Starting phenix.real_space_refine on Sun Jun 15 10:57:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whp_32507/06_2025/7whp_32507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whp_32507/06_2025/7whp_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_32507/06_2025/7whp_32507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whp_32507/06_2025/7whp_32507.map" model { file = "/net/cci-nas-00/data/ceres_data/7whp_32507/06_2025/7whp_32507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whp_32507/06_2025/7whp_32507.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.39, per 1000 atoms: 0.67 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: 4.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.55 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: 6.74 Time building geometry restraints manager: 5.34 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 - 17.67: 9405 17.67 - 35.33: 989 35.33 - 53.00: 210 53.00 - 70.67: 26 70.67 - 88.34: 22 Dihedral angle restraints: 10652 sinusoidal: 4356 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 10649 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: 0.08 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.130 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 15.130 88.336 6576 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP B 2 HIS 0.005 0.001 HIS B 217 PHE 0.014 0.001 PHE A 456 TYR 0.024 0.001 TYR A 963 ARG 0.008 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.24492 ( 656) hydrogen bonds : angle 7.57732 ( 1887) covalent geometry : bond 0.00365 (17420) covalent geometry : angle 0.62325 (23746) *********************** 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 : 2.052 Fit side-chains revert: symmetry clash 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: 0.6544 (t0) REVERT: B 855 MET cc_start: 0.7750 (tpp) cc_final: 0.7507 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3250 time to fit residues: 162.3672 Evaluate side-chains 293 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.1980 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 HIS B 809 GLN ** 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 = 0.3412 r_free = 0.3412 target = 0.138151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.127949 restraints weight = 26950.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129676 restraints weight = 17230.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.130862 restraints weight = 12445.451| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1125 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= 0.140 Angle : 0.553 6.383 23746 Z= 0.292 Chirality : 0.045 0.214 2742 Planarity : 0.005 0.087 3022 Dihedral : 8.522 88.603 2556 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 1.06 % Allowed : 8.65 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2110 helix: 0.31 (0.19), residues: 812 sheet: -0.32 (0.31), residues: 292 loop : -0.73 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.009 0.001 HIS B 806 PHE 0.010 0.001 PHE A 72 TYR 0.018 0.001 TYR A 963 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 656) hydrogen bonds : angle 5.09679 ( 1887) covalent geometry : bond 0.00326 (17420) covalent geometry : angle 0.55303 (23746) *********************** 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 358 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 338 time to evaluate : 2.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8030 (t0) cc_final: 0.7743 (t0) REVERT: A 765 TYR cc_start: 0.8256 (m-80) cc_final: 0.7941 (m-80) REVERT: A 865 ASN cc_start: 0.8016 (m-40) cc_final: 0.7424 (p0) REVERT: B 286 ASN cc_start: 0.6595 (t0) cc_final: 0.6328 (t0) REVERT: B 712 ILE cc_start: 0.8622 (mm) cc_final: 0.8404 (mt) REVERT: B 868 ASP cc_start: 0.7271 (m-30) cc_final: 0.6803 (m-30) outliers start: 20 outliers final: 15 residues processed: 346 average time/residue: 0.3755 time to fit residues: 193.2919 Evaluate side-chains 317 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 302 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 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 6 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 50 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 576 ASN B 618 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** 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 = 0.3387 r_free = 0.3387 target = 0.136102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.125731 restraints weight = 27027.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.127431 restraints weight = 17454.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128618 restraints weight = 12734.009| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17420 Z= 0.183 Angle : 0.588 6.728 23746 Z= 0.308 Chirality : 0.046 0.212 2742 Planarity : 0.005 0.087 3022 Dihedral : 8.199 80.324 2556 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 1.75 % Allowed : 14.01 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2110 helix: 0.39 (0.19), residues: 808 sheet: -0.55 (0.32), residues: 270 loop : -0.80 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.006 0.001 HIS A 217 PHE 0.012 0.001 PHE A 72 TYR 0.019 0.002 TYR A1049 ARG 0.004 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 656) hydrogen bonds : angle 4.85608 ( 1887) covalent geometry : bond 0.00443 (17420) covalent geometry : angle 0.58823 (23746) *********************** 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: 33 poor density : 318 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8030 (t0) cc_final: 0.7787 (t0) REVERT: A 285 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.4841 (mp0) REVERT: A 716 MET cc_start: 0.8474 (mmt) cc_final: 0.8256 (mmt) REVERT: A 765 TYR cc_start: 0.8299 (m-80) cc_final: 0.7939 (m-80) REVERT: A 824 ARG cc_start: 0.7866 (tpp-160) cc_final: 0.7581 (ttt90) REVERT: A 865 ASN cc_start: 0.8085 (m-40) cc_final: 0.7430 (p0) REVERT: B 286 ASN cc_start: 0.6683 (t0) cc_final: 0.6316 (t0) REVERT: B 577 ARG cc_start: 0.7302 (ttt-90) cc_final: 0.7078 (ttt180) outliers start: 33 outliers final: 25 residues processed: 335 average time/residue: 0.3437 time to fit residues: 174.0556 Evaluate side-chains 329 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 519 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 59 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 16 optimal weight: 0.0040 overall best weight: 4.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 737 HIS B 761 GLN ** 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 = 0.3401 r_free = 0.3401 target = 0.137235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.126898 restraints weight = 26956.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.128548 restraints weight = 17460.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129712 restraints weight = 12728.477| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1569 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= 0.149 Angle : 0.542 6.241 23746 Z= 0.284 Chirality : 0.045 0.210 2742 Planarity : 0.005 0.086 3022 Dihedral : 7.937 72.652 2556 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.03 % Favored : 96.92 % Rotamer: Outliers : 2.07 % Allowed : 16.35 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2110 helix: 0.54 (0.19), residues: 808 sheet: -0.49 (0.30), residues: 292 loop : -0.80 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.013 0.001 HIS A 3 PHE 0.011 0.001 PHE A 72 TYR 0.018 0.001 TYR A1049 ARG 0.004 0.000 ARG B 525 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 656) hydrogen bonds : angle 4.65172 ( 1887) covalent geometry : bond 0.00358 (17420) covalent geometry : angle 0.54197 (23746) *********************** 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 367 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 328 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7978 (t0) cc_final: 0.7709 (t0) REVERT: A 285 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.4839 (mp0) REVERT: A 765 TYR cc_start: 0.8262 (m-80) cc_final: 0.7910 (m-80) REVERT: A 824 ARG cc_start: 0.7854 (tpp-160) cc_final: 0.7595 (ttt90) REVERT: A 865 ASN cc_start: 0.8031 (m-40) cc_final: 0.7403 (p0) REVERT: B 116 MET cc_start: 0.8756 (ttp) cc_final: 0.8528 (ttp) REVERT: B 286 ASN cc_start: 0.6573 (t0) cc_final: 0.6172 (t0) outliers start: 39 outliers final: 30 residues processed: 347 average time/residue: 0.2942 time to fit residues: 152.8426 Evaluate side-chains 341 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 310 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 340 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 519 ILE 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 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 558 ILE Chi-restraints excluded: chain B residue 737 HIS 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 52 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 137 optimal weight: 0.0670 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 576 ASN B 618 ASN ** 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 = 0.3440 r_free = 0.3440 target = 0.140561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.130129 restraints weight = 27161.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.131875 restraints weight = 17452.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.133069 restraints weight = 12667.082| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17420 Z= 0.100 Angle : 0.489 6.010 23746 Z= 0.256 Chirality : 0.043 0.207 2742 Planarity : 0.005 0.085 3022 Dihedral : 7.351 67.332 2556 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 2.12 % Allowed : 17.30 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2110 helix: 0.78 (0.19), residues: 818 sheet: -0.49 (0.31), residues: 290 loop : -0.70 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 772 HIS 0.015 0.001 HIS B 737 PHE 0.009 0.001 PHE A 283 TYR 0.015 0.001 TYR A 536 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 656) hydrogen bonds : angle 4.36380 ( 1887) covalent geometry : bond 0.00230 (17420) covalent geometry : angle 0.48903 (23746) *********************** 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 380 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 340 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8001 (t0) cc_final: 0.7742 (t0) REVERT: A 765 TYR cc_start: 0.8223 (m-80) cc_final: 0.7903 (m-80) REVERT: A 824 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7577 (ttt90) REVERT: A 865 ASN cc_start: 0.8040 (m-40) cc_final: 0.7420 (p0) REVERT: B 116 MET cc_start: 0.8734 (ttp) cc_final: 0.8217 (ttm) REVERT: B 286 ASN cc_start: 0.6626 (t0) cc_final: 0.6210 (t0) REVERT: B 304 TYR cc_start: 0.7096 (m-80) cc_final: 0.6869 (m-80) REVERT: B 331 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7234 (mtp180) REVERT: B 737 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: B 926 MET cc_start: 0.8019 (mpp) cc_final: 0.7619 (mpp) outliers start: 40 outliers final: 21 residues processed: 362 average time/residue: 0.3150 time to fit residues: 170.3426 Evaluate side-chains 335 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 313 time to evaluate : 1.891 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 788 ASP 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 556 THR Chi-restraints excluded: chain B residue 558 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 737 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 92 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 214 ASN B 299 GLN B 576 ASN B 737 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.139709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.129335 restraints weight = 27000.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.131278 restraints weight = 18196.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.132522 restraints weight = 12552.007| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17420 Z= 0.114 Angle : 0.505 6.238 23746 Z= 0.263 Chirality : 0.044 0.205 2742 Planarity : 0.005 0.084 3022 Dihedral : 7.125 65.535 2556 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 2.49 % Allowed : 18.37 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2110 helix: 0.87 (0.19), residues: 812 sheet: -0.54 (0.32), residues: 270 loop : -0.69 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.011 0.001 HIS A 3 PHE 0.009 0.001 PHE B 796 TYR 0.017 0.001 TYR A 536 ARG 0.005 0.000 ARG B 981 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 656) hydrogen bonds : angle 4.35476 ( 1887) covalent geometry : bond 0.00269 (17420) covalent geometry : angle 0.50498 (23746) *********************** 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 372 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.5652 (p0) cc_final: 0.5290 (p0) REVERT: A 164 ILE cc_start: 0.8282 (mm) cc_final: 0.8046 (mm) REVERT: A 238 ASP cc_start: 0.7975 (t0) cc_final: 0.7729 (t0) REVERT: A 285 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.5029 (mp0) REVERT: A 765 TYR cc_start: 0.8223 (m-80) cc_final: 0.7875 (m-80) REVERT: A 824 ARG cc_start: 0.7820 (tpp-160) cc_final: 0.7582 (ttt90) REVERT: A 865 ASN cc_start: 0.7994 (m-40) cc_final: 0.7394 (p0) REVERT: B 116 MET cc_start: 0.8746 (ttp) cc_final: 0.7988 (ttp) REVERT: B 286 ASN cc_start: 0.6660 (t0) cc_final: 0.6227 (t0) outliers start: 47 outliers final: 31 residues processed: 352 average time/residue: 0.2856 time to fit residues: 151.6904 Evaluate side-chains 342 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 124 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 177 THR 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 363 ASN 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 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 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 390 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 866 LEU Chi-restraints excluded: chain B residue 868 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 192 optimal weight: 0.1980 chunk 30 optimal weight: 20.0000 chunk 15 optimal weight: 0.0980 chunk 177 optimal weight: 0.0370 chunk 70 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 576 ASN B 782 ASN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.144783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.134671 restraints weight = 26619.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.136680 restraints weight = 17714.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.137789 restraints weight = 12188.355| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2305 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= 0.090 Angle : 0.472 7.268 23746 Z= 0.245 Chirality : 0.042 0.206 2742 Planarity : 0.004 0.083 3022 Dihedral : 6.351 64.302 2556 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 19.85 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2110 helix: 1.05 (0.19), residues: 818 sheet: -0.42 (0.31), residues: 290 loop : -0.57 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 772 HIS 0.009 0.001 HIS A 3 PHE 0.010 0.001 PHE B 672 TYR 0.022 0.001 TYR A 78 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 656) hydrogen bonds : angle 4.09283 ( 1887) covalent geometry : bond 0.00200 (17420) covalent geometry : angle 0.47206 (23746) *********************** 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 376 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 349 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 ILE cc_start: 0.8358 (mm) cc_final: 0.8133 (mm) REVERT: A 417 TYR cc_start: 0.8988 (m-80) cc_final: 0.8705 (m-80) REVERT: A 578 ASN cc_start: 0.6890 (t0) cc_final: 0.6619 (t0) REVERT: A 824 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7428 (ttt90) REVERT: A 865 ASN cc_start: 0.7929 (m-40) cc_final: 0.7292 (p0) REVERT: A 898 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7748 (tt0) REVERT: B 116 MET cc_start: 0.8715 (ttp) cc_final: 0.8000 (ttp) REVERT: B 285 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6838 (mt-10) REVERT: B 286 ASN cc_start: 0.6583 (t0) cc_final: 0.6180 (t0) REVERT: B 395 GLN cc_start: 0.6965 (pm20) cc_final: 0.6410 (pt0) outliers start: 27 outliers final: 11 residues processed: 363 average time/residue: 0.3036 time to fit residues: 164.5967 Evaluate side-chains 325 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 314 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain B residue 41 THR 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 937 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 88 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 83 optimal weight: 0.0030 chunk 149 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 GLN B 299 GLN B 576 ASN B 737 HIS B 782 ASN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.135939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.125540 restraints weight = 27052.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.127211 restraints weight = 17340.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.128371 restraints weight = 12600.239| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17420 Z= 0.201 Angle : 0.612 10.879 23746 Z= 0.315 Chirality : 0.047 0.215 2742 Planarity : 0.005 0.079 3022 Dihedral : 6.953 65.369 2556 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 19.53 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2110 helix: 0.72 (0.19), residues: 810 sheet: -0.53 (0.32), residues: 270 loop : -0.76 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 2 HIS 0.012 0.001 HIS A 3 PHE 0.012 0.002 PHE A 906 TYR 0.025 0.002 TYR A 78 ARG 0.005 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 656) hydrogen bonds : angle 4.56722 ( 1887) covalent geometry : bond 0.00489 (17420) covalent geometry : angle 0.61154 (23746) *********************** 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 363 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 2.149 Fit side-chains revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.4783 (mp0) REVERT: A 578 ASN cc_start: 0.6967 (t0) cc_final: 0.6689 (t0) REVERT: A 824 ARG cc_start: 0.7841 (tpp-160) cc_final: 0.7363 (ttt180) REVERT: A 865 ASN cc_start: 0.7925 (m-40) cc_final: 0.7381 (p0) REVERT: A 926 MET cc_start: 0.8019 (mtm) cc_final: 0.7813 (mtm) REVERT: B 116 MET cc_start: 0.8764 (ttp) cc_final: 0.8024 (ttp) REVERT: B 270 GLN cc_start: 0.7849 (mm-40) cc_final: 0.7505 (mm-40) REVERT: B 285 GLU cc_start: 0.7269 (mt-10) cc_final: 0.7026 (mt-10) REVERT: B 286 ASN cc_start: 0.6614 (t0) cc_final: 0.6186 (t0) REVERT: B 317 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7617 (mmt90) outliers start: 50 outliers final: 35 residues processed: 341 average time/residue: 0.3128 time to fit residues: 159.9666 Evaluate side-chains 340 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 304 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 177 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 358 ILE Chi-restraints excluded: chain A residue 363 ASN 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 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 1005 LEU 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 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 576 ASN 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 924 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 135 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 299 GLN B 576 ASN 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 = 0.3413 r_free = 0.3413 target = 0.138234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.127956 restraints weight = 27122.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129628 restraints weight = 17442.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.130743 restraints weight = 12710.498| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2111 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= 0.126 Angle : 0.549 12.837 23746 Z= 0.281 Chirality : 0.044 0.200 2742 Planarity : 0.005 0.079 3022 Dihedral : 6.697 64.409 2556 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 2.23 % Allowed : 20.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2110 helix: 0.76 (0.19), residues: 814 sheet: -0.52 (0.32), residues: 270 loop : -0.72 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 95 HIS 0.011 0.001 HIS A 3 PHE 0.028 0.001 PHE A 154 TYR 0.022 0.001 TYR A 78 ARG 0.006 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 656) hydrogen bonds : angle 4.41496 ( 1887) covalent geometry : bond 0.00303 (17420) covalent geometry : angle 0.54868 (23746) *********************** 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 360 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5004 (mp0) REVERT: A 416 MET cc_start: 0.8175 (ttp) cc_final: 0.7942 (ttp) REVERT: A 578 ASN cc_start: 0.6790 (t0) cc_final: 0.6540 (t0) REVERT: A 589 ASP cc_start: 0.6969 (t0) cc_final: 0.6621 (t0) REVERT: A 599 ARG cc_start: 0.8110 (tpt170) cc_final: 0.7820 (tpt170) REVERT: A 824 ARG cc_start: 0.7824 (tpp-160) cc_final: 0.7601 (ttt90) REVERT: A 865 ASN cc_start: 0.7994 (m-40) cc_final: 0.7399 (p0) REVERT: B 116 MET cc_start: 0.8741 (ttp) cc_final: 0.8238 (ttm) REVERT: B 270 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7399 (mm110) REVERT: B 285 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 286 ASN cc_start: 0.6632 (t0) cc_final: 0.6171 (t0) REVERT: B 317 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7643 (mmt90) REVERT: B 395 GLN cc_start: 0.6843 (pm20) cc_final: 0.6385 (pt0) outliers start: 42 outliers final: 35 residues processed: 345 average time/residue: 0.2980 time to fit residues: 155.1411 Evaluate side-chains 344 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 308 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 THR 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 363 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 514 LEU 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 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 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 584 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 924 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 55 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN B 576 ASN B 737 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.134155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.123815 restraints weight = 27223.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.125526 restraints weight = 17625.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.126694 restraints weight = 12793.517| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17420 Z= 0.243 Angle : 0.675 11.976 23746 Z= 0.346 Chirality : 0.049 0.237 2742 Planarity : 0.006 0.075 3022 Dihedral : 7.358 69.205 2556 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 2.60 % Allowed : 20.12 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2110 helix: 0.36 (0.19), residues: 810 sheet: -0.63 (0.32), residues: 270 loop : -0.91 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 2 HIS 0.014 0.002 HIS B 737 PHE 0.017 0.002 PHE A 283 TYR 0.020 0.002 TYR A 78 ARG 0.005 0.001 ARG B 970 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 656) hydrogen bonds : angle 4.77809 ( 1887) covalent geometry : bond 0.00591 (17420) covalent geometry : angle 0.67489 (23746) ********************** 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 354 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 305 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.4747 (mp0) REVERT: A 578 ASN cc_start: 0.6828 (t0) cc_final: 0.6560 (t0) REVERT: A 593 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.5053 (pm20) REVERT: B 270 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7505 (mm-40) REVERT: B 285 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 626 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6148 (mt-10) outliers start: 49 outliers final: 38 residues processed: 336 average time/residue: 0.3007 time to fit residues: 151.2844 Evaluate side-chains 338 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 THR 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 358 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 552 MET 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 1005 LEU 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 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 576 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 165 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 299 GLN B 576 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.134368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.124121 restraints weight = 27267.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.125795 restraints weight = 17463.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.126987 restraints weight = 12614.336| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17420 Z= 0.216 Angle : 0.871 59.161 23746 Z= 0.503 Chirality : 0.049 0.558 2742 Planarity : 0.006 0.128 3022 Dihedral : 7.384 69.194 2556 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.55 % Allowed : 20.33 % Favored : 77.12 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2110 helix: 0.36 (0.19), residues: 810 sheet: -0.64 (0.32), residues: 270 loop : -0.91 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 2 HIS 0.162 0.003 HIS B 737 PHE 0.017 0.002 PHE A 283 TYR 0.018 0.002 TYR B 878 ARG 0.006 0.001 ARG B 292 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 656) hydrogen bonds : angle 4.78592 ( 1887) covalent geometry : bond 0.00507 (17420) covalent geometry : angle 0.87067 (23746) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6553.46 seconds wall clock time: 115 minutes 0.32 seconds (6900.32 seconds total)