Starting phenix.real_space_refine on Sun Aug 24 18:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9m_39863/08_2025/8z9m_39863.cif" } resolution = 3.3 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= 0.022 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: 4 Type Number sf(0) Gaussians S 122 5.16 5 C 14072 2.51 5 N 3791 2.21 5 O 4031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s 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: 22016 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2607 Classifications: {'peptide': 328} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 7 Chain: "D" Number of atoms: 8394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8394 Classifications: {'peptide': 1064} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1019} Chain breaks: 7 Chain: "A" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2640 Classifications: {'peptide': 332} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 315} Chain breaks: 7 Chain: "B" Number of atoms: 8375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8375 Classifications: {'peptide': 1062} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 1018} Chain breaks: 7 Time building chain proxies: 5.40, per 1000 atoms: 0.25 Number of scatterers: 22016 At special positions: 0 Unit cell: (130.05, 117.3, 247.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 122 16.00 O 4031 8.00 N 3791 7.00 C 14072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS B1029 " distance=2.66 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: 1.85 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 39 sheets defined 30.8% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.038A pdb=" N THR C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 removed outlier: 4.133A pdb=" N VAL C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 406 " --> pdb=" O HIS C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 427 removed outlier: 4.448A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 422 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 removed outlier: 3.505A pdb=" N LEU C 445 " --> pdb=" O HIS C 441 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 543 removed outlier: 3.753A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 565 Processing helix chain 'C' and resid 586 through 595 removed outlier: 4.094A pdb=" N MET C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 645 removed outlier: 4.009A pdb=" N ASN C 645 " --> pdb=" O GLN C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 716 through 720 removed outlier: 3.742A pdb=" N ASP C 719 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP C 720 " --> pdb=" O GLU C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 716 through 720' Processing helix chain 'C' and resid 734 through 748 removed outlier: 3.514A pdb=" N LYS C 739 " --> pdb=" O GLU C 735 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 741 " --> pdb=" O ASN C 737 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 745 " --> pdb=" O CYS C 741 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 754 Processing helix chain 'C' and resid 755 through 776 removed outlier: 3.550A pdb=" N HIS C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 766 " --> pdb=" O SER C 762 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 24 removed outlier: 3.668A pdb=" N LYS D 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 843 through 847 Processing helix chain 'D' and resid 848 through 861 removed outlier: 3.923A pdb=" N LEU D 853 " --> pdb=" O PRO D 849 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 854 " --> pdb=" O ARG D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 875 removed outlier: 3.748A pdb=" N HIS D 874 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 892 removed outlier: 3.507A pdb=" N LYS D 884 " --> pdb=" O ASN D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 903 Processing helix chain 'D' and resid 908 through 921 Processing helix chain 'D' and resid 923 through 941 removed outlier: 3.798A pdb=" N THR D 930 " --> pdb=" O LEU D 926 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 931 " --> pdb=" O HIS D 927 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 941 " --> pdb=" O HIS D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 964 through 971 removed outlier: 7.063A pdb=" N VAL D 969 " --> pdb=" O CYS D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 972 through 990 removed outlier: 3.589A pdb=" N LYS D 990 " --> pdb=" O LEU D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1007 removed outlier: 3.686A pdb=" N ARG D 998 " --> pdb=" O TYR D 994 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS D 999 " --> pdb=" O ASP D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1018 removed outlier: 3.676A pdb=" N VAL D1014 " --> pdb=" O THR D1010 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN D1015 " --> pdb=" O ASP D1011 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D1016 " --> pdb=" O ARG D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1026 through 1040 Processing helix chain 'D' and resid 1047 through 1061 Processing helix chain 'D' and resid 1062 through 1074 removed outlier: 3.833A pdb=" N GLY D1066 " --> pdb=" O LYS D1062 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP D1074 " --> pdb=" O LEU D1070 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1086 Processing helix chain 'D' and resid 1088 through 1099 Processing helix chain 'D' and resid 1104 through 1117 removed outlier: 3.796A pdb=" N VAL D1108 " --> pdb=" O GLU D1104 " (cutoff:3.500A) Processing helix chain 'D' and resid 1123 through 1134 Processing helix chain 'D' and resid 1136 through 1147 Processing helix chain 'D' and resid 1151 through 1164 Processing helix chain 'D' and resid 1172 through 1189 removed outlier: 3.590A pdb=" N ILE D1176 " --> pdb=" O THR D1172 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1204 removed outlier: 3.520A pdb=" N ALA D1196 " --> pdb=" O PHE D1192 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D1204 " --> pdb=" O ALA D1200 " (cutoff:3.500A) Processing helix chain 'D' and resid 1207 through 1215 Processing helix chain 'A' and resid 383 through 391 removed outlier: 4.034A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 409 removed outlier: 4.512A pdb=" N THR A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.670A pdb=" N LEU A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.703A pdb=" N LEU A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 4.174A pdb=" N LYS A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 587 through 595 Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.517A pdb=" N ILE A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.583A pdb=" N ASN A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 776 removed outlier: 4.513A pdb=" N ASN A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.642A pdb=" N LYS B 24 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.717A pdb=" N TYR B 484 " --> pdb=" O ILE B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 848 through 861 removed outlier: 3.509A pdb=" N SER B 852 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 853 " --> pdb=" O PRO B 849 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 854 " --> pdb=" O ARG B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 removed outlier: 3.955A pdb=" N HIS B 874 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 893 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 908 through 921 Processing helix chain 'B' and resid 923 through 941 removed outlier: 3.530A pdb=" N GLN B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 990 removed outlier: 3.710A pdb=" N LYS B 990 " --> pdb=" O LEU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 Processing helix chain 'B' and resid 1009 through 1018 removed outlier: 3.934A pdb=" N GLN B1015 " --> pdb=" O ASP B1011 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B1016 " --> pdb=" O ARG B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1040 removed outlier: 3.631A pdb=" N CYS B1035 " --> pdb=" O SER B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1060 Processing helix chain 'B' and resid 1063 through 1074 removed outlier: 3.793A pdb=" N ASP B1074 " --> pdb=" O LEU B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1086 removed outlier: 3.761A pdb=" N ALA B1079 " --> pdb=" O LYS B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1099 Processing helix chain 'B' and resid 1104 through 1117 removed outlier: 3.501A pdb=" N VAL B1108 " --> pdb=" O GLU B1104 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'B' and resid 1136 through 1147 Processing helix chain 'B' and resid 1149 through 1164 removed outlier: 3.721A pdb=" N LEU B1155 " --> pdb=" O ASP B1151 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1191 Processing helix chain 'B' and resid 1192 through 1204 removed outlier: 3.569A pdb=" N ALA B1196 " --> pdb=" O PHE B1192 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1215 Processing sheet with id=AA1, first strand: chain 'C' and resid 474 through 475 removed outlier: 5.456A pdb=" N ILE C 378 " --> pdb=" O ASP C 475 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG C 377 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 502 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA C 379 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET C 504 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 381 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N THR C 499 " --> pdb=" O GLN C 520 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ILE C 522 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU C 501 " --> pdb=" O ILE C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 474 through 475 removed outlier: 5.456A pdb=" N ILE C 378 " --> pdb=" O ASP C 475 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG C 377 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 502 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA C 379 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET C 504 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU C 381 " --> pdb=" O MET C 504 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 580 through 583 removed outlier: 6.814A pdb=" N ARG C 569 " --> pdb=" O HIS C 605 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 600 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 820 " --> pdb=" O ILE C 813 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 815 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 612 through 618 removed outlier: 3.648A pdb=" N GLY C 654 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TYR C 655 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU C 725 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C 657 " --> pdb=" O LEU C 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 15 removed outlier: 6.775A pdb=" N ILE D 810 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL D 801 " --> pdb=" O ILE D 810 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA D 812 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.574A pdb=" N ASP D 47 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR D 53 " --> pdb=" O ASP D 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 64 through 69 removed outlier: 3.776A pdb=" N LYS D 66 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS D 107 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 121 removed outlier: 4.448A pdb=" N ASP D 118 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 143 " --> pdb=" O TRP D 153 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP D 153 " --> pdb=" O LEU D 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 161 through 166 removed outlier: 6.735A pdb=" N LEU D 177 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHE D 164 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N THR D 175 " --> pdb=" O PHE D 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 249 through 252 removed outlier: 4.030A pdb=" N GLN D 249 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 251 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET D 260 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 268 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL D 281 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE D 270 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 291 through 296 removed outlier: 7.044A pdb=" N ILE D 312 " --> pdb=" O GLN D 346 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLN D 346 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 314 " --> pdb=" O ARG D 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 358 through 363 removed outlier: 3.797A pdb=" N SER D 360 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 380 " --> pdb=" O LEU D 459 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU D 459 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE D 382 " --> pdb=" O THR D 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 409 through 410 Processing sheet with id=AB5, first strand: chain 'D' and resid 469 through 472 Processing sheet with id=AB6, first strand: chain 'D' and resid 518 through 523 removed outlier: 7.017A pdb=" N VAL D 518 " --> pdb=" O THR D 534 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR D 534 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY D 520 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 532 " --> pdb=" O GLY D 520 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 531 " --> pdb=" O GLN D 548 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 571 through 576 removed outlier: 7.109A pdb=" N VAL D 586 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE D 574 " --> pdb=" O ALA D 584 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA D 584 " --> pdb=" O ILE D 574 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 576 " --> pdb=" O TYR D 582 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR D 582 " --> pdb=" O VAL D 576 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 593 " --> pdb=" O VAL D 585 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG D 604 " --> pdb=" O LEU D 594 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 615 through 618 removed outlier: 4.276A pdb=" N ALA D 615 " --> pdb=" O THR D 682 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 677 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 688 " --> pdb=" O ARG D 703 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG D 703 " --> pdb=" O VAL D 688 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N HIS D 690 " --> pdb=" O SER D 701 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 713 through 719 removed outlier: 4.181A pdb=" N CYS D 715 " --> pdb=" O GLY D 726 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 719 " --> pdb=" O THR D 722 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN D 731 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 732 " --> pdb=" O ILE D 745 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 752 through 757 removed outlier: 6.865A pdb=" N MET D 769 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D 755 " --> pdb=" O ILE D 767 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE D 767 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE D 757 " --> pdb=" O LYS D 765 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS D 765 " --> pdb=" O PHE D 757 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 766 " --> pdb=" O TRP D 777 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY D 773 " --> pdb=" O TYR D 770 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 786 " --> pdb=" O VAL D 776 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 377 through 381 removed outlier: 6.371A pdb=" N ARG A 377 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A 500 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 504 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 499 " --> pdb=" O GLN A 520 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE A 522 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU A 501 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 377 through 381 removed outlier: 6.371A pdb=" N ARG A 377 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A 500 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A 504 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.604A pdb=" N LEU A 476 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 580 through 583 removed outlier: 6.876A pdb=" N ARG A 569 " --> pdb=" O HIS A 605 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 600 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 815 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 612 through 618 removed outlier: 3.516A pdb=" N GLY A 654 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A 655 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A 725 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 657 " --> pdb=" O LEU A 723 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 14 through 15 removed outlier: 4.111A pdb=" N ASP B 800 " --> pdb=" O ALA B 812 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.467A pdb=" N VAL B 43 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 56 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 45 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.565A pdb=" N LYS B 66 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B 107 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 99 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA B 105 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AD2, first strand: chain 'B' and resid 161 through 166 removed outlier: 6.863A pdb=" N LEU B 177 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 164 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR B 175 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 199 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 249 through 252 removed outlier: 4.336A pdb=" N GLN B 249 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 251 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 260 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE B 268 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 281 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 270 " --> pdb=" O VAL B 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 291 through 296 removed outlier: 7.070A pdb=" N ILE B 312 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 346 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 314 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 358 through 363 removed outlier: 4.045A pdb=" N SER B 360 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 380 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 459 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 382 " --> pdb=" O THR B 457 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AD7, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.637A pdb=" N VAL B 497 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 510 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 499 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 518 through 523 removed outlier: 7.195A pdb=" N VAL B 518 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N THR B 534 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 520 " --> pdb=" O PHE B 532 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 532 " --> pdb=" O GLY B 520 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 571 through 576 removed outlier: 4.122A pdb=" N MET B 573 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 594 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 615 through 618 removed outlier: 3.566A pdb=" N GLU B 677 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 688 " --> pdb=" O ARG B 703 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG B 703 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 716 through 719 removed outlier: 3.774A pdb=" N ILE B 745 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 743 " --> pdb=" O PHE B 734 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 755 through 757 removed outlier: 3.939A pdb=" N GLY B 773 " --> pdb=" O TYR B 770 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 774 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER B 787 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B 776 " --> pdb=" O VAL B 785 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2334 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: 5.59 Time building geometry restraints manager: 2.49 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: 7144 1.34 - 1.46: 4158 1.46 - 1.58: 11007 1.58 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 22481 Sorted by residual: bond pdb=" N ARG A 453 " pdb=" CA ARG A 453 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.30e+01 bond pdb=" N ASN C 455 " pdb=" CA ASN C 455 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.29e-02 6.01e+03 8.66e+00 bond pdb=" N HIS A 454 " pdb=" CA HIS A 454 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.27e-02 6.20e+03 7.80e+00 bond pdb=" N LYS A 752 " pdb=" CA LYS A 752 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.88e+00 bond pdb=" N ASP A 457 " pdb=" CA ASP A 457 " ideal model delta sigma weight residual 1.467 1.489 -0.023 8.70e-03 1.32e+04 6.85e+00 ... (remaining 22476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 30087 1.97 - 3.95: 365 3.95 - 5.92: 35 5.92 - 7.89: 3 7.89 - 9.86: 2 Bond angle restraints: 30492 Sorted by residual: angle pdb=" N ILE A 744 " pdb=" CA ILE A 744 " pdb=" C ILE A 744 " ideal model delta sigma weight residual 112.83 107.76 5.07 9.90e-01 1.02e+00 2.62e+01 angle pdb=" N ASP A 457 " pdb=" CA ASP A 457 " pdb=" C ASP A 457 " ideal model delta sigma weight residual 113.21 107.38 5.83 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA ARG B1081 " pdb=" C ARG B1081 " pdb=" O ARG B1081 " ideal model delta sigma weight residual 120.42 116.48 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" N VAL A 647 " pdb=" CA VAL A 647 " pdb=" C VAL A 647 " ideal model delta sigma weight residual 113.07 108.10 4.97 1.37e+00 5.33e-01 1.31e+01 angle pdb=" N LEU A 749 " pdb=" CA LEU A 749 " pdb=" C LEU A 749 " ideal model delta sigma weight residual 112.57 108.48 4.09 1.13e+00 7.83e-01 1.31e+01 ... (remaining 30487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12087 17.94 - 35.88: 1101 35.88 - 53.82: 216 53.82 - 71.76: 54 71.76 - 89.70: 17 Dihedral angle restraints: 13475 sinusoidal: 5379 harmonic: 8096 Sorted by residual: dihedral pdb=" C LYS A 456 " pdb=" N LYS A 456 " pdb=" CA LYS A 456 " pdb=" CB LYS A 456 " ideal model delta harmonic sigma weight residual -122.60 -135.32 12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N LYS A 456 " pdb=" C LYS A 456 " pdb=" CA LYS A 456 " pdb=" CB LYS A 456 " ideal model delta harmonic sigma weight residual 122.80 134.00 -11.20 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" CA ASP B1074 " pdb=" C ASP B1074 " pdb=" N LYS B1075 " pdb=" CA LYS B1075 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 13472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3243 0.081 - 0.162: 259 0.162 - 0.243: 6 0.243 - 0.324: 0 0.324 - 0.405: 1 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CA LYS A 456 " pdb=" N LYS A 456 " pdb=" C LYS A 456 " pdb=" CB LYS A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA HIS A 454 " pdb=" N HIS A 454 " pdb=" C HIS A 454 " pdb=" CB HIS A 454 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL B1040 " pdb=" CA VAL B1040 " pdb=" CG1 VAL B1040 " pdb=" CG2 VAL B1040 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 3506 not shown) Planarity restraints: 3853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 465 " -0.074 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO D 466 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO D 466 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 466 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 610 " 0.037 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO D 611 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 611 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 611 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 619 " -0.035 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO D 620 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 620 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 620 " -0.029 5.00e-02 4.00e+02 ... (remaining 3850 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2897 2.76 - 3.30: 19138 3.30 - 3.83: 33870 3.83 - 4.37: 38920 4.37 - 4.90: 70280 Nonbonded interactions: 165105 Sorted by model distance: nonbonded pdb=" OG SER B 426 " pdb=" OD1 ASP B 428 " model vdw 2.228 3.040 nonbonded pdb=" NH2 ARG A 556 " pdb=" O ASN A 592 " model vdw 2.286 3.120 nonbonded pdb=" OG SER D 426 " pdb=" OD1 ASP D 428 " model vdw 2.291 3.040 nonbonded pdb=" O GLN B 890 " pdb=" OG SER B 893 " model vdw 2.293 3.040 nonbonded pdb=" OG1 THR B 524 " pdb=" OG SER B 528 " model vdw 2.308 3.040 ... (remaining 165100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 376 through 456 or resid 471 through 479 or resid 493 thro \ ugh 664 or resid 715 through 824)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 8 through 441 or resid 447 through 707 or resid 710 throug \ h 1215)) selection = (chain 'D' and (resid 8 through 941 or resid 965 through 1215)) } 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 individual isotropic 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: 7.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.230 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.626 22482 Z= 0.241 Angle : 0.617 48.216 30494 Z= 0.338 Chirality : 0.041 0.405 3509 Planarity : 0.004 0.112 3853 Dihedral : 14.421 89.700 8206 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.24 % Allowed : 0.37 % Favored : 99.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.13 % 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: 0.06 (0.16), residues: 2722 helix: 1.14 (0.20), residues: 752 sheet: 0.97 (0.22), residues: 611 loop : -1.07 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 556 TYR 0.013 0.001 TYR B 975 PHE 0.010 0.001 PHE B 468 TRP 0.010 0.000 TRP D1094 HIS 0.007 0.000 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00201 (22481) covalent geometry : angle 0.51362 (30492) SS BOND : bond 0.62608 ( 1) SS BOND : angle 42.14240 ( 2) hydrogen bonds : bond 0.23563 ( 837) hydrogen bonds : angle 6.84284 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 537 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 MET cc_start: 0.5582 (mpp) cc_final: 0.5375 (mpp) REVERT: C 528 GLU cc_start: 0.6833 (mp0) cc_final: 0.6619 (mp0) REVERT: C 821 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6451 (tm-30) REVERT: D 24 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7766 (ttmm) REVERT: D 513 ILE cc_start: 0.8576 (mm) cc_final: 0.8347 (mm) REVERT: D 822 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7187 (mm-30) REVERT: D 825 MET cc_start: 0.7841 (mtm) cc_final: 0.7616 (mtm) REVERT: D 881 GLU cc_start: 0.6731 (mp0) cc_final: 0.6425 (mp0) REVERT: D 900 LYS cc_start: 0.7906 (ttpt) cc_final: 0.7679 (ttpp) REVERT: D 998 ARG cc_start: 0.6588 (ttp80) cc_final: 0.6338 (ttp80) REVERT: A 392 MET cc_start: 0.4210 (mpp) cc_final: 0.3998 (mpp) REVERT: A 504 MET cc_start: 0.7593 (ptm) cc_final: 0.7339 (ptt) REVERT: A 569 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7506 (mpt180) REVERT: A 593 ASP cc_start: 0.7070 (t0) cc_final: 0.6625 (t0) REVERT: B 148 THR cc_start: 0.8310 (p) cc_final: 0.8099 (p) REVERT: B 180 GLU cc_start: 0.6891 (mp0) cc_final: 0.6433 (mp0) REVERT: B 291 PHE cc_start: 0.7741 (m-80) cc_final: 0.7228 (m-80) REVERT: B 685 ASP cc_start: 0.7184 (m-30) cc_final: 0.6974 (m-30) REVERT: B 1060 ASN cc_start: 0.6901 (m-40) cc_final: 0.6636 (m-40) outliers start: 6 outliers final: 2 residues processed: 542 average time/residue: 0.1946 time to fit residues: 154.0935 Evaluate side-chains 483 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 481 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 752 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 565 GLN C 737 ASN D 501 HIS D 678 HIS A 565 GLN B 977 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098067 restraints weight = 34276.371| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.11 r_work: 0.3007 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22482 Z= 0.173 Angle : 0.608 8.743 30494 Z= 0.311 Chirality : 0.044 0.169 3509 Planarity : 0.005 0.081 3853 Dihedral : 3.954 54.234 2972 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.31 % Allowed : 8.85 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.07 (0.16), residues: 2722 helix: 1.02 (0.19), residues: 783 sheet: 0.98 (0.21), residues: 636 loop : -1.28 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1185 TYR 0.018 0.002 TYR D 975 PHE 0.020 0.002 PHE B 532 TRP 0.019 0.002 TRP D 98 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00400 (22481) covalent geometry : angle 0.60700 (30492) SS BOND : bond 0.00008 ( 1) SS BOND : angle 3.14561 ( 2) hydrogen bonds : bond 0.04884 ( 837) hydrogen bonds : angle 4.56268 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 521 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 MET cc_start: 0.6144 (mpp) cc_final: 0.5943 (mpp) REVERT: C 528 GLU cc_start: 0.7384 (mp0) cc_final: 0.7082 (mp0) REVERT: C 645 ASN cc_start: 0.8249 (m110) cc_final: 0.8047 (m110) REVERT: C 735 GLU cc_start: 0.7672 (tt0) cc_final: 0.7330 (tt0) REVERT: C 739 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7805 (mtmm) REVERT: C 744 ILE cc_start: 0.8428 (mm) cc_final: 0.8213 (tp) REVERT: D 24 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8388 (ttmm) REVERT: D 140 TYR cc_start: 0.8299 (m-80) cc_final: 0.7854 (m-80) REVERT: D 428 ASP cc_start: 0.7745 (p0) cc_final: 0.7541 (p0) REVERT: D 513 ILE cc_start: 0.8740 (mm) cc_final: 0.8430 (mt) REVERT: D 551 ASP cc_start: 0.7959 (t0) cc_final: 0.7759 (t0) REVERT: D 605 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6762 (tm-30) REVERT: D 822 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7785 (mm-30) REVERT: D 881 GLU cc_start: 0.7476 (mp0) cc_final: 0.7190 (mp0) REVERT: D 1210 LEU cc_start: 0.7226 (tp) cc_final: 0.6962 (tt) REVERT: A 380 PHE cc_start: 0.8109 (t80) cc_final: 0.7834 (t80) REVERT: A 569 ARG cc_start: 0.8225 (mmt90) cc_final: 0.7907 (mpt180) REVERT: A 593 ASP cc_start: 0.7931 (t0) cc_final: 0.7490 (t0) REVERT: A 631 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7501 (ttm170) REVERT: B 49 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 148 THR cc_start: 0.8614 (p) cc_final: 0.8269 (p) REVERT: B 150 THR cc_start: 0.8050 (m) cc_final: 0.7792 (m) REVERT: B 175 THR cc_start: 0.8850 (t) cc_final: 0.8595 (m) REVERT: B 180 GLU cc_start: 0.7337 (mp0) cc_final: 0.6946 (mp0) REVERT: B 271 LEU cc_start: 0.8485 (mp) cc_final: 0.8131 (mt) REVERT: B 274 GLU cc_start: 0.7188 (mp0) cc_final: 0.6869 (mp0) REVERT: B 510 GLU cc_start: 0.7840 (tp30) cc_final: 0.7544 (tm-30) REVERT: B 593 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7040 (mt-10) REVERT: B 728 MET cc_start: 0.7864 (mmt) cc_final: 0.7595 (mmm) REVERT: B 831 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7618 (mtm110) REVERT: B 839 GLU cc_start: 0.7444 (pt0) cc_final: 0.7195 (pm20) REVERT: B 865 ASN cc_start: 0.6834 (p0) cc_final: 0.6561 (p0) REVERT: B 1069 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7745 (mp) REVERT: B 1081 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7122 (mtm110) REVERT: B 1103 GLU cc_start: 0.8008 (tp30) cc_final: 0.7759 (tm-30) REVERT: B 1148 ARG cc_start: 0.8345 (mtp85) cc_final: 0.8092 (mtp85) REVERT: B 1163 TYR cc_start: 0.8849 (m-80) cc_final: 0.8601 (m-80) REVERT: B 1173 GLU cc_start: 0.7403 (pt0) cc_final: 0.7116 (pt0) REVERT: B 1182 ASP cc_start: 0.8245 (m-30) cc_final: 0.7875 (m-30) REVERT: B 1185 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8296 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 533 average time/residue: 0.1976 time to fit residues: 152.6758 Evaluate side-chains 506 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 486 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 606 MET Chi-restraints excluded: chain D residue 733 ASN Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 1136 CYS Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1069 LEU Chi-restraints excluded: chain B residue 1073 ILE Chi-restraints excluded: chain B residue 1142 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 179 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 258 optimal weight: 0.0980 chunk 260 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 203 optimal weight: 0.7980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 455 ASN ** C 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 565 GLN C 650 GLN D 299 GLN D 420 ASN D 501 HIS A 497 ASN A 565 GLN A 757 ASN A 811 ASN B 258 ASN B 429 ASN B1068 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098141 restraints weight = 34086.511| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.07 r_work: 0.3063 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22482 Z= 0.108 Angle : 0.491 6.975 30494 Z= 0.255 Chirality : 0.041 0.260 3509 Planarity : 0.004 0.068 3853 Dihedral : 3.710 46.819 2968 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.47 % Allowed : 11.95 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.08 (0.16), residues: 2722 helix: 1.26 (0.19), residues: 783 sheet: 1.03 (0.22), residues: 628 loop : -1.23 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 556 TYR 0.015 0.001 TYR B 975 PHE 0.014 0.001 PHE B 532 TRP 0.011 0.001 TRP D 98 HIS 0.003 0.000 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00250 (22481) covalent geometry : angle 0.49006 (30492) SS BOND : bond 0.00649 ( 1) SS BOND : angle 3.12121 ( 2) hydrogen bonds : bond 0.04221 ( 837) hydrogen bonds : angle 4.25078 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 492 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 392 MET cc_start: 0.6106 (mpp) cc_final: 0.5898 (mpp) REVERT: C 528 GLU cc_start: 0.7407 (mp0) cc_final: 0.7103 (mp0) REVERT: C 644 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7887 (mtm180) REVERT: C 645 ASN cc_start: 0.8229 (m110) cc_final: 0.8027 (m110) REVERT: C 735 GLU cc_start: 0.7650 (tt0) cc_final: 0.7288 (tt0) REVERT: C 744 ILE cc_start: 0.8501 (mm) cc_final: 0.8231 (tp) REVERT: D 24 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8311 (ttmm) REVERT: D 140 TYR cc_start: 0.8312 (m-80) cc_final: 0.7718 (m-80) REVERT: D 428 ASP cc_start: 0.7798 (p0) cc_final: 0.7565 (p0) REVERT: D 479 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7555 (mmtm) REVERT: D 513 ILE cc_start: 0.8749 (mm) cc_final: 0.8440 (mt) REVERT: D 605 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6720 (tm-30) REVERT: D 822 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7748 (mm-30) REVERT: D 879 GLU cc_start: 0.7190 (tt0) cc_final: 0.6959 (tt0) REVERT: D 988 GLU cc_start: 0.7793 (tp30) cc_final: 0.7400 (tm-30) REVERT: A 380 PHE cc_start: 0.8169 (t80) cc_final: 0.7742 (t80) REVERT: A 569 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7899 (mpt180) REVERT: A 593 ASP cc_start: 0.7814 (t0) cc_final: 0.7370 (t0) REVERT: A 652 LEU cc_start: 0.7793 (mp) cc_final: 0.7582 (mp) REVERT: B 148 THR cc_start: 0.8643 (p) cc_final: 0.8271 (p) REVERT: B 150 THR cc_start: 0.8178 (m) cc_final: 0.7899 (m) REVERT: B 175 THR cc_start: 0.8809 (t) cc_final: 0.8530 (m) REVERT: B 180 GLU cc_start: 0.7361 (mp0) cc_final: 0.7026 (mp0) REVERT: B 271 LEU cc_start: 0.8535 (mp) cc_final: 0.8168 (mt) REVERT: B 274 GLU cc_start: 0.7098 (mp0) cc_final: 0.6832 (mp0) REVERT: B 418 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7753 (pp) REVERT: B 510 GLU cc_start: 0.7862 (tp30) cc_final: 0.7503 (tm-30) REVERT: B 728 MET cc_start: 0.7830 (mmt) cc_final: 0.7570 (mmm) REVERT: B 882 GLU cc_start: 0.7666 (mp0) cc_final: 0.7430 (mp0) REVERT: B 889 GLU cc_start: 0.8292 (tp30) cc_final: 0.7978 (tp30) REVERT: B 1069 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 1081 ARG cc_start: 0.7378 (ttp-110) cc_final: 0.7079 (mtm110) REVERT: B 1148 ARG cc_start: 0.8326 (mtp85) cc_final: 0.8059 (mtt90) REVERT: B 1173 GLU cc_start: 0.7355 (pt0) cc_final: 0.7079 (pt0) outliers start: 36 outliers final: 18 residues processed: 509 average time/residue: 0.2013 time to fit residues: 148.6966 Evaluate side-chains 498 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 477 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 644 ARG Chi-restraints excluded: chain C residue 810 LYS Chi-restraints excluded: chain D residue 345 SER Chi-restraints excluded: chain D residue 603 LEU Chi-restraints excluded: chain D residue 733 ASN Chi-restraints excluded: chain D residue 782 VAL Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 817 CYS Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 784 MET Chi-restraints excluded: chain B residue 1006 LEU Chi-restraints excluded: chain B residue 1069 LEU Chi-restraints excluded: chain B residue 1142 GLU Chi-restraints excluded: chain B residue 1210 LEU 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: 68.8348 > 50: distance: 29 - 37: 3.005 distance: 74 - 80: 29.253 distance: 80 - 81: 58.438 distance: 81 - 82: 21.017 distance: 81 - 84: 5.334 distance: 82 - 83: 20.540 distance: 82 - 86: 39.802 distance: 84 - 85: 40.551 distance: 86 - 87: 6.042 distance: 87 - 88: 16.048 distance: 87 - 90: 25.185 distance: 88 - 89: 40.770 distance: 88 - 100: 10.157 distance: 90 - 91: 17.758 distance: 91 - 92: 31.113 distance: 91 - 93: 9.616 distance: 92 - 94: 21.873 distance: 93 - 95: 25.325 distance: 93 - 96: 14.809 distance: 94 - 95: 8.473 distance: 95 - 97: 24.769 distance: 96 - 98: 32.942 distance: 97 - 99: 24.026 distance: 98 - 99: 20.441 distance: 100 - 101: 11.434 distance: 101 - 102: 40.788 distance: 101 - 104: 3.793 distance: 104 - 106: 54.602 distance: 107 - 108: 20.776 distance: 108 - 109: 27.904 distance: 108 - 111: 32.224 distance: 109 - 110: 15.669 distance: 109 - 118: 14.761 distance: 111 - 112: 30.591 distance: 112 - 113: 15.337 distance: 113 - 114: 11.401 distance: 114 - 115: 10.899 distance: 115 - 116: 10.189 distance: 115 - 117: 16.113 distance: 118 - 119: 39.614 distance: 119 - 120: 48.466 distance: 119 - 122: 4.672 distance: 120 - 121: 38.329 distance: 120 - 127: 10.419 distance: 122 - 123: 31.728 distance: 123 - 124: 16.672 distance: 124 - 125: 26.552 distance: 125 - 126: 15.852 distance: 127 - 128: 17.593 distance: 128 - 129: 8.984 distance: 128 - 131: 41.515 distance: 129 - 130: 39.532 distance: 129 - 135: 25.314 distance: 131 - 132: 5.449 distance: 131 - 133: 25.933 distance: 132 - 134: 55.047 distance: 135 - 136: 33.729 distance: 135 - 196: 19.495 distance: 136 - 137: 44.137 distance: 136 - 139: 21.065 distance: 137 - 138: 29.349 distance: 137 - 146: 10.134 distance: 138 - 193: 29.184 distance: 139 - 140: 41.792 distance: 140 - 141: 3.608 distance: 143 - 144: 39.793 distance: 143 - 145: 48.078 distance: 147 - 148: 41.616 distance: 148 - 149: 40.466 distance: 148 - 157: 40.445 distance: 151 - 152: 31.465 distance: 151 - 153: 41.057 distance: 152 - 154: 5.444 distance: 153 - 155: 32.688 distance: 154 - 156: 16.185 distance: 155 - 156: 36.665 distance: 157 - 158: 25.014 distance: 158 - 159: 24.017 distance: 158 - 161: 39.022 distance: 159 - 160: 6.904 distance: 159 - 162: 15.585 distance: 162 - 168: 39.726 distance: 163 - 164: 40.942 distance: 163 - 166: 16.726 distance: 164 - 169: 34.145 distance: 166 - 167: 13.500 distance: 167 - 168: 7.941