Starting phenix.real_space_refine on Mon Oct 26 14:42:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ea6_47826/10_2026/9ea6_47826.map" } resolution = 3.74 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 62 5.49 5 S 116 5.16 5 C 13242 2.51 5 N 3518 2.21 5 O 4109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21048 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7281 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 40, 'TRANS': 857} Chain: "B" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "C" Number of atoms: 7281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7281 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 40, 'TRANS': 857} Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "E" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "P" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'D3T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.21 Number of scatterers: 21048 At special positions: 0 Unit cell: (109.296, 150.696, 144.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 116 16.00 P 62 15.00 O 4109 8.00 N 3518 7.00 C 13242 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: 1.38 Conformation dependent library (CDL) restraints added in 887.7 milliseconds 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4650 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 26 sheets defined 41.3% alpha, 19.1% beta 24 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.998A pdb=" N ALA A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 190 through 205 Processing helix chain 'A' and resid 218 through 238 removed outlier: 8.325A pdb=" N GLU A 233 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ARG A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 308 through 336 removed outlier: 3.640A pdb=" N HIS A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLN A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ARG A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.547A pdb=" N THR A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 435 through 441 removed outlier: 3.815A pdb=" N ALA A 441 " --> pdb=" O HIS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 503 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.592A pdb=" N SER A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 568 removed outlier: 3.763A pdb=" N TYR A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 607 Processing helix chain 'A' and resid 626 through 634 removed outlier: 3.730A pdb=" N ILE A 630 " --> pdb=" O VAL A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 removed outlier: 3.653A pdb=" N PHE A 638 " --> pdb=" O LEU A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 640 through 655 Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.869A pdb=" N MET A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 752 Processing helix chain 'A' and resid 753 through 769 removed outlier: 4.533A pdb=" N ARG A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 3.826A pdb=" N TYR A 788 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 812 removed outlier: 4.333A pdb=" N VAL A 812 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 854 through 862 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'A' and resid 872 through 883 Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.611A pdb=" N PHE A 897 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 893 through 898' Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.609A pdb=" N ASN B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'C' and resid 62 through 76 Processing helix chain 'C' and resid 86 through 96 Processing helix chain 'C' and resid 160 through 166 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.513A pdb=" N LEU C 180 " --> pdb=" O PRO C 176 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.570A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 231 Processing helix chain 'C' and resid 232 through 238 Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 305 through 313 removed outlier: 3.934A pdb=" N ARG C 310 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU C 311 " --> pdb=" O ASN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 336 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.595A pdb=" N THR C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 420 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 441 Processing helix chain 'C' and resid 467 through 503 Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 531 through 568 removed outlier: 4.465A pdb=" N TYR C 564 " --> pdb=" O ILE C 560 " (cutoff:3.500A) removed outlier: 4.758A 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 628 through 634 Processing helix chain 'C' and resid 635 through 638 Processing helix chain 'C' and resid 640 through 656 Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'C' and resid 735 through 752 Processing helix chain 'C' and resid 753 through 769 removed outlier: 4.346A pdb=" N ARG C 769 " --> pdb=" O GLU C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 851 through 861 removed outlier: 4.227A pdb=" N ASP C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 872 removed outlier: 3.579A pdb=" N LEU C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 883 Processing helix chain 'C' and resid 893 through 898 Processing helix chain 'D' and resid 4 through 18 removed outlier: 4.028A pdb=" N ILE D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN D 18 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 65 Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.824A pdb=" N VAL D 100 " --> pdb=" O PRO D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.639A pdb=" N ARG D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 16 removed outlier: 3.563A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 66 removed outlier: 3.642A pdb=" N PHE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 185 through 187 No H-bonds generated for 'chain 'E' and resid 185 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 11 removed outlier: 3.524A pdb=" N PHE A 4 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG A 18 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 8 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 16 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR A 10 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 188 removed outlier: 6.259A pdb=" N PHE A 143 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N MET A 186 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL A 145 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE A 188 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP A 147 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ALA A 109 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE A 210 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 245 through 250 Processing sheet with id=AA5, first strand: chain 'A' and resid 614 through 618 removed outlier: 5.190A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 404 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A 685 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 406 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 681 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 614 through 618 removed outlier: 5.190A pdb=" N ILE A 614 " --> pdb=" O CYS A 625 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N CYS A 625 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 404 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A 685 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 406 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP A 681 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 685 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP A 711 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N GLU A 719 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 430 removed outlier: 7.361A pdb=" N ILE A 427 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASP A 461 " --> pdb=" O ILE A 427 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 429 " --> pdb=" O MET A 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 830 Processing sheet with id=AA9, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AB1, first strand: chain 'B' and resid 28 through 32 Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 75 removed outlier: 4.002A pdb=" N TYR E 165 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE E 147 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 142 " --> pdb=" O PHE E 178 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N PHE E 178 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.603A pdb=" N THR B 177 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 178 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 142 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 147 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 165 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 11 removed outlier: 6.608A pdb=" N ARG C 18 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE C 8 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 16 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N THR C 10 " --> pdb=" O ASN C 14 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.519A pdb=" N PHE C 38 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.541A pdb=" N LYS C 48 " --> pdb=" O VAL C 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 183 through 188 removed outlier: 6.086A pdb=" N PHE C 143 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET C 186 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 145 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE C 188 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 147 " --> pdb=" O PHE C 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 132 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AB9, first strand: chain 'C' and resid 622 through 624 Processing sheet with id=AC1, first strand: chain 'C' and resid 427 through 430 removed outlier: 7.504A pdb=" N ILE C 427 " --> pdb=" O ASP C 461 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP C 461 " --> pdb=" O ILE C 427 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 429 " --> pdb=" O MET C 459 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 698 through 701 removed outlier: 5.688A pdb=" N TRP C 699 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ALA C 706 " --> pdb=" O TRP C 699 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 701 " --> pdb=" O ARG C 704 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASP C 711 " --> pdb=" O GLU C 719 " (cutoff:3.500A) removed outlier: 11.566A 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 782 Processing sheet with id=AC4, first strand: chain 'D' and resid 22 through 23 Processing sheet with id=AC5, first strand: chain 'D' and resid 26 through 32 removed outlier: 5.637A pdb=" N PHE D 28 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N ASP D 46 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 10.618A pdb=" N MET D 30 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N ILE D 44 " --> pdb=" O MET D 30 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N ARG D 32 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 12.141A pdb=" N ALA D 42 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 225 through 227 removed outlier: 6.424A pdb=" N PHE D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 142 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR D 137 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE D 147 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 21 through 23 Processing sheet with id=AC8, first strand: chain 'E' and resid 26 through 32 removed outlier: 5.249A pdb=" N GLN E 27 " --> pdb=" O ILE E 44 " (cutoff:3.500A) 977 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5505 1.33 - 1.46: 4447 1.46 - 1.58: 11345 1.58 - 1.70: 118 1.70 - 1.82: 205 Bond restraints: 21620 Sorted by residual: bond pdb=" O5' D3T T 901 " pdb=" PA D3T T 901 " ideal model delta sigma weight residual 1.655 1.801 -0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" C3' DA T 8 " pdb=" C2' DA T 8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" O3A D3T T 901 " pdb=" PA D3T T 901 " ideal model delta sigma weight residual 1.625 1.557 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" N ILE C 842 " pdb=" CA ILE C 842 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.03e+01 bond pdb=" C3' DT T 19 " pdb=" C2' DT T 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 21615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 28985 2.47 - 4.94: 400 4.94 - 7.41: 44 7.41 - 9.88: 8 9.88 - 12.36: 3 Bond angle restraints: 29440 Sorted by residual: angle pdb=" C THR A 619 " pdb=" CA THR A 619 " pdb=" CB THR A 619 " ideal model delta sigma weight residual 116.54 111.29 5.25 1.15e+00 7.56e-01 2.08e+01 angle pdb=" N3 DT P 15 " pdb=" C4 DT P 15 " pdb=" O4 DT P 15 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT T 18 " pdb=" C4 DT T 18 " pdb=" O4 DT T 18 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT T 34 " pdb=" C4 DT T 34 " pdb=" O4 DT T 34 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 29435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 11729 24.28 - 48.55: 1044 48.55 - 72.83: 175 72.83 - 97.10: 13 97.10 - 121.38: 1 Dihedral angle restraints: 12962 sinusoidal: 5725 harmonic: 7237 Sorted by residual: dihedral pdb=" CA SER A 454 " pdb=" C SER A 454 " pdb=" N PRO A 455 " pdb=" CA PRO A 455 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 787 " pdb=" C LYS A 787 " pdb=" N TYR A 788 " pdb=" CA TYR A 788 " ideal model delta harmonic sigma weight residual -180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE E 29 " pdb=" C ILE E 29 " pdb=" N MET E 30 " pdb=" CA MET E 30 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 12959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3047 0.109 - 0.217: 135 0.217 - 0.326: 1 0.326 - 0.435: 0 0.435 - 0.544: 2 Chirality restraints: 3185 Sorted by residual: chirality pdb=" P DG P 24 " pdb=" OP1 DG P 24 " pdb=" OP2 DG P 24 " pdb=" O5' DG P 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" P DC P 25 " pdb=" OP1 DC P 25 " pdb=" OP2 DC P 25 " pdb=" O5' DC P 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" CA ILE A 113 " pdb=" N ILE A 113 " pdb=" C ILE A 113 " pdb=" CB ILE A 113 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3182 not shown) Planarity restraints: 3587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 832 " -0.255 9.50e-02 1.11e+02 1.14e-01 8.01e+00 pdb=" NE ARG C 832 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 832 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 832 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 832 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 14 " -0.017 2.00e-02 2.50e+03 1.92e-02 6.43e+00 pdb=" CG PHE E 14 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE E 14 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE E 14 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 14 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 14 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 14 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 199 " 0.015 2.00e-02 2.50e+03 1.57e-02 6.14e+00 pdb=" CG TRP D 199 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP D 199 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 199 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 199 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 199 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 199 " 0.001 2.00e-02 2.50e+03 ... (remaining 3584 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1838 2.74 - 3.28: 22126 3.28 - 3.82: 37078 3.82 - 4.36: 42485 4.36 - 4.90: 69529 Nonbonded interactions: 173056 Sorted by model distance: nonbonded pdb=" OG SER B 76 " pdb=" OD1 ASP B 78 " model vdw 2.199 3.040 nonbonded pdb=" OE1 GLN C 386 " pdb=" OH TYR C 575 " model vdw 2.205 3.040 nonbonded pdb=" O GLY C 878 " pdb=" OG SER C 882 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR B 172 " pdb=" O ASN B 176 " model vdw 2.212 3.040 nonbonded pdb=" O LEU A 282 " pdb=" NZ LYS A 825 " model vdw 2.220 3.120 ... (remaining 173051 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' and resid 1 through 898) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.670 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.146 21620 Z= 0.327 Angle : 0.729 12.356 29440 Z= 0.469 Chirality : 0.051 0.544 3185 Planarity : 0.004 0.114 3587 Dihedral : 17.150 121.380 8312 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.33 % Allowed : 21.25 % Favored : 78.43 % 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: -0.16 (0.17), residues: 2470 helix: 0.77 (0.17), residues: 906 sheet: -0.29 (0.23), residues: 479 loop : -0.67 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 131 TYR 0.030 0.002 TYR A 128 PHE 0.044 0.002 PHE E 14 TRP 0.042 0.002 TRP D 199 HIS 0.005 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.33 (21620) covalent geometry : angle 0.72894 / 0.47 (29440) hydrogen bonds : bond 0.13266 / 8.63 ( 1023) hydrogen bonds : angle 6.33874 / 4.48 ( 2862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 293 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7919 (t0) cc_final: 0.7501 (t0) REVERT: A 395 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7306 (mm-30) REVERT: A 869 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7172 (tm-30) REVERT: B 175 GLU cc_start: 0.7389 (pm20) cc_final: 0.6994 (pt0) REVERT: E 39 TYR cc_start: 0.5906 (t80) cc_final: 0.5404 (t80) outliers start: 7 outliers final: 2 residues processed: 297 average time/residue: 0.1425 time to fit residues: 66.8708 Evaluate side-chains 251 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 249 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain C residue 863 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.168704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137863 restraints weight = 39823.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.138086 restraints weight = 56264.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.139523 restraints weight = 44335.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.139603 restraints weight = 28927.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.141101 restraints weight = 24601.556| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21620 Z= 0.238 Angle : 0.646 11.537 29440 Z= 0.355 Chirality : 0.046 0.199 3185 Planarity : 0.004 0.051 3587 Dihedral : 15.422 120.212 3389 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.39 % Allowed : 19.80 % Favored : 76.80 % 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: -0.15 (0.17), residues: 2470 helix: 0.76 (0.17), residues: 914 sheet: -0.37 (0.22), residues: 511 loop : -0.62 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 87 TYR 0.023 0.002 TYR A 317 PHE 0.033 0.002 PHE E 14 TRP 0.020 0.002 TRP D 199 HIS 0.006 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (21620) covalent geometry : angle 0.64623 / 0.36 (29440) hydrogen bonds : bond 0.04993 / 3.29 ( 1023) hydrogen bonds : angle 5.50608 / 3.88 ( 2862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 257 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.6306 (pt0) cc_final: 0.6011 (pt0) REVERT: A 486 MET cc_start: 0.6019 (ptt) cc_final: 0.5729 (ttp) REVERT: A 827 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7221 (mpt) REVERT: B 75 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.5950 (tm-30) outliers start: 73 outliers final: 37 residues processed: 310 average time/residue: 0.1328 time to fit residues: 66.1409 Evaluate side-chains 280 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 863 ASP Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [131, 61, 95, 157, 3, 96, 187, 198, 200, 189, 113] chunk 131 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 30.0000 chunk 157 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 113 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.170638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.140037 restraints weight = 39983.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.140257 restraints weight = 57416.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141679 restraints weight = 43971.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.141964 restraints weight = 28526.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.143517 restraints weight = 24053.318| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21620 Z= 0.178 Angle : 0.597 10.794 29440 Z= 0.328 Chirality : 0.044 0.182 3185 Planarity : 0.004 0.050 3587 Dihedral : 15.345 118.705 3387 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.49 % Allowed : 20.92 % Favored : 75.59 % 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: -0.09 (0.17), residues: 2470 helix: 0.81 (0.17), residues: 920 sheet: -0.34 (0.22), residues: 509 loop : -0.59 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 32 TYR 0.023 0.002 TYR A 317 PHE 0.027 0.002 PHE C 651 TRP 0.021 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (21620) covalent geometry : angle 0.59743 / 0.33 (29440) hydrogen bonds : bond 0.04626 / 3.08 ( 1023) hydrogen bonds : angle 5.32903 / 3.76 ( 2862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7367 (t70) REVERT: A 827 MET cc_start: 0.7599 (mpp) cc_final: 0.7143 (mpt) REVERT: A 869 GLN cc_start: 0.7424 (tm-30) cc_final: 0.7025 (tm-30) REVERT: B 156 GLU cc_start: 0.7388 (pt0) cc_final: 0.6742 (tt0) REVERT: C 259 ILE cc_start: 0.8718 (mt) cc_final: 0.8506 (tt) REVERT: C 320 TYR cc_start: 0.7277 (m-10) cc_final: 0.6964 (m-80) REVERT: C 356 MET cc_start: 0.6988 (OUTLIER) cc_final: 0.6308 (mtp) REVERT: C 459 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5897 (tpt) REVERT: C 671 MET cc_start: 0.5517 (mmt) cc_final: 0.5281 (mmm) REVERT: E 30 MET cc_start: 0.5730 (tpt) cc_final: 0.4436 (ttt) outliers start: 75 outliers final: 49 residues processed: 330 average time/residue: 0.1339 time to fit residues: 70.8703 Evaluate side-chains 303 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 356 MET Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 625 CYS Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [214, 202, 124, 143, 246, 220, 208, 17, 173, 45, 35] chunk 214 optimal weight: 8.9990 chunk 202 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 246 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.168052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136460 restraints weight = 39805.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139505 restraints weight = 66300.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140006 restraints weight = 37818.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140298 restraints weight = 29583.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142212 restraints weight = 23411.730| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21620 Z= 0.252 Angle : 0.650 13.022 29440 Z= 0.353 Chirality : 0.046 0.191 3185 Planarity : 0.004 0.049 3587 Dihedral : 15.419 118.370 3385 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.02 % Allowed : 20.50 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2470 helix: 0.77 (0.17), residues: 922 sheet: -0.45 (0.22), residues: 498 loop : -0.74 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 479 TYR 0.023 0.002 TYR A 317 PHE 0.030 0.002 PHE A 218 TRP 0.025 0.002 TRP D 199 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (21620) covalent geometry : angle 0.65009 / 0.35 (29440) hydrogen bonds : bond 0.04736 / 3.14 ( 1023) hydrogen bonds : angle 5.37209 / 3.77 ( 2862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 263 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7503 (t70) REVERT: A 326 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6809 (tm-30) REVERT: A 581 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.6300 (p) REVERT: A 827 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7071 (mpt) REVERT: C 259 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 459 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6060 (tpt) REVERT: E 30 MET cc_start: 0.5479 (tpt) cc_final: 0.4233 (ttt) REVERT: E 184 MET cc_start: 0.6948 (mmm) cc_final: 0.6631 (mmm) outliers start: 108 outliers final: 64 residues processed: 343 average time/residue: 0.1274 time to fit residues: 71.6823 Evaluate side-chains 309 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 827 MET Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 805 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 216 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [222, 22, 119, 201, 82, 45, 241, 49, 58, 169, 149] chunk 222 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 241 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN C 383 HIS ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.172525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.141134 restraints weight = 39914.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.140880 restraints weight = 56901.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.142631 restraints weight = 44796.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.142815 restraints weight = 28921.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.144335 restraints weight = 24869.420| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21620 Z= 0.126 Angle : 0.582 11.930 29440 Z= 0.315 Chirality : 0.045 0.307 3185 Planarity : 0.004 0.045 3587 Dihedral : 15.349 115.497 3385 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.49 % Allowed : 22.18 % Favored : 74.34 % 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: -0.05 (0.17), residues: 2470 helix: 0.90 (0.16), residues: 927 sheet: -0.35 (0.23), residues: 488 loop : -0.62 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 131 TYR 0.023 0.002 TYR A 317 PHE 0.028 0.002 PHE C 651 TRP 0.027 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (21620) covalent geometry : angle 0.58155 / 0.32 (29440) hydrogen bonds : bond 0.04179 / 2.80 ( 1023) hydrogen bonds : angle 5.08794 / 3.59 ( 2862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7520 (mtm) REVERT: A 315 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7413 (tp40) REVERT: A 869 GLN cc_start: 0.7464 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 459 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5961 (tpt) outliers start: 75 outliers final: 49 residues processed: 336 average time/residue: 0.1267 time to fit residues: 69.0460 Evaluate side-chains 299 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 315 GLN Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 593 TRP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 124 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [49, 244, 101, 185, 36, 248, 160, 23, 61, 107, 180] chunk 49 optimal weight: 8.9990 chunk 244 optimal weight: 40.0000 chunk 101 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 248 optimal weight: 50.0000 chunk 160 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 215 ASN ** 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 = 0.4283 r_free = 0.4283 target = 0.168363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.135680 restraints weight = 39993.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135574 restraints weight = 59177.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.137444 restraints weight = 44371.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137657 restraints weight = 29114.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.139424 restraints weight = 25231.073| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 21620 Z= 0.271 Angle : 0.676 12.957 29440 Z= 0.365 Chirality : 0.047 0.202 3185 Planarity : 0.005 0.049 3587 Dihedral : 15.475 116.009 3385 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.70 % Allowed : 21.80 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2470 helix: 0.80 (0.17), residues: 920 sheet: -0.38 (0.24), residues: 456 loop : -0.75 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 32 TYR 0.025 0.002 TYR A 317 PHE 0.023 0.002 PHE C 651 TRP 0.042 0.003 TRP C 699 HIS 0.005 0.001 HIS A 434 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.27 (21620) covalent geometry : angle 0.67592 / 0.36 (29440) hydrogen bonds : bond 0.04652 / 3.09 ( 1023) hydrogen bonds : angle 5.27347 / 3.70 ( 2862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 254 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7522 (mtm) REVERT: A 137 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7494 (t70) REVERT: A 216 GLU cc_start: 0.7175 (pm20) cc_final: 0.6965 (pm20) REVERT: A 486 MET cc_start: 0.5831 (ptm) cc_final: 0.5251 (ttp) REVERT: A 827 MET cc_start: 0.7913 (mpp) cc_final: 0.7707 (mpp) REVERT: C 459 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6163 (tpt) REVERT: C 671 MET cc_start: 0.6188 (mmt) cc_final: 0.5987 (mmt) REVERT: E 30 MET cc_start: 0.4801 (tpt) cc_final: 0.3580 (ttp) REVERT: E 184 MET cc_start: 0.7151 (mmm) cc_final: 0.6764 (mmm) outliers start: 101 outliers final: 74 residues processed: 329 average time/residue: 0.1244 time to fit residues: 66.6616 Evaluate side-chains 314 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 237 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 614 ILE Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [106, 72, 198, 32, 117, 222, 128, 61, 14, 7, 150] chunk 106 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 150 optimal weight: 0.0870 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.170809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.139623 restraints weight = 40225.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138380 restraints weight = 60352.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.140507 restraints weight = 46932.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140733 restraints weight = 29753.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.142049 restraints weight = 25843.319| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21620 Z= 0.148 Angle : 0.608 11.012 29440 Z= 0.327 Chirality : 0.045 0.276 3185 Planarity : 0.004 0.045 3587 Dihedral : 15.432 114.104 3385 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.58 % Allowed : 23.20 % Favored : 73.22 % 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: -0.07 (0.17), residues: 2470 helix: 0.94 (0.17), residues: 925 sheet: -0.43 (0.24), residues: 457 loop : -0.65 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 32 TYR 0.024 0.002 TYR A 317 PHE 0.027 0.002 PHE C 651 TRP 0.032 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (21620) covalent geometry : angle 0.60797 / 0.33 (29440) hydrogen bonds : bond 0.04180 / 2.79 ( 1023) hydrogen bonds : angle 5.06824 / 3.57 ( 2862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 268 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7489 (mtm) REVERT: A 114 GLU cc_start: 0.5681 (mm-30) cc_final: 0.5278 (mm-30) REVERT: A 316 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7647 (ttt180) REVERT: A 486 MET cc_start: 0.5647 (ptm) cc_final: 0.5119 (ttp) REVERT: A 699 TRP cc_start: 0.8404 (m100) cc_final: 0.8198 (m100) REVERT: C 317 TYR cc_start: 0.7837 (t80) cc_final: 0.7632 (t80) REVERT: C 320 TYR cc_start: 0.7240 (m-80) cc_final: 0.6870 (m-80) REVERT: C 459 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6141 (tpt) REVERT: C 671 MET cc_start: 0.6130 (mmt) cc_final: 0.5891 (mmt) REVERT: E 30 MET cc_start: 0.4426 (tpt) cc_final: 0.3330 (ttp) REVERT: E 184 MET cc_start: 0.6963 (mmm) cc_final: 0.6659 (mmm) outliers start: 77 outliers final: 55 residues processed: 324 average time/residue: 0.1317 time to fit residues: 69.4064 Evaluate side-chains 307 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 249 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 593 TRP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [7, 166, 57, 126, 168, 172, 218, 113, 79, 26, 38] chunk 7 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.0670 overall best weight: 2.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 HIS E 125 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.170959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138884 restraints weight = 39703.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141905 restraints weight = 55864.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142352 restraints weight = 36261.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.142547 restraints weight = 27378.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.144128 restraints weight = 22431.404| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21620 Z= 0.158 Angle : 0.613 11.066 29440 Z= 0.329 Chirality : 0.045 0.247 3185 Planarity : 0.004 0.043 3587 Dihedral : 15.446 113.263 3385 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.53 % Allowed : 23.29 % Favored : 73.18 % 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: -0.04 (0.17), residues: 2470 helix: 0.95 (0.17), residues: 924 sheet: -0.43 (0.23), residues: 464 loop : -0.61 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 32 TYR 0.023 0.002 TYR A 317 PHE 0.026 0.002 PHE C 651 TRP 0.044 0.002 TRP C 699 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (21620) covalent geometry : angle 0.61321 / 0.33 (29440) hydrogen bonds : bond 0.04146 / 2.77 ( 1023) hydrogen bonds : angle 5.05312 / 3.56 ( 2862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: A 114 GLU cc_start: 0.5754 (mm-30) cc_final: 0.5443 (mm-30) REVERT: A 316 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7690 (ttt180) REVERT: A 486 MET cc_start: 0.5558 (ptm) cc_final: 0.5065 (ttp) REVERT: A 699 TRP cc_start: 0.8339 (m100) cc_final: 0.8015 (m100) REVERT: C 317 TYR cc_start: 0.7891 (t80) cc_final: 0.7664 (t80) REVERT: C 459 MET cc_start: 0.6469 (OUTLIER) cc_final: 0.6171 (tpt) REVERT: C 671 MET cc_start: 0.6117 (mmt) cc_final: 0.5876 (mmt) REVERT: D 127 LEU cc_start: 0.8888 (mt) cc_final: 0.8678 (mt) REVERT: E 30 MET cc_start: 0.4327 (tpt) cc_final: 0.3257 (ttp) REVERT: E 184 MET cc_start: 0.6881 (mmm) cc_final: 0.6624 (mmm) outliers start: 76 outliers final: 62 residues processed: 320 average time/residue: 0.1331 time to fit residues: 69.5629 Evaluate side-chains 310 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 593 TRP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 158 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [53, 20, 191, 45, 135, 85, 134, 63, 28, 185, 182] chunk 53 optimal weight: 50.0000 chunk 20 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 185 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.171259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.140069 restraints weight = 39977.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139125 restraints weight = 59189.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.140719 restraints weight = 45005.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142496 restraints weight = 27638.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142838 restraints weight = 23225.438| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21620 Z= 0.133 Angle : 0.610 10.070 29440 Z= 0.325 Chirality : 0.044 0.246 3185 Planarity : 0.004 0.042 3587 Dihedral : 15.439 111.261 3385 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.21 % Allowed : 24.08 % Favored : 72.71 % 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: -0.02 (0.17), residues: 2470 helix: 1.01 (0.17), residues: 923 sheet: -0.49 (0.24), residues: 462 loop : -0.60 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 87 TYR 0.025 0.002 TYR C 320 PHE 0.027 0.002 PHE C 647 TRP 0.039 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (21620) covalent geometry : angle 0.61042 / 0.33 (29440) hydrogen bonds : bond 0.03973 / 2.66 ( 1023) hydrogen bonds : angle 4.95176 / 3.50 ( 2862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7445 (mtm) REVERT: A 114 GLU cc_start: 0.5815 (mm-30) cc_final: 0.5501 (mm-30) REVERT: A 253 MET cc_start: 0.4743 (ppp) cc_final: 0.4484 (ppp) REVERT: A 316 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7341 (ttt180) REVERT: A 320 TYR cc_start: 0.7595 (m-10) cc_final: 0.7280 (m-10) REVERT: A 438 GLU cc_start: 0.6519 (pt0) cc_final: 0.6055 (pt0) REVERT: A 486 MET cc_start: 0.5626 (ptm) cc_final: 0.5103 (ttp) REVERT: A 576 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: C 317 TYR cc_start: 0.7761 (t80) cc_final: 0.7556 (t80) REVERT: C 459 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.6124 (tpt) REVERT: D 127 LEU cc_start: 0.8879 (mt) cc_final: 0.8663 (mt) REVERT: E 30 MET cc_start: 0.4376 (tpt) cc_final: 0.2992 (ttp) outliers start: 69 outliers final: 54 residues processed: 329 average time/residue: 0.1331 time to fit residues: 70.7735 Evaluate side-chains 315 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 593 TRP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 124 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [176, 236, 219, 194, 105, 49, 75, 132, 141, 163, 39] chunk 176 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 163 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.170135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.138857 restraints weight = 39761.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138108 restraints weight = 61723.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139719 restraints weight = 44743.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141381 restraints weight = 27456.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141810 restraints weight = 23111.003| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21620 Z= 0.190 Angle : 0.649 11.078 29440 Z= 0.345 Chirality : 0.045 0.246 3185 Planarity : 0.004 0.041 3587 Dihedral : 15.491 110.410 3385 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.49 % Allowed : 23.94 % Favored : 72.57 % 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: -0.07 (0.17), residues: 2470 helix: 0.94 (0.17), residues: 925 sheet: -0.46 (0.24), residues: 452 loop : -0.63 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 32 TYR 0.035 0.002 TYR C 320 PHE 0.026 0.002 PHE C 651 TRP 0.043 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (21620) covalent geometry : angle 0.64853 / 0.35 (29440) hydrogen bonds : bond 0.04186 / 2.78 ( 1023) hydrogen bonds : angle 5.03247 / 3.54 ( 2862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4940 Ramachandran restraints generated. 2470 Oldfield, 0 Emsley, 2470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7457 (mtm) REVERT: A 114 GLU cc_start: 0.5926 (mm-30) cc_final: 0.5559 (mm-30) REVERT: A 253 MET cc_start: 0.4659 (ppp) cc_final: 0.4431 (ppp) REVERT: A 316 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7473 (ttt180) REVERT: A 320 TYR cc_start: 0.7647 (m-10) cc_final: 0.7378 (m-10) REVERT: A 326 GLU cc_start: 0.7230 (tm-30) cc_final: 0.7002 (tm-30) REVERT: A 486 MET cc_start: 0.5646 (ptm) cc_final: 0.5123 (ttp) REVERT: A 576 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: A 699 TRP cc_start: 0.8353 (m100) cc_final: 0.8019 (m100) REVERT: B 1 MET cc_start: 0.3165 (mmt) cc_final: 0.2759 (mmt) REVERT: C 317 TYR cc_start: 0.7897 (t80) cc_final: 0.7584 (t80) REVERT: C 459 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6039 (tpt) REVERT: C 680 MET cc_start: 0.7098 (mmp) cc_final: 0.6870 (mmp) REVERT: D 127 LEU cc_start: 0.8922 (mt) cc_final: 0.8716 (mt) REVERT: D 136 ASP cc_start: 0.8185 (p0) cc_final: 0.7755 (p0) REVERT: E 184 MET cc_start: 0.7267 (mmm) cc_final: 0.6688 (mmm) outliers start: 75 outliers final: 61 residues processed: 308 average time/residue: 0.1307 time to fit residues: 65.2833 Evaluate side-chains 310 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 687 CYS Chi-restraints excluded: chain A residue 745 SER Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 765 GLU Chi-restraints excluded: chain A residue 842 ILE Chi-restraints excluded: chain A residue 854 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 139 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 593 TRP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 736 LYS Chi-restraints excluded: chain C residue 759 GLU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 LEU Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 124 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: [37, 34, 150, 13, 200, 115, 104, 44, 64, 149, 211] chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 368 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 125 GLN ** E 215 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.170757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138397 restraints weight = 40045.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139181 restraints weight = 56584.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140668 restraints weight = 42806.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.140957 restraints weight = 28819.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142669 restraints weight = 24570.333| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21620 Z= 0.161 Angle : 0.635 10.518 29440 Z= 0.338 Chirality : 0.045 0.243 3185 Planarity : 0.004 0.040 3587 Dihedral : 15.501 108.466 3385 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.53 % Allowed : 23.94 % Favored : 72.52 % 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: -0.06 (0.17), residues: 2470 helix: 0.95 (0.17), residues: 924 sheet: -0.48 (0.24), residues: 452 loop : -0.62 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 87 TYR 0.038 0.002 TYR A 128 PHE 0.026 0.002 PHE C 647 TRP 0.039 0.002 TRP D 199 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (21620) covalent geometry : angle 0.63497 / 0.34 (29440) hydrogen bonds : bond 0.04086 / 2.73 ( 1023) hydrogen bonds : angle 4.98963 / 3.51 ( 2862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2910.27 seconds wall clock time: 51 minutes 29.67 seconds (3089.67 seconds total)