Starting phenix.real_space_refine on Sun Aug 24 16:43:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_16071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_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/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_16071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_16071.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_16071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhw_16071/08_2025/8bhw_16071.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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): 0.02s 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: 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: 4.42, per 1000 atoms: 0.21 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: 1.52 Conformation dependent library (CDL) restraints added in 844.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.61 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: 4.10 Time building geometry restraints manager: 1.96 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: 0.01 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: 7.070 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: 0.040 Extract box with map and model: 0.350 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 19.090 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.820 ------------------------------------------------------------------------------- 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= 0.137 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 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: 3.05 (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 ARG 0.006 0.000 ARG C 85 TYR 0.013 0.001 TYR E 123 PHE 0.015 0.001 PHE G 153 TRP 0.013 0.001 TRP C 111 HIS 0.002 0.000 HIS E 237 Details of bonding type rmsd covalent geometry : bond 0.00299 (21664) covalent geometry : angle 0.56136 (29312) hydrogen bonds : bond 0.17159 ( 1454) hydrogen bonds : angle 5.47504 ( 4242) *********************** 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 : 0.553 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: 0.1349 time to fit residues: 27.6481 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 : 0.497 ------------------------------------------------------------------------------- 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 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 50.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN C 270 ASN G 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.093198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.061752 restraints weight = 93383.422| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 5.25 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21664 Z= 0.168 Angle : 0.529 7.061 29312 Z= 0.276 Chirality : 0.036 0.161 3184 Planarity : 0.004 0.041 3840 Dihedral : 4.039 63.409 2971 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.49 % Allowed : 18.66 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.28 (0.17), residues: 2640 helix: 3.26 (0.12), residues: 1760 sheet: 1.93 (0.47), residues: 156 loop : -0.71 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.011 0.001 TYR E 123 PHE 0.013 0.001 PHE D 181 TRP 0.012 0.001 TRP D 111 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00361 (21664) covalent geometry : angle 0.52914 (29312) hydrogen bonds : bond 0.05367 ( 1454) hydrogen bonds : angle 4.01420 ( 4242) *********************** REFINEMENT MACRO_CYCLE 2 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 161 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8384 (mtp180) REVERT: D 224 MET cc_start: 0.8822 (tpp) cc_final: 0.8527 (tpp) REVERT: E 272 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9083 (mt0) REVERT: F 224 MET cc_start: 0.8818 (tpp) cc_final: 0.8535 (tpp) REVERT: G 36 MET cc_start: 0.6925 (ppp) cc_final: 0.6713 (ppp) REVERT: G 97 MET cc_start: 0.9037 (mpp) cc_final: 0.8760 (mmm) REVERT: H 224 MET cc_start: 0.8797 (tpp) cc_final: 0.8510 (tpp) outliers start: 33 outliers final: 15 residues processed: 160 average time/residue: 0.1508 time to fit residues: 36.9145 Evaluate side-chains 144 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 45 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.093875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.062672 restraints weight = 93251.078| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 5.08 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21664 Z= 0.125 Angle : 0.484 7.239 29312 Z= 0.251 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.041 3840 Dihedral : 3.414 13.920 2960 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.49 % Allowed : 18.89 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.31 (0.17), residues: 2640 helix: 3.22 (0.12), residues: 1784 sheet: 1.91 (0.48), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 85 TYR 0.012 0.001 TYR A 123 PHE 0.010 0.001 PHE H 181 TRP 0.013 0.001 TRP B 32 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00261 (21664) covalent geometry : angle 0.48418 (29312) hydrogen bonds : bond 0.04526 ( 1454) hydrogen bonds : angle 3.70504 ( 4242) *********************** REFINEMENT MACRO_CYCLE 3 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 164 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8430 (mtt180) REVERT: B 224 MET cc_start: 0.8786 (tpp) cc_final: 0.8511 (tpp) REVERT: D 224 MET cc_start: 0.8782 (tpp) cc_final: 0.8511 (tpp) REVERT: F 224 MET cc_start: 0.8805 (tpp) cc_final: 0.8508 (tpp) REVERT: G 36 MET cc_start: 0.6594 (ppp) cc_final: 0.6360 (ppp) REVERT: H 224 MET cc_start: 0.8770 (tpp) cc_final: 0.8506 (tpp) outliers start: 33 outliers final: 21 residues processed: 163 average time/residue: 0.1374 time to fit residues: 34.6419 Evaluate side-chains 148 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 239 optimal weight: 0.8980 chunk 64 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.081174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.051162 restraints weight = 83831.413| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 4.79 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21664 Z= 0.131 Angle : 0.491 7.450 29312 Z= 0.251 Chirality : 0.035 0.155 3184 Planarity : 0.003 0.039 3840 Dihedral : 3.393 13.807 2960 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.99 % Allowed : 18.93 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.34 (0.17), residues: 2640 helix: 3.26 (0.12), residues: 1784 sheet: 1.86 (0.48), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 155 TYR 0.011 0.001 TYR A 123 PHE 0.020 0.001 PHE C 40 TRP 0.012 0.001 TRP H 111 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00281 (21664) covalent geometry : angle 0.49055 (29312) hydrogen bonds : bond 0.04357 ( 1454) hydrogen bonds : angle 3.62257 ( 4242) *********************** REFINEMENT MACRO_CYCLE 4 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 172 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8379 (mtt180) REVERT: B 112 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8813 (m-30) REVERT: B 224 MET cc_start: 0.8833 (tpp) cc_final: 0.8418 (tpp) REVERT: C 263 MET cc_start: 0.9366 (mmm) cc_final: 0.9155 (mmp) REVERT: D 224 MET cc_start: 0.8835 (tpp) cc_final: 0.8420 (tpp) REVERT: E 36 MET cc_start: 0.7706 (ppp) cc_final: 0.7247 (ppp) REVERT: F 112 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8818 (m-30) REVERT: F 224 MET cc_start: 0.8867 (tpp) cc_final: 0.8436 (tpp) REVERT: G 36 MET cc_start: 0.5910 (ppp) cc_final: 0.5623 (ppp) REVERT: H 112 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8827 (m-30) REVERT: H 224 MET cc_start: 0.8822 (tpp) cc_final: 0.8426 (tpp) outliers start: 44 outliers final: 27 residues processed: 171 average time/residue: 0.1217 time to fit residues: 32.8515 Evaluate side-chains 158 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 87 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 190 optimal weight: 0.9990 chunk 222 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.094239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.063108 restraints weight = 92540.452| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.12 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21664 Z= 0.109 Angle : 0.477 9.659 29312 Z= 0.244 Chirality : 0.035 0.156 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.335 13.430 2960 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.68 % Allowed : 19.43 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.41 (0.17), residues: 2640 helix: 3.32 (0.12), residues: 1784 sheet: 1.94 (0.49), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 85 TYR 0.011 0.001 TYR A 123 PHE 0.011 0.001 PHE C 40 TRP 0.013 0.001 TRP D 111 HIS 0.003 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00221 (21664) covalent geometry : angle 0.47730 (29312) hydrogen bonds : bond 0.04098 ( 1454) hydrogen bonds : angle 3.49051 ( 4242) *********************** REFINEMENT MACRO_CYCLE 5 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 167 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8413 (mtt180) REVERT: B 224 MET cc_start: 0.8792 (tpp) cc_final: 0.8423 (tpp) REVERT: C 97 MET cc_start: 0.8939 (mpp) cc_final: 0.8657 (mmm) REVERT: D 224 MET cc_start: 0.8801 (tpp) cc_final: 0.8400 (tpp) REVERT: F 224 MET cc_start: 0.8827 (tpp) cc_final: 0.8411 (tpp) REVERT: G 36 MET cc_start: 0.6375 (ppp) cc_final: 0.6102 (ppp) REVERT: H 224 MET cc_start: 0.8799 (tpp) cc_final: 0.8427 (tpp) outliers start: 37 outliers final: 30 residues processed: 167 average time/residue: 0.1438 time to fit residues: 36.8268 Evaluate side-chains 160 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 159 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.081522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051686 restraints weight = 83224.803| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.76 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21664 Z= 0.116 Angle : 0.491 8.649 29312 Z= 0.247 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.302 13.963 2960 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.99 % Allowed : 19.66 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.49 (0.17), residues: 2640 helix: 3.38 (0.12), residues: 1784 sheet: 1.99 (0.49), residues: 156 loop : -0.66 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 155 TYR 0.011 0.001 TYR A 123 PHE 0.009 0.001 PHE C 40 TRP 0.013 0.001 TRP D 111 HIS 0.002 0.001 HIS B 189 Details of bonding type rmsd covalent geometry : bond 0.00244 (21664) covalent geometry : angle 0.49148 (29312) hydrogen bonds : bond 0.04025 ( 1454) hydrogen bonds : angle 3.43708 ( 4242) *********************** REFINEMENT MACRO_CYCLE 6 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 175 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: B 112 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: B 224 MET cc_start: 0.8800 (tpp) cc_final: 0.8348 (tpp) REVERT: C 68 MET cc_start: 0.8676 (ttp) cc_final: 0.8219 (ptp) REVERT: D 112 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8802 (m-30) REVERT: D 224 MET cc_start: 0.8857 (tpp) cc_final: 0.8380 (tpp) REVERT: E 272 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9200 (mt0) REVERT: F 112 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8791 (m-30) REVERT: F 224 MET cc_start: 0.8894 (tpp) cc_final: 0.8417 (tpp) REVERT: G 36 MET cc_start: 0.5671 (ppp) cc_final: 0.5362 (ppp) REVERT: G 68 MET cc_start: 0.8711 (ttp) cc_final: 0.8191 (ptp) REVERT: G 155 ARG cc_start: 0.9262 (mtm-85) cc_final: 0.8551 (mpp80) REVERT: H 112 ASP cc_start: 0.9074 (OUTLIER) cc_final: 0.8797 (m-30) REVERT: H 224 MET cc_start: 0.8847 (tpp) cc_final: 0.8395 (tpp) outliers start: 44 outliers final: 33 residues processed: 175 average time/residue: 0.1518 time to fit residues: 40.7401 Evaluate side-chains 166 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 209 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 165 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.081659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051846 restraints weight = 83252.168| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.77 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21664 Z= 0.112 Angle : 0.487 8.402 29312 Z= 0.244 Chirality : 0.034 0.152 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.289 13.466 2960 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.17 % Allowed : 19.66 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.55 (0.17), residues: 2640 helix: 3.42 (0.12), residues: 1784 sheet: 2.03 (0.49), residues: 156 loop : -0.65 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 85 TYR 0.011 0.001 TYR C 123 PHE 0.010 0.001 PHE C 153 TRP 0.013 0.001 TRP D 111 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00234 (21664) covalent geometry : angle 0.48730 (29312) hydrogen bonds : bond 0.03926 ( 1454) hydrogen bonds : angle 3.37724 ( 4242) *********************** REFINEMENT MACRO_CYCLE 7 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 176 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8456 (mtt180) REVERT: B 112 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: B 224 MET cc_start: 0.8834 (tpp) cc_final: 0.8368 (tpp) REVERT: C 97 MET cc_start: 0.8967 (mpp) cc_final: 0.8700 (mmm) REVERT: C 155 ARG cc_start: 0.9326 (mtm110) cc_final: 0.9091 (mtm110) REVERT: D 88 MET cc_start: 0.7890 (mmp) cc_final: 0.7489 (mmp) REVERT: D 112 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8778 (m-30) REVERT: D 224 MET cc_start: 0.8872 (tpp) cc_final: 0.8379 (tpp) REVERT: E 68 MET cc_start: 0.8698 (ttp) cc_final: 0.8208 (ptm) REVERT: E 142 MET cc_start: 0.9099 (mtm) cc_final: 0.8830 (mtm) REVERT: E 272 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9194 (mt0) REVERT: F 112 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: F 224 MET cc_start: 0.8895 (tpp) cc_final: 0.8429 (tpp) REVERT: G 36 MET cc_start: 0.5466 (ppp) cc_final: 0.5141 (ppp) REVERT: G 53 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: H 112 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8787 (m-30) REVERT: H 224 MET cc_start: 0.8858 (tpp) cc_final: 0.8402 (tpp) outliers start: 48 outliers final: 34 residues processed: 175 average time/residue: 0.1375 time to fit residues: 38.2869 Evaluate side-chains 168 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 116 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 236 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.081646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051814 restraints weight = 83196.288| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.76 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21664 Z= 0.115 Angle : 0.501 9.801 29312 Z= 0.248 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.259 13.454 2960 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.08 % Allowed : 19.84 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.61 (0.17), residues: 2640 helix: 3.47 (0.12), residues: 1788 sheet: 2.03 (0.49), residues: 156 loop : -0.63 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 85 TYR 0.011 0.001 TYR A 123 PHE 0.010 0.001 PHE G 153 TRP 0.012 0.001 TRP D 111 HIS 0.002 0.001 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00242 (21664) covalent geometry : angle 0.50142 (29312) hydrogen bonds : bond 0.03893 ( 1454) hydrogen bonds : angle 3.33970 ( 4242) *********************** REFINEMENT MACRO_CYCLE 8 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 174 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8402 (mtt180) REVERT: B 88 MET cc_start: 0.7934 (mmp) cc_final: 0.7457 (mmp) REVERT: B 112 ASP cc_start: 0.9053 (OUTLIER) cc_final: 0.8775 (m-30) REVERT: B 224 MET cc_start: 0.8852 (tpp) cc_final: 0.8362 (tpp) REVERT: C 68 MET cc_start: 0.8715 (ttp) cc_final: 0.8231 (ptm) REVERT: C 97 MET cc_start: 0.8964 (mpp) cc_final: 0.8690 (mmm) REVERT: C 155 ARG cc_start: 0.9349 (mtm110) cc_final: 0.9123 (mtm110) REVERT: D 88 MET cc_start: 0.7923 (mmp) cc_final: 0.7557 (mmp) REVERT: D 112 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: D 224 MET cc_start: 0.8866 (tpp) cc_final: 0.8344 (tpp) REVERT: E 272 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.9189 (mt0) REVERT: F 88 MET cc_start: 0.7947 (mmp) cc_final: 0.7575 (mmp) REVERT: F 112 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8782 (m-30) REVERT: F 224 MET cc_start: 0.8884 (tpp) cc_final: 0.8394 (tpp) REVERT: G 36 MET cc_start: 0.5448 (ppp) cc_final: 0.5105 (ppp) REVERT: G 53 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7824 (mm-40) REVERT: G 68 MET cc_start: 0.8739 (ttp) cc_final: 0.8353 (ptm) REVERT: H 88 MET cc_start: 0.7870 (mmp) cc_final: 0.7504 (mmp) REVERT: H 112 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: H 224 MET cc_start: 0.8863 (tpp) cc_final: 0.8377 (tpp) outliers start: 46 outliers final: 36 residues processed: 173 average time/residue: 0.1402 time to fit residues: 38.5238 Evaluate side-chains 170 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 272 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 121 optimal weight: 8.9990 chunk 257 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 216 optimal weight: 0.7980 chunk 162 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.081838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052089 restraints weight = 83164.548| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.75 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21664 Z= 0.109 Angle : 0.503 10.390 29312 Z= 0.248 Chirality : 0.035 0.151 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.266 14.592 2960 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.95 % Allowed : 19.97 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.63 (0.17), residues: 2640 helix: 3.49 (0.12), residues: 1788 sheet: 2.06 (0.49), residues: 156 loop : -0.65 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.011 0.001 TYR A 123 PHE 0.008 0.001 PHE H 181 TRP 0.013 0.001 TRP D 111 HIS 0.002 0.000 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00229 (21664) covalent geometry : angle 0.50339 (29312) hydrogen bonds : bond 0.03827 ( 1454) hydrogen bonds : angle 3.31394 ( 4242) *********************** REFINEMENT MACRO_CYCLE 9 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 172 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (mtt180) REVERT: B 88 MET cc_start: 0.7941 (mmp) cc_final: 0.7569 (mmp) REVERT: B 112 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8764 (m-30) REVERT: B 224 MET cc_start: 0.8857 (tpp) cc_final: 0.8360 (tpp) REVERT: C 97 MET cc_start: 0.8949 (mpp) cc_final: 0.8673 (mmm) REVERT: D 88 MET cc_start: 0.7932 (mmp) cc_final: 0.7640 (mmp) REVERT: D 112 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8773 (m-30) REVERT: D 224 MET cc_start: 0.8880 (tpp) cc_final: 0.8353 (tpp) REVERT: E 68 MET cc_start: 0.8719 (ttp) cc_final: 0.8418 (ptm) REVERT: F 88 MET cc_start: 0.7919 (mmp) cc_final: 0.7578 (mmp) REVERT: F 112 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8772 (m-30) REVERT: F 224 MET cc_start: 0.8907 (tpp) cc_final: 0.8416 (tpp) REVERT: G 36 MET cc_start: 0.5373 (ppp) cc_final: 0.5025 (ppp) REVERT: G 53 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7833 (mm-40) REVERT: G 68 MET cc_start: 0.8725 (ttp) cc_final: 0.8203 (ptm) REVERT: H 88 MET cc_start: 0.7848 (mmp) cc_final: 0.7549 (mmp) REVERT: H 112 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: H 224 MET cc_start: 0.8871 (tpp) cc_final: 0.8385 (tpp) outliers start: 43 outliers final: 35 residues processed: 170 average time/residue: 0.1377 time to fit residues: 36.9477 Evaluate side-chains 170 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 229 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 127 optimal weight: 0.0070 chunk 181 optimal weight: 0.6980 chunk 158 optimal weight: 0.5980 chunk 194 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.081980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.052253 restraints weight = 83882.999| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.77 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21664 Z= 0.106 Angle : 0.512 11.295 29312 Z= 0.249 Chirality : 0.034 0.153 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.244 16.083 2960 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.86 % Allowed : 20.06 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.65 (0.17), residues: 2640 helix: 3.54 (0.12), residues: 1780 sheet: 1.79 (0.43), residues: 208 loop : -0.81 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 85 TYR 0.011 0.001 TYR A 123 PHE 0.010 0.001 PHE E 40 TRP 0.013 0.001 TRP D 111 HIS 0.002 0.000 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00220 (21664) covalent geometry : angle 0.51231 (29312) hydrogen bonds : bond 0.03739 ( 1454) hydrogen bonds : angle 3.27495 ( 4242) ********************** REFINEMENT MACRO_CYCLE 10 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 169 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8394 (mtt180) REVERT: B 88 MET cc_start: 0.7932 (mmp) cc_final: 0.7616 (mmp) REVERT: B 112 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8763 (m-30) REVERT: B 224 MET cc_start: 0.8842 (tpp) cc_final: 0.8362 (tpp) REVERT: C 36 MET cc_start: 0.7583 (ppp) cc_final: 0.7105 (ppp) REVERT: C 97 MET cc_start: 0.8953 (mpp) cc_final: 0.8682 (mmm) REVERT: D 88 MET cc_start: 0.7924 (mmp) cc_final: 0.7675 (mmp) REVERT: D 112 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: D 224 MET cc_start: 0.8891 (tpp) cc_final: 0.8429 (tpp) REVERT: E 68 MET cc_start: 0.8709 (ttp) cc_final: 0.8361 (ptm) REVERT: F 88 MET cc_start: 0.7925 (mmp) cc_final: 0.7650 (mmp) REVERT: F 112 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8768 (m-30) REVERT: F 224 MET cc_start: 0.8914 (tpp) cc_final: 0.8418 (tpp) REVERT: G 36 MET cc_start: 0.5256 (ppp) cc_final: 0.4897 (ppp) REVERT: G 53 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7858 (mm-40) REVERT: G 68 MET cc_start: 0.8743 (ttp) cc_final: 0.8218 (ptm) REVERT: H 88 MET cc_start: 0.7858 (mmp) cc_final: 0.7566 (mmp) REVERT: H 112 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: H 224 MET cc_start: 0.8880 (tpp) cc_final: 0.8387 (tpp) outliers start: 41 outliers final: 35 residues processed: 167 average time/residue: 0.1436 time to fit residues: 37.9226 Evaluate side-chains 168 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 307 TYR Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 182 optimal weight: 0.8980 chunk 253 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 66 optimal weight: 0.0870 chunk 135 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.094003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.062853 restraints weight = 93071.881| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.05 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21664 Z= 0.116 Angle : 0.515 11.151 29312 Z= 0.251 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.229 14.557 2960 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.13 % Allowed : 19.93 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 3.67 (0.17), residues: 2640 helix: 3.62 (0.12), residues: 1756 sheet: 1.74 (0.43), residues: 208 loop : -0.83 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 155 TYR 0.011 0.001 TYR A 123 PHE 0.010 0.001 PHE G 153 TRP 0.012 0.001 TRP D 111 HIS 0.002 0.000 HIS F 189 Details of bonding type rmsd covalent geometry : bond 0.00247 (21664) covalent geometry : angle 0.51477 (29312) hydrogen bonds : bond 0.03788 ( 1454) hydrogen bonds : angle 3.27149 ( 4242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.96 seconds wall clock time: 68 minutes 13.22 seconds (4093.22 seconds total)