Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bhw_16071/11_2024/8bhw_16071.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 120 5.16 5 C 13416 2.51 5 N 3800 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "D" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 10.73, per 1000 atoms: 0.51 Number of scatterers: 21240 At special positions: 0 Unit cell: (126.14, 126.14, 170.66, 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 120 16.00 O 3904 8.00 N 3800 7.00 C 13416 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 70.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.775A pdb=" N ARG A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.532A pdb=" N ILE A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.984A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 4.344A pdb=" N SER A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.668A pdb=" N GLN A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.630A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 239 removed outlier: 3.616A pdb=" N ASN A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 260 through 275 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.587A pdb=" N ASP A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 348 removed outlier: 3.549A pdb=" N MET A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.748A pdb=" N ARG B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 50 removed outlier: 4.149A pdb=" N ALA B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.568A pdb=" N GLY B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 110 through 121 removed outlier: 3.522A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.638A pdb=" N LYS B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 removed outlier: 3.586A pdb=" N ASN B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 238 removed outlier: 3.972A pdb=" N LEU B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 279 through 295 removed outlier: 3.551A pdb=" N ASP B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 348 Processing helix chain 'C' and resid 18 through 29 removed outlier: 3.779A pdb=" N ARG C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 27 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 50 removed outlier: 3.555A pdb=" N ILE C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.897A pdb=" N GLY C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 4.273A pdb=" N SER C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 110 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.662A pdb=" N GLN C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.630A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 239 removed outlier: 3.554A pdb=" N ASN C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 260 through 275 Processing helix chain 'C' and resid 279 through 295 removed outlier: 3.586A pdb=" N ASP C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.535A pdb=" N ARG C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 removed outlier: 3.973A pdb=" N ARG D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 50 removed outlier: 4.121A pdb=" N ALA D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 47 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.570A pdb=" N GLY D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.555A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.809A pdb=" N LYS D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 144 removed outlier: 3.585A pdb=" N ASN D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 238 removed outlier: 3.971A pdb=" N LEU D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.577A pdb=" N ASP D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 348 Processing helix chain 'E' and resid 18 through 29 removed outlier: 3.806A pdb=" N ARG E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP E 27 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.567A pdb=" N ILE E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 36 " --> pdb=" O TRP E 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.861A pdb=" N GLY E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 86 removed outlier: 4.256A pdb=" N SER E 74 " --> pdb=" O GLY E 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 85 " --> pdb=" O ASN E 81 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 removed outlier: 3.513A pdb=" N SER E 110 " --> pdb=" O MET E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 120 removed outlier: 3.629A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 Processing helix chain 'E' and resid 167 through 239 removed outlier: 3.550A pdb=" N ASN E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 260 through 275 Processing helix chain 'E' and resid 279 through 295 removed outlier: 3.603A pdb=" N ASP E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 295 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 347 removed outlier: 3.670A pdb=" N ARG E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N CYS E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.838A pdb=" N ARG F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 50 removed outlier: 3.513A pdb=" N LEU F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA F 39 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA F 41 " --> pdb=" O GLY F 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR F 47 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 70 removed outlier: 3.563A pdb=" N GLY F 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 83 Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 110 through 121 removed outlier: 3.521A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.719A pdb=" N LYS F 125 " --> pdb=" O THR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.581A pdb=" N ASN F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 238 removed outlier: 3.970A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 Processing helix chain 'F' and resid 279 through 295 removed outlier: 3.557A pdb=" N ASP F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY F 295 " --> pdb=" O THR F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 348 Processing helix chain 'G' and resid 18 through 29 removed outlier: 3.698A pdb=" N ARG G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.837A pdb=" N LEU G 38 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 70 removed outlier: 3.870A pdb=" N GLY G 70 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 removed outlier: 4.267A pdb=" N SER G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.652A pdb=" N GLN G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.623A pdb=" N ILE G 146 " --> pdb=" O MET G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 239 removed outlier: 3.615A pdb=" N ASN G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 260 through 275 Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.585A pdb=" N ASP G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY G 295 " --> pdb=" O THR G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 347 removed outlier: 3.649A pdb=" N ILE G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 removed outlier: 3.835A pdb=" N ARG H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 50 removed outlier: 4.167A pdb=" N ALA H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR H 47 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE H 49 " --> pdb=" O LEU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 70 removed outlier: 3.571A pdb=" N GLY H 70 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 83 Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 110 through 121 removed outlier: 3.553A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.801A pdb=" N LYS H 125 " --> pdb=" O THR H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.589A pdb=" N ASN H 144 " --> pdb=" O ASP H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 238 removed outlier: 3.972A pdb=" N LEU H 175 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 Processing helix chain 'H' and resid 279 through 295 removed outlier: 3.558A pdb=" N ASP H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY H 295 " --> pdb=" O THR H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 348 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 149 removed outlier: 6.256A pdb=" N ILE A 60 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 147 through 149 removed outlier: 6.806A pdb=" N ASP B 62 " --> pdb=" O TYR B 307 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR B 307 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 147 through 149 removed outlier: 6.258A pdb=" N ILE C 60 " --> pdb=" O LEU C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 147 through 149 removed outlier: 6.791A pdb=" N ASP D 62 " --> pdb=" O TYR D 307 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N TYR D 307 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 147 through 149 removed outlier: 6.246A pdb=" N ILE E 60 " --> pdb=" O LEU E 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 147 through 149 removed outlier: 6.790A pdb=" N ASP F 62 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR F 307 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 147 through 149 removed outlier: 6.258A pdb=" N ILE G 60 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 147 through 149 removed outlier: 6.780A pdb=" N ASP H 62 " --> pdb=" O TYR H 307 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR H 307 " --> pdb=" O ASP H 62 " (cutoff:3.500A) 1454 hydrogen bonds defined for protein. 4242 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: 4.22 Time building geometry restraints manager: 4.28 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: 7188 1.34 - 1.46: 4811 1.46 - 1.58: 9433 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 21664 Sorted by residual: bond pdb=" CB ARG B 85 " pdb=" CG ARG B 85 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CB ARG H 85 " pdb=" CG ARG H 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" CB ARG D 85 " pdb=" CG ARG D 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 bond pdb=" CB ARG F 85 " pdb=" CG ARG F 85 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.54e-01 ... (remaining 21659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 28962 2.07 - 4.14: 264 4.14 - 6.21: 61 6.21 - 8.29: 19 8.29 - 10.36: 6 Bond angle restraints: 29312 Sorted by residual: angle pdb=" CB MET A 36 " pdb=" CG MET A 36 " pdb=" SD MET A 36 " ideal model delta sigma weight residual 112.70 123.06 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CB MET B 224 " pdb=" CG MET B 224 " pdb=" SD MET B 224 " ideal model delta sigma weight residual 112.70 122.74 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CB MET H 263 " pdb=" CG MET H 263 " pdb=" SD MET H 263 " ideal model delta sigma weight residual 112.70 122.26 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET D 263 " pdb=" CG MET D 263 " pdb=" SD MET D 263 " ideal model delta sigma weight residual 112.70 122.26 -9.56 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB ARG E 85 " pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 111.30 118.45 -7.15 2.30e+00 1.89e-01 9.67e+00 ... (remaining 29307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 11270 17.00 - 34.00: 1420 34.00 - 51.00: 389 51.00 - 68.00: 70 68.00 - 85.00: 19 Dihedral angle restraints: 13168 sinusoidal: 5392 harmonic: 7776 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" CB ASP A 62 " pdb=" CG ASP A 62 " pdb=" OD1 ASP A 62 " ideal model delta sinusoidal sigma weight residual -30.00 -88.13 58.13 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP E 62 " pdb=" CB ASP E 62 " pdb=" CG ASP E 62 " pdb=" OD1 ASP E 62 " ideal model delta sinusoidal sigma weight residual -30.00 -87.92 57.92 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP C 62 " pdb=" CB ASP C 62 " pdb=" CG ASP C 62 " pdb=" OD1 ASP C 62 " ideal model delta sinusoidal sigma weight residual -30.00 -87.90 57.90 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 13165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1918 0.025 - 0.050: 833 0.050 - 0.075: 287 0.075 - 0.100: 96 0.100 - 0.125: 50 Chirality restraints: 3184 Sorted by residual: chirality pdb=" CA ARG G 301 " pdb=" N ARG G 301 " pdb=" C ARG G 301 " pdb=" CB ARG G 301 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 149 " pdb=" N ILE B 149 " pdb=" C ILE B 149 " pdb=" CB ILE B 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ARG C 301 " pdb=" N ARG C 301 " pdb=" C ARG C 301 " pdb=" CB ARG C 301 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 3181 not shown) Planarity restraints: 3840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 319 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO E 320 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO E 320 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 320 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 319 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO C 320 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 320 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 320 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " -0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 247 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.015 5.00e-02 4.00e+02 ... (remaining 3837 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1139 2.73 - 3.27: 21538 3.27 - 3.82: 36251 3.82 - 4.36: 38042 4.36 - 4.90: 68509 Nonbonded interactions: 165479 Sorted by model distance: nonbonded pdb=" O LEU E 108 " pdb=" OH TYR E 178 " model vdw 2.188 3.040 nonbonded pdb=" O LEU G 108 " pdb=" OH TYR G 178 " model vdw 2.190 3.040 nonbonded pdb=" O LEU A 108 " pdb=" OH TYR A 178 " model vdw 2.191 3.040 nonbonded pdb=" O LEU C 108 " pdb=" OH TYR C 178 " model vdw 2.192 3.040 nonbonded pdb=" OD1 ASP C 83 " pdb=" NH2 ARG C 201 " model vdw 2.235 3.120 ... (remaining 165474 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.360 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.003 0.031 21664 Z= 0.194 Angle : 0.561 10.356 29312 Z= 0.280 Chirality : 0.034 0.125 3184 Planarity : 0.003 0.035 3840 Dihedral : 16.119 85.004 8128 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.18 % Allowed : 19.16 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2640 helix: 3.26 (0.13), residues: 1648 sheet: 2.23 (0.48), residues: 156 loop : -0.71 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.002 0.000 HIS E 237 PHE 0.015 0.001 PHE G 153 TYR 0.013 0.001 TYR E 123 ARG 0.006 0.000 ARG C 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 75 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8415 (mm-40) REVERT: F 75 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8447 (mm-40) REVERT: G 68 MET cc_start: 0.9153 (ttm) cc_final: 0.8857 (ttm) REVERT: G 97 MET cc_start: 0.9056 (mpp) cc_final: 0.8745 (mmm) outliers start: 4 outliers final: 2 residues processed: 132 average time/residue: 0.2341 time to fit residues: 48.1172 Evaluate side-chains 130 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: