: B 175 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7608 (tm-30) REVERT: C 112 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: C 216 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: C 253 MET cc_start: 0.5617 (ttp) cc_final: 0.5334 (ttt) REVERT: C 356 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.5439 (tmt) REVERT: C 432 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7800 (tmtt) REVERT: C 439 TYR cc_start: 0.8029 (m-80) cc_final: 0.7567 (m-80) REVERT: C 575 TYR cc_start: 0.8292 (t80) cc_final: 0.8083 (t80) REVERT: C 600 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: C 699 TRP cc_start: 0.8366 (m100) cc_final: 0.7990 (m100) REVERT: C 764 PHE cc_start: 0.8526 (t80) cc_final: 0.7974 (t80) REVERT: C 872 PHE cc_start: 0.7212 (t80) cc_final: 0.6911 (t80) REVERT: D 22 MET cc_start: 0.5028 (mmm) cc_final: 0.4646 (tpt) REVERT: D 51 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7026 (p0) REVERT: D 149 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7954 (mp) REVERT: E 1 MET cc_start: 0.4596 (tpt) cc_final: 0.4310 (mmm) REVERT: E 12 LYS cc_start: 0.8741 (mmtt) cc_final: 0.7981 (mmtt) outliers start: 90 outliers final: 60 residues processed: 325 average time/residue: 0.1421 time to fit residues: 72.0859 Evaluate side-chains 305 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 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 139 ILE 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 294 GLU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 409 LEU 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 554 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 667 LEU 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 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 112 ASP 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 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 410 THR 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 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 38 THR 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 183 ASN Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain D residue 223 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 187 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** A 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 864 HIS E 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.161107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.110132 restraints weight = 45625.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.108970 restraints weight = 24160.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.110306 restraints weight = 20503.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.110451 restraints weight = 17193.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110573 restraints weight = 16377.640| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21445 Z= 0.225 Angle : 0.653 14.711 29172 Z= 0.346 Chirality : 0.045 0.176 3159 Planarity : 0.004 0.045 3578 Dihedral : 15.741 169.027 3288 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.88 % Allowed : 25.57 % Favored : 69.55 % 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: -0.48 (0.17), residues: 2468 helix: 0.86 (0.17), residues: 921 sheet: -1.04 (0.22), residues: 535 loop : -0.89 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 674 TYR 0.025 0.002 TYR C 887 PHE 0.016 0.002 PHE A 764 TRP 0.016 0.002 TRP A 362 HIS 0.009 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00527 (21445) covalent geometry : angle 0.65292 (29172) hydrogen bonds : bond 0.04412 ( 1005) hydrogen bonds : angle 5.08243 ( 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 356 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 251 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8314 (mmm) cc_final: 0.7530 (tpp) REVERT: A 129 GLU cc_start: 0.6722 (pt0) cc_final: 0.6311 (mp0) REVERT: A 182 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8026 (mtm180) REVERT: A 216 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 224 MET cc_start: 0.9095 (mmm) cc_final: 0.8839 (mmm) REVERT: A 486 MET cc_start: 0.8997 (tmm) cc_final: 0.8571 (tmm) REVERT: A 530 TYR cc_start: 0.3570 (OUTLIER) cc_final: 0.2839 (m-10) REVERT: A 667 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.5792 (mp) REVERT: A 678 MET cc_start: 0.5289 (tmm) cc_final: 0.4077 (mtt) REVERT: A 840 LYS cc_start: 0.8331 (pttt) cc_final: 0.7965 (tptt) REVERT: A 859 LEU cc_start: 0.7101 (pp) cc_final: 0.6854 (mm) REVERT: B 1 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.4678 (pmm) REVERT: B 175 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7631 (tm-30) REVERT: B 212 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8087 (pm20) REVERT: C 63 MET cc_start: 0.8444 (mmt) cc_final: 0.8116 (mmt) REVERT: C 216 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: C 253 MET cc_start: 0.5557 (ttp) cc_final: 0.5275 (ttt) REVERT: C 356 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.5611 (tmt) REVERT: C 432 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7823 (tmtt) REVERT: C 600 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: C 699 TRP cc_start: 0.8471 (m100) cc_final: 0.8081 (m100) REVERT: C 764 PHE cc_start: 0.8541 (t80) cc_final: 0.7952 (t80) REVERT: C 827 MET cc_start: 0.6371 (mpp) cc_final: 0.6094 (mpp) REVERT: C 872 PHE cc_start: 0.7509 (t80) cc_final: 0.7267 (t80) REVERT: D 22 MET cc_start: 0.5212 (mmm) cc_final: 0.4798 (tpt) REVERT: D 51 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7067 (p0) REVERT: D 149 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (mp) REVERT: D 187 MET cc_start: 0.8851 (ppp) cc_final: 0.8630 (ppp) REVERT: E 55 TYR cc_start: 0.5572 (OUTLIER) cc_final: 0.5098 (m-80) outliers start: 105 outliers final: 70 residues processed: 326 average time/residue: 0.1383 time to fit residues: 70.9465 Evaluate side-chains 318 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 239 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 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 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 409 LEU 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 500 ILE 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 577 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 778 GLU 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 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 216 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 306 ILE 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 410 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 506 SER Chi-restraints excluded: chain C residue 548 LEU 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 670 TYR Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 38 THR 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 184 MET Chi-restraints excluded: chain D residue 199 TRP Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 PHE 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 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: 0.7980 chunk 203 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 chunk 26 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN C 368 ASN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4306 r_free = 0.4306 target = 0.159987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110225 restraints weight = 45932.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106073 restraints weight = 26386.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.107850 restraints weight = 22122.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108076 restraints weight = 17495.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108244 restraints weight = 16910.578| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21445 Z= 0.246 Angle : 0.671 12.908 29172 Z= 0.357 Chirality : 0.045 0.174 3159 Planarity : 0.004 0.049 3578 Dihedral : 15.771 165.065 3288 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.74 % Allowed : 25.80 % Favored : 69.46 % 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: -0.62 (0.17), residues: 2468 helix: 0.76 (0.17), residues: 921 sheet: -1.15 (0.22), residues: 539 loop : -0.97 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 674 TYR 0.023 0.002 TYR C 887 PHE 0.021 0.002 PHE A 519 TRP 0.015 0.002 TRP A 362 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00576 (21445) covalent geometry : angle 0.67079 (29172) hydrogen bonds : bond 0.04573 ( 1005) hydrogen bonds : angle 5.16818 ( 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 344 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 242 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 HIS cc_start: 0.8462 (OUTLIER) cc_final: 0.8179 (t-90) REVERT: A 63 MET cc_start: 0.8362 (mmt) cc_final: 0.7851 (mtm) REVERT: A 83 MET cc_start: 0.8339 (mmm) cc_final: 0.7508 (tpp) REVERT: A 129 GLU cc_start: 0.6896 (pt0) cc_final: 0.6463 (mp0) REVERT: A 216 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 288 GLU cc_start: 0.8922 (pm20) cc_final: 0.8302 (mm-30) REVERT: A 329 GLN cc_start: 0.9058 (tp40) cc_final: 0.8692 (tp40) REVERT: A 486 MET cc_start: 0.8993 (tmm) cc_final: 0.8540 (tmm) REVERT: A 487 PHE cc_start: 0.8739 (m-80) cc_final: 0.8461 (m-80) REVERT: A 530 TYR cc_start: 0.3500 (OUTLIER) cc_final: 0.2763 (m-10) REVERT: A 613 PHE cc_start: 0.8097 (m-80) cc_final: 0.7742 (m-10) REVERT: A 667 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.5855 (mp) REVERT: A 678 MET cc_start: 0.5244 (tmm) cc_final: 0.4509 (mtt) REVERT: B 1 MET cc_start: 0.5296 (OUTLIER) cc_final: 0.3925 (pmm) REVERT: B 175 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7673 (tm-30) REVERT: B 212 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8117 (pm20) REVERT: C 63 MET cc_start: 0.8445 (mmt) cc_final: 0.8060 (mmt) REVERT: C 83 MET cc_start: 0.5785 (mtp) cc_final: 0.5552 (mtm) REVERT: C 216 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: C 253 MET cc_start: 0.5564 (ttp) cc_final: 0.5283 (ttt) REVERT: C 356 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.5749 (tmt) REVERT: C 432 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7770 (tmtt) REVERT: C 600 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: C 699 TRP cc_start: 0.8507 (m100) cc_final: 0.8102 (m100) REVERT: C 764 PHE cc_start: 0.8593 (t80) cc_final: 0.7970 (t80) REVERT: C 827 MET cc_start: 0.6406 (mpp) cc_final: 0.6125 (mpp) REVERT: C 872 PHE cc_start: 0.7545 (t80) cc_final: 0.7344 (t80) REVERT: D 22 MET cc_start: 0.5497 (mmm) cc_final: 0.5073 (tpt) REVERT: D 23 LEU cc_start: 0.8103 (tp) cc_final: 0.7725 (tp) REVERT: D 149 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8234 (mp) REVERT: E 1 MET cc_start: 0.4172 (tpt) cc_final: 0.3864 (mmm) outliers start: 102 outliers final: 74 residues processed: 317 average time/residue: 0.1391 time to fit residues: 69.7304 Evaluate side-chains 318 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 236 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 70 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 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 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 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 667 LEU 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 40 HIS 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 216 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE 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 410 THR 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 548 LEU 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 724 ILE Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 38 THR 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 184 MET 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 28 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 143 optimal weight: 0.7980 chunk 163 optimal weight: 50.0000 chunk 34 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 207 optimal weight: 30.0000 chunk 216 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 236 optimal weight: 50.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 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 = 0.4320 r_free = 0.4320 target = 0.161171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111194 restraints weight = 45164.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108724 restraints weight = 25746.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110263 restraints weight = 20997.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110425 restraints weight = 17568.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110549 restraints weight = 17061.573| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21445 Z= 0.189 Angle : 0.634 13.517 29172 Z= 0.335 Chirality : 0.044 0.176 3159 Planarity : 0.004 0.045 3578 Dihedral : 15.714 164.255 3288 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.46 % Allowed : 26.08 % Favored : 69.46 % 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: -0.53 (0.17), residues: 2468 helix: 0.81 (0.17), residues: 921 sheet: -1.08 (0.22), residues: 538 loop : -0.90 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 674 TYR 0.020 0.002 TYR C 887 PHE 0.015 0.002 PHE A 764 TRP 0.014 0.002 TRP C 593 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00440 (21445) covalent geometry : angle 0.63371 (29172) hydrogen bonds : bond 0.04243 ( 1005) hydrogen bonds : angle 5.04137 ( 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 350 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 254 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 40 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.8191 (t-90) REVERT: A 63 MET cc_start: 0.8336 (mmt) cc_final: 0.7822 (mtm) REVERT: A 83 MET cc_start: 0.8336 (mmm) cc_final: 0.7510 (tpp) REVERT: A 129 GLU cc_start: 0.6844 (pt0) cc_final: 0.6467 (mp0) REVERT: A 182 ARG cc_start: 0.8311 (mtm110) cc_final: 0.7960 (mtm180) REVERT: A 186 MET cc_start: 0.8617 (pmm) cc_final: 0.7972 (pmm) REVERT: A 216 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 224 MET cc_start: 0.8857 (mmm) cc_final: 0.8494 (mmm) REVERT: A 288 GLU cc_start: 0.8892 (pm20) cc_final: 0.8307 (mm-30) REVERT: A 329 GLN cc_start: 0.9089 (tp40) cc_final: 0.8691 (tp40) REVERT: A 486 MET cc_start: 0.9018 (tmm) cc_final: 0.8553 (tmm) REVERT: A 487 PHE cc_start: 0.8743 (m-80) cc_final: 0.8444 (m-80) REVERT: A 530 TYR cc_start: 0.3640 (OUTLIER) cc_final: 0.2926 (m-10) REVERT: A 613 PHE cc_start: 0.8029 (m-80) cc_final: 0.7723 (m-10) REVERT: A 667 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.5783 (mp) REVERT: A 678 MET cc_start: 0.5171 (tmm) cc_final: 0.4935 (mtt) REVERT: A 840 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8261 (mmmm) REVERT: A 894 ASP cc_start: 0.8831 (t0) cc_final: 0.8483 (p0) REVERT: B 1 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4049 (pmm) REVERT: B 175 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7675 (tm-30) REVERT: B 212 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8083 (pm20) REVERT: C 63 MET cc_start: 0.8425 (mmt) cc_final: 0.8064 (mmt) REVERT: C 216 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: C 253 MET cc_start: 0.5385 (ttp) cc_final: 0.5108 (ttt) REVERT: C 356 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.5698 (tmt) REVERT: C 432 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7745 (tmtt) REVERT: C 600 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: C 699 TRP cc_start: 0.8478 (m100) cc_final: 0.8097 (m100) REVERT: C 725 MET cc_start: 0.8552 (ptp) cc_final: 0.8088 (pmm) REVERT: C 764 PHE cc_start: 0.8608 (t80) cc_final: 0.7954 (t80) REVERT: C 827 MET cc_start: 0.6586 (mpp) cc_final: 0.6382 (mpp) REVERT: D 22 MET cc_start: 0.5385 (mmm) cc_final: 0.4963 (tpt) REVERT: D 126 LEU cc_start: 0.9592 (tp) cc_final: 0.9312 (pp) REVERT: D 149 ILE cc_start: 0.8446 (pt) cc_final: 0.8238 (mp) REVERT: D 186 ASN cc_start: 0.8792 (t0) cc_final: 0.8459 (m-40) REVERT: E 1 MET cc_start: 0.4004 (tpt) cc_final: 0.3713 (mmm) REVERT: E 55 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.5152 (m-80) outliers start: 96 outliers final: 72 residues processed: 323 average time/residue: 0.1288 time to fit residues: 66.8978 Evaluate side-chains 317 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 237 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 70 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 357 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 397 LYS 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 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 577 LEU Chi-restraints excluded: chain A residue 667 LEU 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 778 GLU 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 40 HIS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 300 LEU 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 410 THR 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 548 LEU 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 29 ILE Chi-restraints excluded: chain D residue 30 MET Chi-restraints excluded: chain D residue 38 THR 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 D residue 184 MET Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 247 optimal weight: 20.0000 chunk 206 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 73 optimal weight: 0.0010 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 421 ASN D 124 GLN ** D 204 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 = 0.4352 r_free = 0.4352 target = 0.163687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.114947 restraints weight = 45752.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114220 restraints weight = 24759.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114308 restraints weight = 19813.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.115028 restraints weight = 19805.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.115450 restraints weight = 16177.426| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21445 Z= 0.131 Angle : 0.608 13.173 29172 Z= 0.318 Chirality : 0.043 0.156 3159 Planarity : 0.004 0.043 3578 Dihedral : 15.545 166.538 3285 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.11 % Allowed : 27.71 % Favored : 69.18 % 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: -0.30 (0.17), residues: 2468 helix: 0.96 (0.17), residues: 919 sheet: -0.83 (0.22), residues: 519 loop : -0.83 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.017 0.001 TYR C 575 PHE 0.032 0.001 PHE D 180 TRP 0.028 0.002 TRP C 69 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00298 (21445) covalent geometry : angle 0.60790 (29172) hydrogen bonds : bond 0.03855 ( 1005) hydrogen bonds : angle 4.84913 ( 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 335 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8451 (tm-30) REVERT: A 83 MET cc_start: 0.8272 (mmm) cc_final: 0.7401 (tpp) REVERT: A 129 GLU cc_start: 0.6944 (pt0) cc_final: 0.6609 (mp0) REVERT: A 182 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8111 (mtm180) REVERT: A 186 MET cc_start: 0.8456 (pmm) cc_final: 0.8156 (pmm) REVERT: A 224 MET cc_start: 0.8843 (mmm) cc_final: 0.8427 (mmm) REVERT: A 288 GLU cc_start: 0.8880 (pm20) cc_final: 0.8309 (mm-30) REVERT: A 421 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8226 (t0) REVERT: A 486 MET cc_start: 0.8995 (tmm) cc_final: 0.8539 (tmm) REVERT: A 489 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 530 TYR cc_start: 0.3760 (OUTLIER) cc_final: 0.3027 (m-10) REVERT: A 650 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7936 (mp10) REVERT: A 667 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5645 (mp) REVERT: A 680 MET cc_start: 0.6820 (mmm) cc_final: 0.6306 (mmm) REVERT: A 840 LYS cc_start: 0.8691 (mmtm) cc_final: 0.8319 (mmmm) REVERT: B 1 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.4189 (pmm) REVERT: B 175 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7689 (tm-30) REVERT: B 184 MET cc_start: 0.8932 (mmm) cc_final: 0.8367 (mmm) REVERT: B 212 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8081 (pm20) REVERT: C 63 MET cc_start: 0.8424 (mmt) cc_final: 0.8078 (mmt) REVERT: C 253 MET cc_start: 0.5342 (ttp) cc_final: 0.5050 (ttt) REVERT: C 356 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.5421 (tmt) REVERT: C 432 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7765 (tmtt) REVERT: C 491 MET cc_start: 0.8937 (mpp) cc_final: 0.8096 (tmm) REVERT: C 600 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8655 (tm-30) REVERT: C 699 TRP cc_start: 0.8407 (m100) cc_final: 0.8059 (m100) REVERT: C 725 MET cc_start: 0.8525 (ptp) cc_final: 0.8290 (pmm) REVERT: C 764 PHE cc_start: 0.8710 (t80) cc_final: 0.8391 (t80) REVERT: C 766 LYS cc_start: 0.8857 (mmmt) cc_final: 0.8588 (mmtm) REVERT: D 1 MET cc_start: 0.7223 (mmm) cc_final: 0.6192 (mpp) REVERT: D 22 MET cc_start: 0.5548 (mmm) cc_final: 0.5064 (tpt) REVERT: D 23 LEU cc_start: 0.8159 (tp) cc_final: 0.7949 (tt) REVERT: D 126 LEU cc_start: 0.9607 (tp) cc_final: 0.9326 (pp) REVERT: D 149 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8234 (mp) REVERT: D 186 ASN cc_start: 0.8686 (t0) cc_final: 0.8449 (m-40) REVERT: D 190 GLN cc_start: 0.8144 (tt0) cc_final: 0.7657 (tm-30) REVERT: E 1 MET cc_start: 0.3796 (tpt) cc_final: 0.3170 (mmm) REVERT: E 55 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.5171 (m-80) outliers start: 67 outliers final: 47 residues processed: 314 average time/residue: 0.1333 time to fit residues: 65.8143 Evaluate side-chains 308 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 253 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET 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 379 GLN Chi-restraints excluded: chain A residue 421 ASN 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 530 TYR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 667 LEU 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 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 40 HIS Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 322 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 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 589 VAL 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 38 THR 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 184 MET 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 203 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 236 optimal weight: 50.0000 chunk 92 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 chunk 89 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.161406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111028 restraints weight = 45671.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110352 restraints weight = 27241.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110904 restraints weight = 19856.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111513 restraints weight = 18367.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111615 restraints weight = 16300.669| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21445 Z= 0.189 Angle : 0.639 13.288 29172 Z= 0.336 Chirality : 0.044 0.181 3159 Planarity : 0.004 0.043 3578 Dihedral : 15.567 167.210 3285 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.98 % Allowed : 27.85 % Favored : 69.18 % 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: -0.38 (0.17), residues: 2468 helix: 0.93 (0.17), residues: 920 sheet: -1.00 (0.22), residues: 535 loop : -0.83 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 206 TYR 0.020 0.002 TYR C 887 PHE 0.048 0.002 PHE D 180 TRP 0.046 0.002 TRP C 69 HIS 0.006 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00443 (21445) covalent geometry : angle 0.63877 (29172) hydrogen bonds : bond 0.04127 ( 1005) hydrogen bonds : angle 4.92731 ( 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 314 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8341 (mmt) cc_final: 0.7811 (mtp) REVERT: A 83 MET cc_start: 0.8134 (mmm) cc_final: 0.7405 (tpp) REVERT: A 129 GLU cc_start: 0.6901 (pt0) cc_final: 0.6609 (mp0) REVERT: A 182 ARG cc_start: 0.8357 (mtm110) cc_final: 0.8107 (mtm180) REVERT: A 186 MET cc_start: 0.8467 (pmm) cc_final: 0.8054 (pmm) REVERT: A 216 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 224 MET cc_start: 0.8930 (mmm) cc_final: 0.8591 (mmm) REVERT: A 288 GLU cc_start: 0.8845 (pm20) cc_final: 0.8279 (mm-30) REVERT: A 317 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 421 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8194 (t0) REVERT: A 486 MET cc_start: 0.8951 (tmm) cc_final: 0.8549 (tmm) REVERT: A 489 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 530 TYR cc_start: 0.3721 (OUTLIER) cc_final: 0.2973 (m-10) REVERT: A 667 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.5894 (mp) REVERT: A 840 LYS cc_start: 0.8679 (mmtm) cc_final: 0.8303 (mmmm) REVERT: B 1 MET cc_start: 0.5366 (OUTLIER) cc_final: 0.4040 (pmm) REVERT: B 175 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7680 (tm-30) REVERT: B 212 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8105 (pm20) REVERT: C 63 MET cc_start: 0.8404 (mmt) cc_final: 0.8023 (mmt) REVERT: C 253 MET cc_start: 0.5354 (ttp) cc_final: 0.5073 (ttt) REVERT: C 356 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.5477 (tmt) REVERT: C 432 LYS cc_start: 0.8151 (tmtt) cc_final: 0.7815 (tmtt) REVERT: C 491 MET cc_start: 0.8827 (mpp) cc_final: 0.8266 (tmm) REVERT: C 699 TRP cc_start: 0.8510 (m100) cc_final: 0.8131 (m100) REVERT: C 725 MET cc_start: 0.8521 (ptp) cc_final: 0.8263 (pmm) REVERT: C 764 PHE cc_start: 0.8731 (t80) cc_final: 0.8394 (t80) REVERT: C 766 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8602 (mmtm) REVERT: D 1 MET cc_start: 0.7362 (mmm) cc_final: 0.6477 (mpp) REVERT: D 22 MET cc_start: 0.5642 (mmm) cc_final: 0.5241 (tpt) REVERT: D 23 LEU cc_start: 0.8223 (tp) cc_final: 0.7729 (tt) REVERT: D 149 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8232 (mp) REVERT: D 186 ASN cc_start: 0.8739 (t0) cc_final: 0.8512 (m-40) REVERT: E 1 MET cc_start: 0.3717 (tpt) cc_final: 0.2853 (mmm) REVERT: E 12 LYS cc_start: 0.8671 (mmtt) cc_final: 0.7881 (mmtt) REVERT: E 55 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5152 (m-80) outliers start: 64 outliers final: 51 residues processed: 292 average time/residue: 0.1411 time to fit residues: 64.8290 Evaluate side-chains 300 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET 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 294 GLU Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain A residue 421 ASN 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 570 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 667 LEU 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 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 40 HIS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 300 LEU 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 388 PHE Chi-restraints excluded: chain C residue 408 ASP 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 589 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 38 THR 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 184 MET 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: 50.0000 chunk 247 optimal weight: 20.0000 chunk 240 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 234 optimal weight: 8.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN A 421 ASN ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 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 = 0.4299 r_free = 0.4299 target = 0.159119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107485 restraints weight = 45671.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105881 restraints weight = 25154.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107134 restraints weight = 20726.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.107290 restraints weight = 16503.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.107492 restraints weight = 15726.232| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21445 Z= 0.266 Angle : 0.700 13.199 29172 Z= 0.371 Chirality : 0.046 0.185 3159 Planarity : 0.005 0.060 3578 Dihedral : 15.676 164.834 3285 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.39 % Allowed : 27.52 % Favored : 69.08 % 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: 0.76 (0.17), residues: 921 sheet: -1.05 (0.22), residues: 533 loop : -0.96 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 674 TYR 0.024 0.002 TYR C 623 PHE 0.023 0.002 PHE C 872 TRP 0.038 0.002 TRP C 69 HIS 0.008 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00625 (21445) covalent geometry : angle 0.69989 (29172) hydrogen bonds : bond 0.04575 ( 1005) hydrogen bonds : angle 5.13414 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3537.94 seconds wall clock time: 62 minutes 0.11 seconds (3720.11 seconds total)