Starting phenix.real_space_refine on Tue Aug 26 10:01:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p7n_20267/08_2025/6p7n_20267.map" } resolution = 4.9 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17892 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 4 5.21 5 S 56 5.16 5 C 12876 2.51 5 N 3362 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 20356 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 847 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8796 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 1048} Chain breaks: 7 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 533 Classifications: {'DNA': 1, 'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 16} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G:plan': 1, ' G:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: G, E, F Time building chain proxies: 8.54, per 1000 atoms: 0.42 Number of scatterers: 20356 At special positions: 0 Unit cell: (152.1, 165.6, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 50 15.00 Mg 4 11.99 O 4008 8.00 N 3362 7.00 C 12876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 934.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4500 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 48.9% alpha, 13.3% beta 12 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'C' and resid 128 through 148 Processing helix chain 'C' and resid 151 through 155 removed outlier: 3.552A pdb=" N ARG C 155 " --> pdb=" O TYR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'G' and resid 129 through 148 Processing helix chain 'G' and resid 151 through 155 removed outlier: 3.553A pdb=" N ARG G 155 " --> pdb=" O TYR G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 204 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 38 through 66 removed outlier: 4.581A pdb=" N LYS A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.670A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE A 119 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 150 Processing helix chain 'A' and resid 151 through 159 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.762A pdb=" N GLU A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 312 through 327 Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 409 through 431 Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.649A pdb=" N PHE A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 718 through 728 removed outlier: 4.083A pdb=" N PHE A 728 " --> pdb=" O PHE A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Processing helix chain 'A' and resid 872 through 886 Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.609A pdb=" N GLU A 894 " --> pdb=" O TRP A 890 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 917 " --> pdb=" O GLU A 913 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 955 Processing helix chain 'A' and resid 969 through 973 removed outlier: 4.244A pdb=" N GLY A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE A1052 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1120 through 1135 removed outlier: 4.256A pdb=" N TYR A1124 " --> pdb=" O ASP A1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A1125 " --> pdb=" O LYS A1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1178 through 1201 removed outlier: 3.680A pdb=" N VAL A1191 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1214 through 1225 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 26 through 33 Processing helix chain 'E' and resid 38 through 66 removed outlier: 4.583A pdb=" N LYS E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.671A pdb=" N ARG E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 114 through 120 removed outlier: 4.221A pdb=" N PHE E 119 " --> pdb=" O LYS E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 127 through 132 removed outlier: 3.597A pdb=" N LEU E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 144 removed outlier: 3.968A pdb=" N LEU E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 150 Processing helix chain 'E' and resid 151 through 159 Processing helix chain 'E' and resid 170 through 178 removed outlier: 3.763A pdb=" N GLU E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 201 through 211 removed outlier: 4.355A pdb=" N ILE E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 312 through 327 Processing helix chain 'E' and resid 341 through 352 removed outlier: 3.709A pdb=" N SER E 345 " --> pdb=" O GLY E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 removed outlier: 3.974A pdb=" N ILE E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 392 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 409 through 431 Processing helix chain 'E' and resid 433 through 437 removed outlier: 3.650A pdb=" N PHE E 436 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 471 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 483 through 498 removed outlier: 4.456A pdb=" N ASP E 489 " --> pdb=" O SER E 485 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 512 Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 718 through 728 removed outlier: 4.082A pdb=" N PHE E 728 " --> pdb=" O PHE E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 791 removed outlier: 4.115A pdb=" N GLU E 791 " --> pdb=" O ARG E 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 811 through 822 Processing helix chain 'E' and resid 872 through 886 Processing helix chain 'E' and resid 890 through 919 removed outlier: 3.608A pdb=" N GLU E 894 " --> pdb=" O TRP E 890 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS E 909 " --> pdb=" O SER E 905 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS E 917 " --> pdb=" O GLU E 913 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 955 Processing helix chain 'E' and resid 969 through 973 removed outlier: 4.243A pdb=" N GLY E 973 " --> pdb=" O ALA E 970 " (cutoff:3.500A) Processing helix chain 'E' and resid 1020 through 1029 Processing helix chain 'E' and resid 1048 through 1052 removed outlier: 3.506A pdb=" N PHE E1052 " --> pdb=" O TYR E1049 " (cutoff:3.500A) Processing helix chain 'E' and resid 1091 through 1102 Processing helix chain 'E' and resid 1111 through 1116 Processing helix chain 'E' and resid 1120 through 1135 removed outlier: 4.257A pdb=" N TYR E1124 " --> pdb=" O ASP E1120 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER E1125 " --> pdb=" O LYS E1121 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E1135 " --> pdb=" O MET E1131 " (cutoff:3.500A) Processing helix chain 'E' and resid 1165 through 1167 No H-bonds generated for 'chain 'E' and resid 1165 through 1167' Processing helix chain 'E' and resid 1178 through 1201 removed outlier: 3.679A pdb=" N VAL E1191 " --> pdb=" O ILE E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1205 through 1209 Processing helix chain 'E' and resid 1214 through 1225 Processing sheet with id=AA1, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C 157 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 222 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 206 through 207 removed outlier: 6.894A pdb=" N CYS C 195 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS C 185 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 197 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN G 157 " --> pdb=" O VAL G 213 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 222 " --> pdb=" O ILE G 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 206 through 207 removed outlier: 6.893A pdb=" N CYS G 195 " --> pdb=" O CYS G 185 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 185 " --> pdb=" O CYS G 195 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR G 197 " --> pdb=" O GLY G 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 737 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR A 553 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 794 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 765 through 766 Processing sheet with id=AA9, first strand: chain 'A' and resid 850 through 855 removed outlier: 6.464A pdb=" N VAL A 843 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN A 853 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE A 841 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 925 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 922 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 996 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 924 " --> pdb=" O ILE A 996 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 863 removed outlier: 3.503A pdb=" N ILE A 868 " --> pdb=" O ASN A 861 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU A1065 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1070 through 1073 Processing sheet with id=AB4, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR A1162 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 737 " --> pdb=" O ALA E 801 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 545 through 549 removed outlier: 4.866A pdb=" N TYR E 553 " --> pdb=" O ILE E 704 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR E 794 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'E' and resid 765 through 766 Processing sheet with id=AB9, first strand: chain 'E' and resid 850 through 855 removed outlier: 6.465A pdb=" N VAL E 843 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN E 853 " --> pdb=" O ILE E 841 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE E 841 " --> pdb=" O GLN E 853 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU E 925 " --> pdb=" O ILE E 831 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE E 922 " --> pdb=" O PHE E 994 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE E 996 " --> pdb=" O ILE E 922 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU E 924 " --> pdb=" O ILE E 996 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 858 through 863 removed outlier: 3.504A pdb=" N ILE E 868 " --> pdb=" O ASN E 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 1033 through 1037 removed outlier: 3.793A pdb=" N LEU E1065 " --> pdb=" O PHE E1045 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1070 through 1073 Processing sheet with id=AC4, first strand: chain 'E' and resid 1151 through 1155 removed outlier: 4.724A pdb=" N TYR E1162 " --> pdb=" O SER E1152 " (cutoff:3.500A) 909 hydrogen bonds defined for protein. 2499 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.00 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: 6240 1.34 - 1.46: 3449 1.46 - 1.57: 10977 1.57 - 1.69: 100 1.69 - 1.81: 94 Bond restraints: 20860 Sorted by residual: bond pdb=" CB GLU E 443 " pdb=" CG GLU E 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 bond pdb=" CB GLU A 443 " pdb=" CG GLU A 443 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.26e-01 bond pdb=" CA ASP C 137 " pdb=" C ASP C 137 " ideal model delta sigma weight residual 1.522 1.509 0.013 1.40e-02 5.10e+03 7.97e-01 bond pdb=" CA ASP G 137 " pdb=" C ASP G 137 " ideal model delta sigma weight residual 1.522 1.509 0.012 1.40e-02 5.10e+03 7.52e-01 bond pdb=" CG LEU A1130 " pdb=" CD2 LEU A1130 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.10e-01 ... (remaining 20855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 28130 2.48 - 4.97: 160 4.97 - 7.45: 16 7.45 - 9.93: 2 9.93 - 12.41: 2 Bond angle restraints: 28310 Sorted by residual: angle pdb=" N LEU C 138 " pdb=" CA LEU C 138 " pdb=" C LEU C 138 " ideal model delta sigma weight residual 111.36 107.38 3.98 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N LEU G 138 " pdb=" CA LEU G 138 " pdb=" C LEU G 138 " ideal model delta sigma weight residual 111.36 107.39 3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" CA LEU C 138 " pdb=" CB LEU C 138 " pdb=" CG LEU C 138 " ideal model delta sigma weight residual 116.30 128.71 -12.41 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA LEU G 138 " pdb=" CB LEU G 138 " pdb=" CG LEU G 138 " ideal model delta sigma weight residual 116.30 128.66 -12.36 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C LEU A 497 " pdb=" N LEU A 498 " pdb=" CA LEU A 498 " ideal model delta sigma weight residual 122.31 116.41 5.90 2.00e+00 2.50e-01 8.71e+00 ... (remaining 28305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.28: 12230 31.28 - 62.57: 382 62.57 - 93.85: 42 93.85 - 125.13: 0 125.13 - 156.41: 2 Dihedral angle restraints: 12656 sinusoidal: 5686 harmonic: 6970 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.59 156.41 1 1.70e+01 3.46e-03 6.37e+01 dihedral pdb=" O4' U F 14 " pdb=" C1' U F 14 " pdb=" N1 U F 14 " pdb=" C2 U F 14 " ideal model delta sinusoidal sigma weight residual 232.00 75.67 156.33 1 1.70e+01 3.46e-03 6.36e+01 dihedral pdb=" CA ALA E 195 " pdb=" C ALA E 195 " pdb=" N ILE E 196 " pdb=" CA ILE E 196 " ideal model delta harmonic sigma weight residual 180.00 157.44 22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 12653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2246 0.039 - 0.078: 632 0.078 - 0.117: 182 0.117 - 0.156: 31 0.156 - 0.195: 5 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C1' C B 9 " pdb=" O4' C B 9 " pdb=" C2' C B 9 " pdb=" N1 C B 9 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" C1' C F 9 " pdb=" O4' C F 9 " pdb=" C2' C F 9 " pdb=" N1 C F 9 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CB THR G 140 " pdb=" CA THR G 140 " pdb=" OG1 THR G 140 " pdb=" CG2 THR G 140 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 3093 not shown) Planarity restraints: 3434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 136 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C ILE G 136 " 0.057 2.00e-02 2.50e+03 pdb=" O ILE G 136 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP G 137 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " 0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ILE C 136 " -0.057 2.00e-02 2.50e+03 pdb=" O ILE C 136 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 137 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 176 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ILE E 176 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 176 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN E 177 " -0.017 2.00e-02 2.50e+03 ... (remaining 3431 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 594 2.70 - 3.25: 20158 3.25 - 3.80: 31076 3.80 - 4.35: 43031 4.35 - 4.90: 70067 Nonbonded interactions: 164926 Sorted by model distance: nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.152 3.040 nonbonded pdb=" O SER E 68 " pdb=" OG SER E 68 " model vdw 2.152 3.040 nonbonded pdb=" OP2 A B 17 " pdb="MG MG A1301 " model vdw 2.195 2.170 nonbonded pdb=" OP2 A F 17 " pdb="MG MG E1301 " model vdw 2.202 2.170 nonbonded pdb=" OE1 GLU C 184 " pdb=" O5' A B 1 " model vdw 2.209 3.040 ... (remaining 164921 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'G' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.002 0.029 20860 Z= 0.099 Angle : 0.533 12.414 28310 Z= 0.298 Chirality : 0.040 0.195 3096 Planarity : 0.004 0.042 3434 Dihedral : 15.216 156.413 8156 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.33 % Allowed : 3.84 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.30 (0.15), residues: 2316 helix: -1.44 (0.14), residues: 1052 sheet: -3.27 (0.29), residues: 212 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 187 TYR 0.011 0.001 TYR C 188 PHE 0.013 0.001 PHE E 946 TRP 0.010 0.001 TRP A1193 HIS 0.006 0.001 HIS E 909 Details of bonding type rmsd covalent geometry : bond 0.00186 (20860) covalent geometry : angle 0.53270 (28310) hydrogen bonds : bond 0.15089 ( 887) hydrogen bonds : angle 6.22256 ( 2547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4632 Ramachandran restraints generated. 2316 Oldfield, 0 Emsley, 2316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8618 (pm20) REVERT: C 224 MET cc_start: 0.7124 (mtp) cc_final: 0.6570 (mtm) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0759 time to fit residues: 2.2053 Evaluate side-chains 16 residues out of total 100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.027 Evaluate side-chains 79 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 701 MET cc_start: 0.9055 (ttm) cc_final: 0.8792 (tpp) REVERT: A 796 LEU cc_start: 0.9855 (tp) cc_final: 0.9629 (pp) outliers start: 13 outliers final: 3 residues processed: 78 average time/residue: 0.1013 time to fit residues: 10.8009 Evaluate side-chains 38 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.219 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0049 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 704, in refine_xyz self.minimization_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 794, in minimization_ncs weight = 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 394, 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 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ 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/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = 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: 61.0546 > 50: distance: 0 - 1: 17.933 distance: 1 - 2: 16.262 distance: 1 - 4: 13.997 distance: 2 - 3: 25.663 distance: 2 - 7: 19.193 distance: 4 - 5: 12.269 distance: 4 - 6: 11.780 distance: 7 - 8: 20.252 distance: 8 - 9: 9.924 distance: 8 - 11: 12.099 distance: 9 - 10: 11.736 distance: 9 - 16: 12.667 distance: 11 - 12: 42.732 distance: 13 - 14: 20.030 distance: 14 - 15: 11.885 distance: 16 - 17: 13.621 distance: 17 - 18: 30.499 distance: 17 - 20: 25.572 distance: 18 - 19: 25.249 distance: 18 - 28: 6.186 distance: 20 - 21: 5.395 distance: 21 - 22: 13.631 distance: 21 - 23: 4.587 distance: 22 - 24: 10.810 distance: 23 - 25: 16.188 distance: 24 - 26: 9.067 distance: 25 - 26: 10.867 distance: 26 - 27: 17.133 distance: 28 - 29: 12.903 distance: 29 - 30: 28.470 distance: 29 - 32: 39.458 distance: 30 - 31: 26.289 distance: 30 - 35: 23.442 distance: 32 - 33: 27.994 distance: 32 - 34: 40.164 distance: 35 - 36: 39.207 distance: 36 - 37: 11.455 distance: 36 - 39: 20.725 distance: 37 - 38: 15.272 distance: 37 - 41: 14.463 distance: 38 - 62: 44.013 distance: 39 - 40: 24.604 distance: 41 - 42: 4.065 distance: 42 - 43: 34.214 distance: 42 - 45: 36.765 distance: 43 - 44: 13.434 distance: 43 - 49: 8.277 distance: 44 - 68: 29.167 distance: 45 - 46: 11.431 distance: 45 - 47: 18.947 distance: 46 - 48: 23.663 distance: 49 - 50: 33.182 distance: 50 - 51: 20.940 distance: 50 - 53: 23.696 distance: 51 - 52: 11.343 distance: 51 - 54: 16.540 distance: 54 - 55: 20.318 distance: 55 - 56: 18.277 distance: 55 - 58: 6.926 distance: 56 - 57: 27.336 distance: 56 - 62: 13.491 distance: 58 - 59: 22.993 distance: 59 - 60: 17.194 distance: 59 - 61: 19.225 distance: 62 - 63: 23.285 distance: 63 - 64: 14.568 distance: 63 - 66: 16.474 distance: 64 - 65: 9.374 distance: 64 - 68: 21.123 distance: 66 - 67: 3.035 distance: 68 - 69: 6.598 distance: 69 - 70: 8.937 distance: 69 - 72: 14.545 distance: 70 - 71: 3.486 distance: 72 - 73: 5.322 distance: 73 - 74: 4.518 distance: 74 - 75: 7.144 distance: 75 - 76: 4.149