Starting phenix.real_space_refine on Sat Jul 4 00:43:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.map" model { file = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7whp_32507/07_2026/7whp_32507.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 94 5.16 5 C 10770 2.51 5 N 2948 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 5, 'PTRANS': 47, 'TRANS': 1004} Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 1004} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM A1102 " pdbres="ATP A1103 " Chain breaks: 1 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM B1102 " pdbres="ATP B1103 " Chain breaks: 1 Time building chain proxies: 3.45, per 1000 atoms: 0.20 Number of scatterers: 17038 At special positions: 0 Unit cell: (160.362, 107.262, 204.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 6 15.00 O 3220 8.00 N 2948 7.00 C 10770 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: 1.31 Conformation dependent library (CDL) restraints added in 636.6 milliseconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 27 sheets defined 41.2% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 21 through 26 removed outlier: 4.131A pdb=" N THR A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.511A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 128 through 137 removed outlier: 3.705A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 145 through 158 removed outlier: 4.063A pdb=" N PHE A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.578A pdb=" N ARG A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 223 through 247 removed outlier: 3.526A pdb=" N MET A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.502A pdb=" N TYR A 279 " --> pdb=" O ILE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.381A pdb=" N THR A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 292 through 306 removed outlier: 3.647A pdb=" N ALA A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 330 through 343 removed outlier: 3.946A pdb=" N LEU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.615A pdb=" N MET A 416 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.809A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.607A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 499 Processing helix chain 'A' and resid 529 through 543 removed outlier: 4.260A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 4.342A pdb=" N ASN A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 643 removed outlier: 3.592A pdb=" N MET A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.602A pdb=" N SER A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 788 through 795 Processing helix chain 'A' and resid 804 through 809 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 866 through 871 removed outlier: 3.706A pdb=" N ILE A 869 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER A 870 " --> pdb=" O ALA A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 935 through 951 Processing helix chain 'A' and resid 965 through 972 removed outlier: 4.336A pdb=" N THR A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1011 Processing helix chain 'A' and resid 1020 through 1031 Processing helix chain 'A' and resid 1036 through 1049 removed outlier: 4.372A pdb=" N ALA A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A1044 " --> pdb=" O GLY A1040 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 26 removed outlier: 4.080A pdb=" N THR B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 84 through 97 Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.757A pdb=" N ARG B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 147 through 158 removed outlier: 4.682A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 removed outlier: 3.746A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 223 through 248 removed outlier: 3.700A pdb=" N ASP B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 Processing helix chain 'B' and resid 280 through 285 removed outlier: 4.459A pdb=" N THR B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 removed outlier: 3.593A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.544A pdb=" N ASP B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.797A pdb=" N LEU B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.504A pdb=" N MET B 416 " --> pdb=" O VAL B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.525A pdb=" N ASP B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 443 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 460 Processing helix chain 'B' and resid 461 through 466 Processing helix chain 'B' and resid 466 through 480 removed outlier: 3.655A pdb=" N LYS B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 497 Processing helix chain 'B' and resid 528 through 543 removed outlier: 3.903A pdb=" N MET B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.937A pdb=" N ASN B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 642 Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.631A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 718 removed outlier: 3.810A pdb=" N ARG B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N TYR B 715 " --> pdb=" O MET B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.905A pdb=" N SER B 764 " --> pdb=" O GLN B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 795 Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.502A pdb=" N GLN B 809 " --> pdb=" O TYR B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 812 No H-bonds generated for 'chain 'B' and resid 810 through 812' Processing helix chain 'B' and resid 832 through 852 removed outlier: 3.578A pdb=" N LEU B 851 " --> pdb=" O GLU B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 871 removed outlier: 3.577A pdb=" N ILE B 869 " --> pdb=" O LEU B 866 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER B 870 " --> pdb=" O ALA B 867 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 871 " --> pdb=" O ASP B 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 866 through 871' Processing helix chain 'B' and resid 888 through 895 removed outlier: 3.549A pdb=" N LYS B 894 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 951 Processing helix chain 'B' and resid 965 through 972 removed outlier: 4.146A pdb=" N THR B 969 " --> pdb=" O ALA B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1011 Processing helix chain 'B' and resid 1020 through 1031 removed outlier: 3.623A pdb=" N TYR B1031 " --> pdb=" O ALA B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1049 removed outlier: 4.082A pdb=" N ALA B1041 " --> pdb=" O SER B1037 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP B1044 " --> pdb=" O GLY B1040 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B1048 " --> pdb=" O ASP B1044 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B1049 " --> pdb=" O VAL B1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 3.878A pdb=" N VAL A 251 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.614A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 48 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 165 removed outlier: 6.655A pdb=" N VAL A 205 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.148A pdb=" N LEU A 326 " --> pdb=" O TYR A 353 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE A 355 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N MET A 328 " --> pdb=" O PHE A 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376 removed outlier: 5.279A pdb=" N GLU A 768 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG A 786 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 747 " --> pdb=" O HIS A 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.758A pdb=" N GLY A 817 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 383 through 384 Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB1, first strand: chain 'A' and resid 401 through 406 removed outlier: 6.280A pdb=" N THR A 402 " --> pdb=" O GLU A 825 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG A 827 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N SER A 404 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N MET A 829 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL A 406 " --> pdb=" O MET A 829 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG A1034 " --> pdb=" O ARG A 827 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET A 829 " --> pdb=" O ARG A1034 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 419 through 422 removed outlier: 3.918A pdb=" N THR A 690 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 612 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 614 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 585 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AB4, first strand: chain 'A' and resid 980 through 983 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 8 removed outlier: 7.190A pdb=" N THR B 5 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 253 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE B 7 " --> pdb=" O ALA B 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 38 through 43 Processing sheet with id=AB7, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AB8, first strand: chain 'B' and resid 161 through 165 removed outlier: 6.553A pdb=" N VAL B 205 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 326 through 329 removed outlier: 6.337A pdb=" N LEU B 326 " --> pdb=" O TYR B 353 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE B 355 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 328 " --> pdb=" O PHE B 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 373 through 376 removed outlier: 5.509A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER B 729 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS B 747 " --> pdb=" O SER B 729 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.594A pdb=" N GLY B 817 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC5, first strand: chain 'B' and resid 401 through 406 removed outlier: 7.109A pdb=" N VAL B 406 " --> pdb=" O ARG B 827 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET B 829 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG B1034 " --> pdb=" O ARG B 827 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET B 829 " --> pdb=" O ARG B1034 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 419 through 422 removed outlier: 3.734A pdb=" N ILE B 614 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 559 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY B 586 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 505 through 507 removed outlier: 3.804A pdb=" N VAL B 506 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 897 through 900 removed outlier: 6.391A pdb=" N TYR B 878 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN B 900 " --> pdb=" O TYR B 878 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B 880 " --> pdb=" O GLN B 900 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 857 " --> pdb=" O ASN B 916 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 917 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 980 through 982 662 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5561 1.34 - 1.46: 2638 1.46 - 1.57: 9035 1.57 - 1.69: 10 1.69 - 1.81: 176 Bond restraints: 17420 Sorted by residual: bond pdb=" C2 SAM A1102 " pdb=" N3 SAM A1102 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C2 SAM B1101 " pdb=" N3 SAM B1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" C2 SAM A1101 " pdb=" N3 SAM A1101 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C2 SAM B1102 " pdb=" N3 SAM B1102 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" C8 SAM B1102 " pdb=" N7 SAM B1102 " ideal model delta sigma weight residual 1.298 1.352 -0.054 2.00e-02 2.50e+03 7.21e+00 ... (remaining 17415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 23428 2.27 - 4.54: 258 4.54 - 6.80: 43 6.80 - 9.07: 16 9.07 - 11.34: 1 Bond angle restraints: 23746 Sorted by residual: angle pdb=" C ILE B 519 " pdb=" N PRO B 520 " pdb=" CA PRO B 520 " ideal model delta sigma weight residual 120.52 112.93 7.59 9.90e-01 1.02e+00 5.89e+01 angle pdb=" N GLU A 564 " pdb=" CA GLU A 564 " pdb=" C GLU A 564 " ideal model delta sigma weight residual 110.97 106.77 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N GLU A 566 " pdb=" CA GLU A 566 " pdb=" C GLU A 566 " ideal model delta sigma weight residual 109.42 114.97 -5.55 1.48e+00 4.57e-01 1.41e+01 angle pdb=" N ARG A 112 " pdb=" CA ARG A 112 " pdb=" C ARG A 112 " ideal model delta sigma weight residual 109.23 103.84 5.39 1.55e+00 4.16e-01 1.21e+01 angle pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.86e+00 ... (remaining 23741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 9311 17.24 - 34.49: 945 34.49 - 51.73: 170 51.73 - 68.98: 17 68.98 - 86.22: 19 Dihedral angle restraints: 10462 sinusoidal: 4166 harmonic: 6296 Sorted by residual: dihedral pdb=" CA LEU A 816 " pdb=" C LEU A 816 " pdb=" N GLY A 817 " pdb=" CA GLY A 817 " ideal model delta harmonic sigma weight residual -180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU A 551 " pdb=" C LEU A 551 " pdb=" N MET A 552 " pdb=" CA MET A 552 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 590 " pdb=" CD ARG B 590 " pdb=" NE ARG B 590 " pdb=" CZ ARG B 590 " ideal model delta sinusoidal sigma weight residual -180.00 -135.13 -44.87 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1937 0.042 - 0.083: 568 0.083 - 0.125: 207 0.125 - 0.166: 24 0.166 - 0.208: 6 Chirality restraints: 2742 Sorted by residual: chirality pdb=" C1' SAM A1102 " pdb=" C2' SAM A1102 " pdb=" N9 SAM A1102 " pdb=" O4' SAM A1102 " both_signs ideal model delta sigma weight residual False 2.30 2.51 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' SAM B1102 " pdb=" C1' SAM B1102 " pdb=" C3' SAM B1102 " pdb=" O2' SAM B1102 " both_signs ideal model delta sigma weight residual False -2.76 -2.57 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 2739 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 553 " -0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO A 554 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 554 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 554 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 553 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 554 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 554 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 554 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 74 " -0.047 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO A 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.039 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1712 2.75 - 3.29: 16964 3.29 - 3.82: 27227 3.82 - 4.36: 33062 4.36 - 4.90: 57189 Nonbonded interactions: 136154 Sorted by model distance: nonbonded pdb=" OG SER B 301 " pdb=" OH TYR B 316 " model vdw 2.209 3.040 nonbonded pdb=" O ARG B 324 " pdb=" OH TYR B 349 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR A 856 " pdb=" O ASN A 916 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 842 " pdb=" O SAM A1102 " model vdw 2.226 3.040 nonbonded pdb=" O VAL A 733 " pdb=" OH TYR A 741 " model vdw 2.228 3.040 ... (remaining 136149 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.004 0.066 17420 Z= 0.162 Angle : 0.623 11.338 23746 Z= 0.305 Chirality : 0.045 0.208 2742 Planarity : 0.005 0.094 3022 Dihedral : 14.193 86.221 6386 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.85 (0.18), residues: 2110 helix: -0.24 (0.18), residues: 826 sheet: -0.36 (0.32), residues: 286 loop : -0.78 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 583 TYR 0.024 0.001 TYR A 963 PHE 0.014 0.001 PHE A 456 TRP 0.009 0.001 TRP B 2 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17420) covalent geometry : angle 0.62325 / 0.30 (23746) hydrogen bonds : bond 0.24492 / 16.32 ( 656) hydrogen bonds : angle 7.57732 / 5.50 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.561 Fit side-chains REVERT: A 865 ASN cc_start: 0.7830 (m-40) cc_final: 0.7431 (p0) REVERT: B 36 THR cc_start: 0.7805 (p) cc_final: 0.7532 (p) REVERT: B 286 ASN cc_start: 0.6816 (t0) cc_final: 0.6541 (t0) REVERT: B 855 MET cc_start: 0.7750 (tpp) cc_final: 0.7508 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1224 time to fit residues: 61.8671 Evaluate side-chains 292 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 114 ASN B 761 GLN B 806 HIS B 809 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.138654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128551 restraints weight = 26854.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130215 restraints weight = 17111.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.131420 restraints weight = 12330.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.132233 restraints weight = 9660.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.132783 restraints weight = 8104.071| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17420 Z= 0.134 Angle : 0.547 6.325 23746 Z= 0.289 Chirality : 0.045 0.214 2742 Planarity : 0.005 0.087 3022 Dihedral : 4.726 53.957 2366 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 1.11 % Allowed : 9.18 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.48 (0.18), residues: 2110 helix: 0.30 (0.19), residues: 812 sheet: -0.35 (0.31), residues: 292 loop : -0.74 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.018 0.001 TYR A 963 PHE 0.010 0.001 PHE A 72 TRP 0.007 0.001 TRP B 115 HIS 0.009 0.001 HIS B 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (17420) covalent geometry : angle 0.54710 / 0.29 (23746) hydrogen bonds : bond 0.04713 / 3.17 ( 656) hydrogen bonds : angle 5.01530 / 3.61 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 347 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8024 (t0) cc_final: 0.7734 (t0) REVERT: A 440 ASP cc_start: 0.7345 (m-30) cc_final: 0.7144 (m-30) REVERT: A 765 TYR cc_start: 0.8252 (m-80) cc_final: 0.7962 (m-80) REVERT: A 865 ASN cc_start: 0.7966 (m-40) cc_final: 0.7382 (p0) REVERT: B 286 ASN cc_start: 0.6633 (t0) cc_final: 0.6383 (t0) REVERT: B 712 ILE cc_start: 0.8603 (mm) cc_final: 0.8398 (mt) REVERT: B 868 ASP cc_start: 0.7198 (m-30) cc_final: 0.6710 (m-30) outliers start: 21 outliers final: 16 residues processed: 355 average time/residue: 0.1174 time to fit residues: 62.3799 Evaluate side-chains 325 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 309 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 558 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 166 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 136 optimal weight: 10.0000 chunk 163 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 339 GLN B 299 GLN B 576 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1047 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 = 0.3373 r_free = 0.3373 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.124479 restraints weight = 27357.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.126206 restraints weight = 17681.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.127392 restraints weight = 12863.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.128179 restraints weight = 10204.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.128714 restraints weight = 8628.605| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17420 Z= 0.212 Angle : 0.621 7.097 23746 Z= 0.324 Chirality : 0.047 0.216 2742 Planarity : 0.006 0.087 3022 Dihedral : 5.054 51.959 2366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.96 % Allowed : 14.65 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.61 (0.18), residues: 2110 helix: 0.29 (0.18), residues: 808 sheet: -0.58 (0.32), residues: 270 loop : -0.84 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1034 TYR 0.021 0.002 TYR A1049 PHE 0.012 0.002 PHE A 906 TRP 0.009 0.001 TRP A 184 HIS 0.007 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (17420) covalent geometry : angle 0.62092 / 0.32 (23746) hydrogen bonds : bond 0.05216 / 3.50 ( 656) hydrogen bonds : angle 4.94263 / 3.55 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.4873 (mp0) REVERT: A 339 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7097 (mp10) REVERT: A 824 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7599 (ttt90) REVERT: A 865 ASN cc_start: 0.8042 (m-40) cc_final: 0.7410 (p0) REVERT: B 286 ASN cc_start: 0.6723 (t0) cc_final: 0.6349 (t0) REVERT: B 577 ARG cc_start: 0.7275 (ttt-90) cc_final: 0.7054 (ttt180) outliers start: 37 outliers final: 26 residues processed: 333 average time/residue: 0.1140 time to fit residues: 57.8631 Evaluate side-chains 321 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 558 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 299 GLN B 737 HIS ** B1047 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 = 0.3393 r_free = 0.3393 target = 0.136618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.126173 restraints weight = 26959.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.127887 restraints weight = 17411.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.129078 restraints weight = 12664.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129887 restraints weight = 10037.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.130414 restraints weight = 8461.577| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17420 Z= 0.155 Angle : 0.554 6.302 23746 Z= 0.290 Chirality : 0.045 0.212 2742 Planarity : 0.005 0.086 3022 Dihedral : 4.903 53.287 2366 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 2.39 % Allowed : 16.40 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 2110 helix: 0.47 (0.19), residues: 808 sheet: -0.61 (0.31), residues: 270 loop : -0.83 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 525 TYR 0.018 0.001 TYR A1049 PHE 0.022 0.001 PHE A 154 TRP 0.007 0.001 TRP A 184 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17420) covalent geometry : angle 0.55350 / 0.29 (23746) hydrogen bonds : bond 0.04428 / 2.98 ( 656) hydrogen bonds : angle 4.70118 / 3.37 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8009 (t0) cc_final: 0.7765 (t0) REVERT: A 285 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.4703 (mp0) REVERT: A 765 TYR cc_start: 0.8286 (m-80) cc_final: 0.7904 (m-80) REVERT: A 824 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.7582 (ttt90) REVERT: A 865 ASN cc_start: 0.7973 (m-40) cc_final: 0.7393 (p0) REVERT: A 1055 LEU cc_start: 0.8724 (mt) cc_final: 0.8507 (mt) REVERT: B 286 ASN cc_start: 0.6672 (t0) cc_final: 0.6264 (t0) REVERT: B 577 ARG cc_start: 0.7255 (ttt-90) cc_final: 0.7022 (ttt180) REVERT: B 926 MET cc_start: 0.7950 (mpp) cc_final: 0.7555 (mpp) outliers start: 45 outliers final: 38 residues processed: 343 average time/residue: 0.1203 time to fit residues: 62.6804 Evaluate side-chains 347 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 127 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 197 optimal weight: 0.0670 overall best weight: 6.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 339 GLN B 299 GLN B 576 ASN B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.134631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.124349 restraints weight = 27263.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.126046 restraints weight = 17541.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.127239 restraints weight = 12705.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.128037 restraints weight = 9989.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128567 restraints weight = 8439.380| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17420 Z= 0.215 Angle : 0.617 6.978 23746 Z= 0.321 Chirality : 0.047 0.212 2742 Planarity : 0.005 0.085 3022 Dihedral : 5.182 53.770 2366 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 3.45 % Allowed : 17.94 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.69 (0.18), residues: 2110 helix: 0.30 (0.18), residues: 808 sheet: -0.69 (0.31), residues: 270 loop : -0.94 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1034 TYR 0.020 0.002 TYR A1049 PHE 0.022 0.002 PHE A 154 TRP 0.010 0.002 TRP B 2 HIS 0.014 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 (17420) covalent geometry : angle 0.61669 / 0.32 (23746) hydrogen bonds : bond 0.04909 / 3.29 ( 656) hydrogen bonds : angle 4.85526 / 3.48 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 317 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8024 (t0) cc_final: 0.7803 (t0) REVERT: A 285 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.4863 (mp0) REVERT: A 339 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7181 (mp10) REVERT: A 593 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4967 (pm20) REVERT: A 824 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7583 (ttt90) REVERT: A 1055 LEU cc_start: 0.8750 (mt) cc_final: 0.8537 (mt) REVERT: B 285 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 286 ASN cc_start: 0.6679 (t0) cc_final: 0.6246 (t0) REVERT: B 577 ARG cc_start: 0.7271 (ttt180) cc_final: 0.7040 (ttt180) REVERT: B 737 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7011 (t-90) outliers start: 65 outliers final: 44 residues processed: 356 average time/residue: 0.1146 time to fit residues: 61.8538 Evaluate side-chains 355 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 784 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 876 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 155 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 865 ASN B 299 GLN B 737 HIS ** B1047 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 = 0.3418 r_free = 0.3418 target = 0.138701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.128548 restraints weight = 26919.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.130326 restraints weight = 17555.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.131522 restraints weight = 12667.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.132315 restraints weight = 9725.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.132821 restraints weight = 8152.338| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17420 Z= 0.113 Angle : 0.508 5.948 23746 Z= 0.266 Chirality : 0.044 0.206 2742 Planarity : 0.005 0.085 3022 Dihedral : 4.726 54.580 2366 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 2.60 % Allowed : 19.16 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.40 (0.18), residues: 2110 helix: 0.60 (0.19), residues: 818 sheet: -0.61 (0.31), residues: 270 loop : -0.82 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 525 TYR 0.020 0.001 TYR A 878 PHE 0.025 0.001 PHE A 154 TRP 0.006 0.001 TRP A 184 HIS 0.012 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (17420) covalent geometry : angle 0.50821 / 0.27 (23746) hydrogen bonds : bond 0.03735 / 2.49 ( 656) hydrogen bonds : angle 4.47265 / 3.21 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 339 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8027 (t0) cc_final: 0.7763 (t0) REVERT: A 765 TYR cc_start: 0.8261 (m-80) cc_final: 0.7916 (m-80) REVERT: A 824 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7595 (ttt90) REVERT: A 855 MET cc_start: 0.7528 (mmt) cc_final: 0.7220 (mmt) REVERT: A 865 ASN cc_start: 0.8082 (m-40) cc_final: 0.7367 (p0) REVERT: A 1055 LEU cc_start: 0.8761 (mt) cc_final: 0.8501 (mt) REVERT: B 286 ASN cc_start: 0.6593 (t0) cc_final: 0.6134 (t0) outliers start: 49 outliers final: 31 residues processed: 370 average time/residue: 0.1144 time to fit residues: 64.2688 Evaluate side-chains 350 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 319 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 885 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 101 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 299 GLN B 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.137072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.126866 restraints weight = 27193.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128564 restraints weight = 17623.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.129731 restraints weight = 12784.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.130485 restraints weight = 10161.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.131005 restraints weight = 8611.512| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17420 Z= 0.138 Angle : 0.542 7.210 23746 Z= 0.281 Chirality : 0.045 0.205 2742 Planarity : 0.005 0.082 3022 Dihedral : 4.805 53.230 2366 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 2.87 % Allowed : 19.96 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2110 helix: 0.66 (0.19), residues: 810 sheet: -0.64 (0.31), residues: 270 loop : -0.82 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.018 0.001 TYR A 878 PHE 0.009 0.001 PHE A 72 TRP 0.007 0.001 TRP A 184 HIS 0.012 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (17420) covalent geometry : angle 0.54240 / 0.28 (23746) hydrogen bonds : bond 0.03977 / 2.66 ( 656) hydrogen bonds : angle 4.50779 / 3.23 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 329 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8361 (mm) cc_final: 0.8144 (mm) REVERT: A 238 ASP cc_start: 0.8015 (t0) cc_final: 0.7774 (t0) REVERT: A 285 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.4928 (mp0) REVERT: A 578 ASN cc_start: 0.6790 (t0) cc_final: 0.6528 (t0) REVERT: A 824 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7590 (ttt90) REVERT: A 855 MET cc_start: 0.7567 (mmt) cc_final: 0.7245 (mmt) REVERT: A 865 ASN cc_start: 0.8100 (m-40) cc_final: 0.7417 (p0) REVERT: B 286 ASN cc_start: 0.6630 (t0) cc_final: 0.6208 (t0) REVERT: B 739 ASN cc_start: 0.6346 (m-40) cc_final: 0.5686 (t0) outliers start: 54 outliers final: 44 residues processed: 359 average time/residue: 0.1140 time to fit residues: 62.2891 Evaluate side-chains 364 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 937 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 51 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 chunk 184 optimal weight: 9.9990 chunk 177 optimal weight: 0.0870 chunk 182 optimal weight: 6.9990 chunk 167 optimal weight: 20.0000 chunk 7 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 overall best weight: 1.2560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 299 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.140871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.130523 restraints weight = 26755.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.132492 restraints weight = 18489.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.133683 restraints weight = 12675.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.134231 restraints weight = 9848.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.135119 restraints weight = 8418.696| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 17420 Z= 0.097 Angle : 0.495 9.208 23746 Z= 0.257 Chirality : 0.043 0.202 2742 Planarity : 0.004 0.081 3022 Dihedral : 4.528 53.993 2366 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 2.34 % Allowed : 20.91 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.18 (0.18), residues: 2110 helix: 0.84 (0.19), residues: 812 sheet: -0.56 (0.31), residues: 290 loop : -0.71 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 52 TYR 0.016 0.001 TYR A 878 PHE 0.010 0.001 PHE A 283 TRP 0.006 0.001 TRP A 772 HIS 0.010 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (17420) covalent geometry : angle 0.49482 / 0.26 (23746) hydrogen bonds : bond 0.03325 / 2.22 ( 656) hydrogen bonds : angle 4.31314 / 3.08 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8385 (mm) cc_final: 0.8171 (mm) REVERT: A 238 ASP cc_start: 0.7984 (t0) cc_final: 0.7733 (t0) REVERT: A 285 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.4857 (mp0) REVERT: A 578 ASN cc_start: 0.6805 (t0) cc_final: 0.6554 (t0) REVERT: A 824 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7590 (ttt90) REVERT: A 829 MET cc_start: 0.8077 (ptt) cc_final: 0.7735 (ptt) REVERT: A 855 MET cc_start: 0.7630 (mmt) cc_final: 0.7313 (mmt) REVERT: A 865 ASN cc_start: 0.8105 (m-40) cc_final: 0.7355 (p0) REVERT: A 898 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7693 (tt0) REVERT: B 286 ASN cc_start: 0.6703 (t0) cc_final: 0.6225 (t0) REVERT: B 474 TYR cc_start: 0.8180 (t80) cc_final: 0.7961 (t80) REVERT: B 737 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7085 (t-90) REVERT: B 739 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5248 (t0) outliers start: 44 outliers final: 29 residues processed: 375 average time/residue: 0.1205 time to fit residues: 67.9895 Evaluate side-chains 349 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 317 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 889 THR Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 937 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 90 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 chunk 121 optimal weight: 9.9990 chunk 13 optimal weight: 0.0570 chunk 178 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 148 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 214 ASN B 270 GLN B 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.139053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128763 restraints weight = 26836.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.130710 restraints weight = 18057.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.131838 restraints weight = 12575.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.132471 restraints weight = 9786.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.133151 restraints weight = 8399.919| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17420 Z= 0.124 Angle : 0.537 12.838 23746 Z= 0.275 Chirality : 0.044 0.199 2742 Planarity : 0.005 0.078 3022 Dihedral : 4.599 50.804 2366 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 2.28 % Allowed : 21.34 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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 (0.18), residues: 2110 helix: 0.80 (0.19), residues: 812 sheet: -0.59 (0.32), residues: 270 loop : -0.74 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 981 TYR 0.020 0.001 TYR A 320 PHE 0.029 0.001 PHE A 154 TRP 0.007 0.001 TRP A 184 HIS 0.012 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (17420) covalent geometry : angle 0.53684 / 0.27 (23746) hydrogen bonds : bond 0.03707 / 2.47 ( 656) hydrogen bonds : angle 4.37605 / 3.13 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 163 ASP cc_start: 0.5641 (p0) cc_final: 0.5228 (p0) REVERT: A 164 ILE cc_start: 0.8358 (mm) cc_final: 0.8115 (mm) REVERT: A 238 ASP cc_start: 0.7981 (t0) cc_final: 0.7733 (t0) REVERT: A 285 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5034 (mp0) REVERT: A 578 ASN cc_start: 0.6856 (t0) cc_final: 0.6611 (t0) REVERT: A 824 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7585 (ttt90) REVERT: A 829 MET cc_start: 0.8104 (ptt) cc_final: 0.7763 (ptt) REVERT: A 855 MET cc_start: 0.7632 (mmt) cc_final: 0.7319 (mmt) REVERT: A 865 ASN cc_start: 0.8077 (m-40) cc_final: 0.7411 (p0) REVERT: A 898 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7728 (tt0) REVERT: B 286 ASN cc_start: 0.6673 (t0) cc_final: 0.6206 (t0) REVERT: B 474 TYR cc_start: 0.8185 (t80) cc_final: 0.7928 (t80) REVERT: B 626 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5678 (mt-10) outliers start: 43 outliers final: 35 residues processed: 346 average time/residue: 0.1222 time to fit residues: 64.7202 Evaluate side-chains 345 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 308 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 866 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 196 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS B 299 GLN B 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.136282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125934 restraints weight = 26932.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.127567 restraints weight = 17445.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.128690 restraints weight = 12844.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.129487 restraints weight = 10243.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.129948 restraints weight = 8694.216| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17420 Z= 0.172 Angle : 0.591 12.706 23746 Z= 0.304 Chirality : 0.046 0.201 2742 Planarity : 0.005 0.075 3022 Dihedral : 4.895 50.318 2366 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 2.55 % Allowed : 21.28 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.18), residues: 2110 helix: 0.60 (0.19), residues: 810 sheet: -0.63 (0.32), residues: 270 loop : -0.85 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 271 TYR 0.019 0.002 TYR A 536 PHE 0.010 0.001 PHE A 283 TRP 0.009 0.001 TRP B 2 HIS 0.013 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (17420) covalent geometry : angle 0.59080 / 0.30 (23746) hydrogen bonds : bond 0.04290 / 2.86 ( 656) hydrogen bonds : angle 4.57554 / 3.28 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.540 Fit side-chains REVERT: A 164 ILE cc_start: 0.8373 (mm) cc_final: 0.8151 (mm) REVERT: A 238 ASP cc_start: 0.8005 (t0) cc_final: 0.7747 (t0) REVERT: A 285 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.4654 (mp0) REVERT: A 578 ASN cc_start: 0.6897 (t0) cc_final: 0.6658 (t0) REVERT: A 824 ARG cc_start: 0.7815 (tpp-160) cc_final: 0.7598 (ttt90) REVERT: A 829 MET cc_start: 0.8185 (ptt) cc_final: 0.7811 (ptt) REVERT: A 855 MET cc_start: 0.7609 (mmt) cc_final: 0.7241 (mmt) REVERT: A 865 ASN cc_start: 0.8135 (m-40) cc_final: 0.7398 (p0) REVERT: A 926 MET cc_start: 0.8161 (mtm) cc_final: 0.7874 (mtm) REVERT: A 1055 LEU cc_start: 0.8710 (mt) cc_final: 0.8494 (mt) REVERT: B 286 ASN cc_start: 0.6705 (t0) cc_final: 0.6219 (t0) REVERT: B 626 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5875 (mt-10) outliers start: 48 outliers final: 42 residues processed: 336 average time/residue: 0.1297 time to fit residues: 66.2271 Evaluate side-chains 340 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 296 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 891 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 690 THR Chi-restraints excluded: chain B residue 737 HIS Chi-restraints excluded: chain B residue 816 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 876 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 79 optimal weight: 0.6980 chunk 188 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 HIS A 910 ASN B 299 GLN B 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.140151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.129796 restraints weight = 26848.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.131780 restraints weight = 18334.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.132926 restraints weight = 12668.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.133608 restraints weight = 9888.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.134372 restraints weight = 8410.571| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17420 Z= 0.107 Angle : 0.521 13.306 23746 Z= 0.268 Chirality : 0.044 0.199 2742 Planarity : 0.005 0.074 3022 Dihedral : 4.579 51.231 2366 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 21.55 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % 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: -0.24 (0.18), residues: 2110 helix: 0.77 (0.19), residues: 812 sheet: -0.55 (0.31), residues: 290 loop : -0.75 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 981 TYR 0.018 0.001 TYR A 320 PHE 0.033 0.001 PHE A 154 TRP 0.006 0.001 TRP A 772 HIS 0.011 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17420) covalent geometry : angle 0.52078 / 0.27 (23746) hydrogen bonds : bond 0.03487 / 2.32 ( 656) hydrogen bonds : angle 4.35032 / 3.11 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.07 seconds wall clock time: 48 minutes 33.22 seconds (2913.22 seconds total)