Starting phenix.real_space_refine on Sun Aug 24 05:16:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7whp_32507/08_2025/7whp_32507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7whp_32507/08_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_32507/08_2025/7whp_32507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7whp_32507/08_2025/7whp_32507.map" model { file = "/net/cci-nas-00/data/ceres_data/7whp_32507/08_2025/7whp_32507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7whp_32507/08_2025/7whp_32507.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 94 5.16 5 C 10770 2.51 5 N 2948 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 5, 'PTRANS': 47, 'TRANS': 1004} Chain: "B" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8434 Classifications: {'peptide': 1057} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 1004} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM A1102 " pdbres="ATP A1103 " Chain breaks: 1 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'ATP': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="SAM B1102 " pdbres="ATP B1103 " Chain breaks: 1 Time building chain proxies: 3.65, per 1000 atoms: 0.21 Number of scatterers: 17038 At special positions: 0 Unit cell: (160.362, 107.262, 204.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 94 16.00 P 6 15.00 O 3220 8.00 N 2948 7.00 C 10770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 695.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 27 sheets defined 41.2% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 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: 2.84 Time building geometry restraints manager: 1.66 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.580 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.18), residues: 2110 helix: -0.24 (0.18), residues: 826 sheet: -0.36 (0.32), residues: 286 loop : -0.78 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 583 TYR 0.024 0.001 TYR A 963 PHE 0.014 0.001 PHE A 456 TRP 0.009 0.001 TRP B 2 HIS 0.005 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00365 (17420) covalent geometry : angle 0.62325 (23746) hydrogen bonds : bond 0.24492 ( 656) hydrogen bonds : angle 7.57732 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.410 Fit side-chains REVERT: A 865 ASN cc_start: 0.7830 (m-40) cc_final: 0.7431 (p0) REVERT: B 36 THR cc_start: 0.7805 (p) cc_final: 0.7532 (p) REVERT: B 286 ASN cc_start: 0.6816 (t0) cc_final: 0.6541 (t0) REVERT: B 855 MET cc_start: 0.7750 (tpp) cc_final: 0.7508 (tpp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1354 time to fit residues: 67.4626 Evaluate side-chains 292 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS B 114 ASN B 761 GLN B 806 HIS B 809 GLN ** B1047 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.138614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.128407 restraints weight = 26838.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.130117 restraints weight = 17205.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.131318 restraints weight = 12417.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.132118 restraints weight = 9785.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.132670 restraints weight = 8201.893| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17420 Z= 0.135 Angle : 0.549 6.312 23746 Z= 0.290 Chirality : 0.045 0.214 2742 Planarity : 0.005 0.087 3022 Dihedral : 8.442 88.763 2556 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 1.06 % Allowed : 9.08 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.18), residues: 2110 helix: 0.32 (0.19), residues: 812 sheet: -0.34 (0.31), residues: 292 loop : -0.75 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 122 TYR 0.018 0.001 TYR A 963 PHE 0.010 0.001 PHE A 72 TRP 0.007 0.001 TRP B 115 HIS 0.009 0.001 HIS B 806 Details of bonding type rmsd covalent geometry : bond 0.00314 (17420) covalent geometry : angle 0.54870 (23746) hydrogen bonds : bond 0.04789 ( 656) hydrogen bonds : angle 5.03309 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 346 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8033 (t0) cc_final: 0.7743 (t0) REVERT: A 440 ASP cc_start: 0.7352 (m-30) cc_final: 0.7146 (m-30) REVERT: A 765 TYR cc_start: 0.8260 (m-80) cc_final: 0.7971 (m-80) REVERT: A 865 ASN cc_start: 0.7961 (m-40) cc_final: 0.7381 (p0) REVERT: B 286 ASN cc_start: 0.6622 (t0) cc_final: 0.6349 (t0) REVERT: B 712 ILE cc_start: 0.8605 (mm) cc_final: 0.8402 (mt) REVERT: B 868 ASP cc_start: 0.7226 (m-30) cc_final: 0.6750 (m-30) outliers start: 20 outliers final: 15 residues processed: 353 average time/residue: 0.1268 time to fit residues: 66.7326 Evaluate side-chains 321 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 306 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 166 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3397 r_free = 0.3397 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.126526 restraints weight = 27244.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.128248 restraints weight = 17619.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.129429 restraints weight = 12806.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.130247 restraints weight = 10120.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.130779 restraints weight = 8531.065| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1415 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= 0.167 Angle : 0.568 6.461 23746 Z= 0.297 Chirality : 0.046 0.213 2742 Planarity : 0.005 0.087 3022 Dihedral : 8.123 81.297 2556 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.96 % Allowed : 13.69 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.18), residues: 2110 helix: 0.45 (0.19), residues: 810 sheet: -0.41 (0.31), residues: 292 loop : -0.79 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1034 TYR 0.018 0.001 TYR A1049 PHE 0.011 0.001 PHE A 72 TRP 0.007 0.001 TRP A 184 HIS 0.006 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00404 (17420) covalent geometry : angle 0.56841 (23746) hydrogen bonds : bond 0.04755 ( 656) hydrogen bonds : angle 4.80697 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4220 Ramachandran restraints generated. 2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 238 ASP cc_start: 0.8021 (t0) cc_final: 0.7773 (t0) REVERT: A 285 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.4786 (mp0) REVERT: A 716 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8131 (mmt) REVERT: A 765 TYR cc_start: 0.8295 (m-80) cc_final: 0.7985 (m-80) REVERT: A 824 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7558 (ttt90) REVERT: A 865 ASN cc_start: 0.8073 (m-40) cc_final: 0.7411 (p0) REVERT: B 286 ASN cc_start: 0.6707 (t0) cc_final: 0.6350 (t0) REVERT: B 577 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.7058 (ttt180) outliers start: 37 outliers final: 26 residues processed: 330 average time/residue: 0.1242 time to fit residues: 61.4416 Evaluate side-chains 328 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 558 ILE Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 788 ASP Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 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 391 ILE 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3706 > 50: distance: 59 - 79: 14.541 distance: 63 - 90: 22.064 distance: 71 - 98: 24.471 distance: 74 - 79: 13.623 distance: 79 - 80: 9.976 distance: 80 - 81: 7.315 distance: 80 - 83: 16.064 distance: 81 - 82: 7.862 distance: 81 - 90: 17.798 distance: 83 - 84: 34.027 distance: 84 - 85: 10.146 distance: 85 - 86: 13.341 distance: 86 - 87: 8.827 distance: 87 - 88: 8.809 distance: 90 - 91: 5.995 distance: 91 - 92: 19.369 distance: 91 - 94: 35.627 distance: 92 - 93: 23.595 distance: 92 - 98: 20.810 distance: 94 - 95: 21.667 distance: 95 - 96: 15.379 distance: 95 - 97: 13.530 distance: 98 - 99: 6.473 distance: 99 - 100: 14.077 distance: 99 - 102: 27.411 distance: 100 - 101: 39.574 distance: 100 - 106: 6.273 distance: 102 - 103: 19.080 distance: 103 - 104: 14.497 distance: 103 - 105: 30.050 distance: 106 - 107: 22.911 distance: 107 - 108: 13.592 distance: 107 - 110: 10.949 distance: 108 - 109: 14.797 distance: 108 - 115: 25.365 distance: 110 - 111: 25.817 distance: 111 - 112: 7.830 distance: 112 - 113: 14.932 distance: 112 - 114: 12.883 distance: 115 - 116: 7.913 distance: 116 - 117: 16.070 distance: 116 - 119: 21.814 distance: 117 - 118: 18.707 distance: 117 - 121: 24.292 distance: 119 - 120: 19.635 distance: 121 - 122: 16.896 distance: 122 - 123: 10.571 distance: 122 - 125: 14.312 distance: 123 - 124: 25.092 distance: 123 - 128: 17.842 distance: 125 - 126: 6.559 distance: 125 - 127: 30.916 distance: 129 - 130: 9.308 distance: 129 - 132: 16.723 distance: 130 - 131: 24.646 distance: 130 - 133: 14.237 distance: 133 - 134: 7.144 distance: 134 - 135: 9.305 distance: 134 - 137: 14.422 distance: 135 - 136: 3.113 distance: 135 - 143: 19.498 distance: 137 - 138: 6.543 distance: 138 - 140: 4.252 distance: 139 - 141: 4.650 distance: 140 - 142: 3.493 distance: 141 - 142: 4.289 distance: 143 - 144: 7.389 distance: 144 - 145: 28.527 distance: 144 - 147: 24.122 distance: 145 - 146: 40.437 distance: 145 - 152: 8.302 distance: 147 - 148: 19.108 distance: 148 - 149: 22.832 distance: 149 - 150: 22.819 distance: 150 - 151: 26.896 distance: 152 - 153: 12.805 distance: 153 - 154: 11.771 distance: 153 - 156: 35.763 distance: 154 - 155: 8.779 distance: 154 - 159: 21.564 distance: 156 - 157: 27.093 distance: 156 - 158: 22.195