Starting phenix.real_space_refine on Sat Aug 23 18:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.map" model { file = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iff_35415/08_2025/8iff_35415.cif" } resolution = 3.1 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= 0.002 sd= 0.088 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 104 5.16 5 C 8705 2.51 5 N 2366 2.21 5 O 2523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 13698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6800 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6812 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.22 Number of scatterers: 13698 At special positions: 0 Unit cell: (113.05, 122.4, 139.4, 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 104 16.00 O 2523 8.00 N 2366 7.00 C 8705 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 541.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 17 sheets defined 39.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.668A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 380 through 426 removed outlier: 3.970A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.870A pdb=" N GLN A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 467 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.554A pdb=" N ALA A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.088A pdb=" N ILE A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.159A pdb=" N ILE A 794 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 876 through 922 removed outlier: 3.780A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 927 through 948 Processing helix chain 'A' and resid 969 through 980 removed outlier: 4.364A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 removed outlier: 3.528A pdb=" N SER A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 4.133A pdb=" N VAL A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 3.634A pdb=" N PHE A1019 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A1022 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1026 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1080 through 1082 No H-bonds generated for 'chain 'A' and resid 1080 through 1082' Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.825A pdb=" N MET A1087 " --> pdb=" O GLY A1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.806A pdb=" N LYS B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 4.143A pdb=" N GLU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.641A pdb=" N SER B 131 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 132 " --> pdb=" O ILE B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.081A pdb=" N LEU B 152 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 219 through 235 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 removed outlier: 3.767A pdb=" N MET B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 Processing helix chain 'B' and resid 402 through 414 removed outlier: 3.600A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.657A pdb=" N VAL B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 489 through 494 removed outlier: 3.710A pdb=" N ALA B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 4.428A pdb=" N LEU B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 502' Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.939A pdb=" N ILE B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 820 through 832 removed outlier: 3.601A pdb=" N VAL B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 922 removed outlier: 3.619A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 927 through 948 removed outlier: 3.900A pdb=" N GLN B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 removed outlier: 3.839A pdb=" N THR B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 removed outlier: 4.002A pdb=" N MET B1001 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1011 through 1017 Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1026 removed outlier: 3.688A pdb=" N ASN B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B1026 " --> pdb=" O MET B1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1021 through 1026' Processing helix chain 'B' and resid 1065 through 1073 removed outlier: 3.547A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B1072 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B1073 " --> pdb=" O LEU B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.740A pdb=" N LEU B1095 " --> pdb=" O LYS B1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.658A pdb=" N ALA A 88 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.541A pdb=" N GLY A 250 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.306A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 removed outlier: 3.759A pdb=" N GLY A 804 " --> pdb=" O CYS A 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1035 through 1037 removed outlier: 4.259A pdb=" N SER A1110 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A1103 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 4.040A pdb=" N HIS A1049 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1117 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.497A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 99 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 86 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 182 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 removed outlier: 3.676A pdb=" N GLY B 250 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.831A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.502A pdb=" N ALA B 448 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY B 484 " --> pdb=" O LYS B 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.913A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 559 " --> pdb=" O VAL B 530 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.509A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 858 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 967 through 969 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 7.408A pdb=" N ARG B 991 " --> pdb=" O LEU B1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 3.592A pdb=" N LEU B1057 " --> pdb=" O PHE B1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 4.166A pdb=" N HIS B1049 " --> pdb=" O ALA B1119 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1629 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: 2.58 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3046 1.33 - 1.45: 2848 1.45 - 1.57: 7890 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 13952 Sorted by residual: bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.383 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBC O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.357 1.410 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 13947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18520 2.10 - 4.20: 275 4.20 - 6.30: 35 6.30 - 8.40: 6 8.40 - 10.50: 3 Bond angle restraints: 18839 Sorted by residual: angle pdb=" CA LYS A 807 " pdb=" CB LYS A 807 " pdb=" CG LYS A 807 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N ASN A 758 " pdb=" CA ASN A 758 " pdb=" C ASN A 758 " ideal model delta sigma weight residual 109.81 102.75 7.06 2.21e+00 2.05e-01 1.02e+01 angle pdb=" C ALA A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta sigma weight residual 121.14 115.76 5.38 1.75e+00 3.27e-01 9.45e+00 angle pdb=" CA LEU A 939 " pdb=" CB LEU A 939 " pdb=" CG LEU A 939 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 9.00e+00 angle pdb=" CA LYS A 807 " pdb=" C LYS A 807 " pdb=" N SER A 808 " ideal model delta sigma weight residual 118.30 114.64 3.66 1.26e+00 6.30e-01 8.44e+00 ... (remaining 18834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7177 18.00 - 36.01: 998 36.01 - 54.01: 287 54.01 - 72.01: 47 72.01 - 90.02: 22 Dihedral angle restraints: 8531 sinusoidal: 3507 harmonic: 5024 Sorted by residual: dihedral pdb=" CA THR A 969 " pdb=" C THR A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A 871 " pdb=" C PHE A 871 " pdb=" N LEU A 872 " pdb=" CA LEU A 872 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " pdb=" OD1 ASP A 441 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1522 0.039 - 0.078: 463 0.078 - 0.117: 121 0.117 - 0.156: 38 0.156 - 0.195: 3 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.52 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2144 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.329 2.00e-02 2.50e+03 2.42e-01 1.47e+03 pdb=" CAP O6E B1201 " -0.118 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.131 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.191 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.087 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.491 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.063 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.383 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.337 2.00e-02 2.50e+03 2.00e-01 1.00e+03 pdb=" CAP O6E A1201 " 0.178 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.136 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.088 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.409 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.128 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " -0.051 2.00e-02 2.50e+03 1.72e-01 7.42e+02 pdb=" CAO O6E A1201 " -0.167 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.295 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " 0.019 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.079 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " 0.024 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.043 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.070 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.407 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 13044 3.25 - 3.80: 20343 3.80 - 4.35: 25515 4.35 - 4.90: 44201 Nonbonded interactions: 103462 Sorted by model distance: nonbonded pdb=" OG SER A 100 " pdb=" OD1 ASN A 102 " model vdw 2.153 3.040 nonbonded pdb=" O ASN A 909 " pdb=" OG SER A 912 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN B 330 " pdb=" NE2 HIS B 549 " model vdw 2.256 3.120 nonbonded pdb=" N GLU A 262 " pdb=" OE1 GLU A 262 " model vdw 2.300 3.120 ... (remaining 103457 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 71 through 187 or resid 194 or resid 196 through 1201)) selection = (chain 'B' and (resid 71 through 187 or resid 195 through 1201)) } 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: 1.300 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.180 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.007 0.442 13954 Z= 0.554 Angle : 0.634 10.498 18839 Z= 0.322 Chirality : 0.042 0.195 2147 Planarity : 0.010 0.242 2400 Dihedral : 18.236 90.017 5267 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.27 % Allowed : 29.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.43 (0.20), residues: 1712 helix: 1.28 (0.23), residues: 544 sheet: -0.05 (0.30), residues: 303 loop : -1.43 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 497 TYR 0.016 0.001 TYR A 242 PHE 0.019 0.002 PHE A 871 TRP 0.017 0.002 TRP B 366 HIS 0.006 0.001 HIS A 467 Details of bonding type rmsd covalent geometry : bond 0.00409 (13952) covalent geometry : angle 0.63369 (18839) hydrogen bonds : bond 0.12922 ( 582) hydrogen bonds : angle 6.24402 ( 1629) Misc. bond : bond 0.43781 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8051 (t) cc_final: 0.7653 (p) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.1218 time to fit residues: 24.6200 Evaluate side-chains 132 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 532 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 50.3331 > 50: distance: 13 - 17: 12.212 distance: 17 - 18: 10.115 distance: 18 - 19: 18.500 distance: 18 - 21: 17.599 distance: 19 - 20: 18.244 distance: 19 - 22: 13.532 distance: 20 - 41: 29.323 distance: 22 - 23: 3.505 distance: 23 - 24: 10.009 distance: 23 - 26: 32.753 distance: 24 - 25: 43.347 distance: 24 - 27: 14.497 distance: 25 - 49: 21.285 distance: 27 - 28: 15.563 distance: 28 - 29: 11.033 distance: 28 - 31: 22.538 distance: 29 - 30: 11.240 distance: 29 - 36: 12.719 distance: 30 - 56: 10.537 distance: 31 - 32: 18.800 distance: 32 - 33: 8.737 distance: 33 - 34: 21.364 distance: 34 - 35: 9.915 distance: 36 - 37: 7.692 distance: 37 - 38: 13.403 distance: 37 - 40: 26.569 distance: 38 - 39: 16.023 distance: 38 - 41: 5.101 distance: 39 - 67: 13.479 distance: 41 - 42: 6.350 distance: 42 - 43: 6.005 distance: 42 - 45: 8.851 distance: 43 - 44: 12.528 distance: 43 - 49: 9.372 distance: 44 - 75: 12.013 distance: 45 - 46: 13.162 distance: 45 - 47: 11.296 distance: 46 - 48: 17.615 distance: 49 - 50: 11.091 distance: 51 - 52: 8.188 distance: 52 - 84: 7.008 distance: 53 - 54: 14.102 distance: 53 - 55: 15.314 distance: 56 - 57: 3.062 distance: 57 - 58: 4.124 distance: 57 - 60: 4.876 distance: 58 - 59: 10.413 distance: 58 - 67: 4.816 distance: 60 - 61: 9.618 distance: 61 - 62: 7.612 distance: 62 - 63: 8.348 distance: 63 - 64: 4.505 distance: 64 - 65: 8.932 distance: 64 - 66: 4.476 distance: 67 - 68: 6.695 distance: 68 - 69: 25.790 distance: 68 - 71: 12.936 distance: 69 - 70: 7.497 distance: 69 - 75: 21.702 distance: 71 - 72: 12.554 distance: 72 - 73: 17.600 distance: 72 - 74: 18.558 distance: 75 - 76: 14.064 distance: 76 - 77: 7.705 distance: 76 - 79: 14.249 distance: 77 - 78: 9.580 distance: 77 - 84: 5.269 distance: 79 - 80: 7.054 distance: 80 - 81: 7.759 distance: 81 - 82: 6.487 distance: 81 - 83: 5.868 distance: 84 - 85: 5.090 distance: 85 - 86: 6.569 distance: 85 - 88: 10.008 distance: 86 - 87: 7.671 distance: 86 - 90: 6.260 distance: 88 - 89: 7.460