Starting phenix.real_space_refine on Wed Jun 18 15:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhw_16071/06_2025/8bhw_16071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhw_16071/06_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_16071/06_2025/8bhw_16071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhw_16071/06_2025/8bhw_16071.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhw_16071/06_2025/8bhw_16071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhw_16071/06_2025/8bhw_16071.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 13416 2.51 5 N 3800 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "B" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "D" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "F" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "G" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "H" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2655 Classifications: {'peptide': 332} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Time building chain proxies: 13.52, per 1000 atoms: 0.64 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: 5.35 Conformation dependent library (CDL) restraints added in 2.8 seconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 70.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 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: 6.09 Time building geometry restraints manager: 6.30 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: 0.02 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.640 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.17), residues: 2640 helix: 3.26 (0.13), residues: 1648 sheet: 2.23 (0.48), residues: 156 loop : -0.71 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 111 HIS 0.002 0.000 HIS E 237 PHE 0.015 0.001 PHE G 153 TYR 0.013 0.001 TYR E 123 ARG 0.006 0.000 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.17159 ( 1454) hydrogen bonds : angle 5.47504 ( 4242) covalent geometry : bond 0.00299 (21664) covalent geometry : angle 0.56136 (29312) *********************** 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 : 2.748 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: 0.3393 time to fit residues: 70.0889 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 : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain F residue 75 GLN Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3801 r_free = 0.3801 target = 0.080532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.050545 restraints weight = 83505.462| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.77 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21664 Z= 0.171 Angle : 0.534 7.082 29312 Z= 0.278 Chirality : 0.036 0.165 3184 Planarity : 0.004 0.041 3840 Dihedral : 4.060 63.252 2971 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.68 % Allowed : 18.39 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.17), residues: 2640 helix: 3.17 (0.12), residues: 1784 sheet: 1.91 (0.47), residues: 156 loop : -0.69 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 111 HIS 0.002 0.001 HIS F 189 PHE 0.013 0.001 PHE D 181 TYR 0.011 0.001 TYR E 123 ARG 0.004 0.000 ARG A 185 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 1454) hydrogen bonds : angle 3.98925 ( 4242) covalent geometry : bond 0.00370 (21664) covalent geometry : angle 0.53355 (29312) *********************** 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 165 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8363 (mtp180) REVERT: C 68 MET cc_start: 0.9017 (ttm) cc_final: 0.8769 (ttm) REVERT: C 97 MET cc_start: 0.9019 (mpp) cc_final: 0.8642 (mmm) REVERT: D 224 MET cc_start: 0.8864 (tpp) cc_final: 0.8521 (tpp) REVERT: E 68 MET cc_start: 0.9032 (ttm) cc_final: 0.8775 (ttm) REVERT: E 272 GLN cc_start: 0.9464 (OUTLIER) cc_final: 0.9166 (mt0) REVERT: F 224 MET cc_start: 0.8882 (tpp) cc_final: 0.8554 (tpp) REVERT: G 36 MET cc_start: 0.6397 (ppp) cc_final: 0.6118 (ppp) REVERT: G 68 MET cc_start: 0.9034 (ttm) cc_final: 0.8786 (ttp) REVERT: G 97 MET cc_start: 0.9034 (mpp) cc_final: 0.8729 (mmm) REVERT: H 224 MET cc_start: 0.8845 (tpp) cc_final: 0.8512 (tpp) outliers start: 37 outliers final: 18 residues processed: 164 average time/residue: 0.3603 time to fit residues: 91.5435 Evaluate side-chains 147 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 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 42 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 215 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 153 optimal weight: 0.9980 chunk 229 optimal weight: 10.0000 chunk 170 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.081645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051874 restraints weight = 82341.030| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.74 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 21664 Z= 0.112 Angle : 0.480 7.335 29312 Z= 0.248 Chirality : 0.035 0.149 3184 Planarity : 0.003 0.040 3840 Dihedral : 3.402 14.172 2960 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.54 % Allowed : 18.89 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.17), residues: 2640 helix: 3.22 (0.12), residues: 1784 sheet: 1.95 (0.48), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 32 HIS 0.003 0.001 HIS F 189 PHE 0.009 0.001 PHE C 117 TYR 0.011 0.001 TYR A 123 ARG 0.008 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 1454) hydrogen bonds : angle 3.68665 ( 4242) covalent geometry : bond 0.00225 (21664) covalent geometry : angle 0.48026 (29312) *********************** 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: 34 poor density : 130 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8500 (mtp85) REVERT: B 224 MET cc_start: 0.8827 (tpp) cc_final: 0.8509 (tpp) REVERT: C 68 MET cc_start: 0.9007 (ttm) cc_final: 0.8770 (ttm) REVERT: D 224 MET cc_start: 0.8811 (tpp) cc_final: 0.8492 (tpp) REVERT: E 68 MET cc_start: 0.9035 (ttm) cc_final: 0.8782 (ttm) REVERT: F 224 MET cc_start: 0.8836 (tpp) cc_final: 0.8455 (tpp) REVERT: G 36 MET cc_start: 0.6016 (ppp) cc_final: 0.5752 (ppp) REVERT: G 68 MET cc_start: 0.9016 (ttm) cc_final: 0.8778 (ttp) REVERT: H 224 MET cc_start: 0.8854 (tpp) cc_final: 0.8502 (tpp) outliers start: 34 outliers final: 20 residues processed: 162 average time/residue: 0.3452 time to fit residues: 86.1298 Evaluate side-chains 146 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 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 247 optimal weight: 0.5980 chunk 99 optimal weight: 50.0000 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 219 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.094132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.062922 restraints weight = 93649.112| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.98 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1371 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= 0.120 Angle : 0.482 7.351 29312 Z= 0.247 Chirality : 0.035 0.157 3184 Planarity : 0.003 0.039 3840 Dihedral : 3.365 14.042 2960 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.68 % Allowed : 19.29 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.17), residues: 2640 helix: 3.25 (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 TRP 0.012 0.001 TRP H 111 HIS 0.003 0.001 HIS B 189 PHE 0.020 0.001 PHE C 40 TYR 0.011 0.001 TYR A 123 ARG 0.006 0.000 ARG C 155 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 1454) hydrogen bonds : angle 3.60159 ( 4242) covalent geometry : bond 0.00253 (21664) covalent geometry : angle 0.48162 (29312) *********************** 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 165 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8407 (mtt180) REVERT: B 224 MET cc_start: 0.8829 (tpp) cc_final: 0.8460 (tpp) REVERT: C 68 MET cc_start: 0.8885 (ttm) cc_final: 0.8679 (ttp) REVERT: D 224 MET cc_start: 0.8812 (tpp) cc_final: 0.8445 (tpp) REVERT: E 36 MET cc_start: 0.7824 (ppp) cc_final: 0.7441 (ppp) REVERT: E 68 MET cc_start: 0.8894 (ttm) cc_final: 0.8689 (ttm) REVERT: F 112 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8751 (m-30) REVERT: F 224 MET cc_start: 0.8846 (tpp) cc_final: 0.8459 (tpp) REVERT: G 36 MET cc_start: 0.6347 (ppp) cc_final: 0.6075 (ppp) REVERT: G 68 MET cc_start: 0.8883 (ttm) cc_final: 0.8681 (ttp) REVERT: H 224 MET cc_start: 0.8798 (tpp) cc_final: 0.8448 (tpp) outliers start: 37 outliers final: 26 residues processed: 165 average time/residue: 0.3205 time to fit residues: 83.6778 Evaluate side-chains 155 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 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 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 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 113 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 252 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 135 optimal weight: 0.0070 chunk 112 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.081790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052004 restraints weight = 83369.054| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.75 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1526 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 : 0.475 9.261 29312 Z= 0.242 Chirality : 0.035 0.155 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.312 13.586 2960 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.68 % Allowed : 19.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.17), residues: 2640 helix: 3.32 (0.12), residues: 1784 sheet: 1.96 (0.49), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 111 HIS 0.002 0.001 HIS D 189 PHE 0.011 0.001 PHE C 40 TYR 0.011 0.001 TYR A 123 ARG 0.008 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1454) hydrogen bonds : angle 3.47461 ( 4242) covalent geometry : bond 0.00223 (21664) covalent geometry : angle 0.47525 (29312) *********************** 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 166 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8385 (mtt180) REVERT: B 112 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: B 224 MET cc_start: 0.8844 (tpp) cc_final: 0.8426 (tpp) REVERT: C 68 MET cc_start: 0.9020 (ttm) cc_final: 0.8749 (ttp) REVERT: C 97 MET cc_start: 0.8945 (mpp) cc_final: 0.8642 (mmm) REVERT: D 224 MET cc_start: 0.8848 (tpp) cc_final: 0.8389 (tpp) REVERT: E 36 MET cc_start: 0.7601 (ppp) cc_final: 0.7386 (ppp) REVERT: E 68 MET cc_start: 0.9024 (ttm) cc_final: 0.8771 (ttm) REVERT: F 112 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: F 224 MET cc_start: 0.8874 (tpp) cc_final: 0.8401 (tpp) REVERT: G 36 MET cc_start: 0.5768 (ppp) cc_final: 0.5466 (ppp) REVERT: G 68 MET cc_start: 0.9030 (ttm) cc_final: 0.8775 (ttp) REVERT: H 112 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: H 224 MET cc_start: 0.8840 (tpp) cc_final: 0.8408 (tpp) outliers start: 37 outliers final: 27 residues processed: 166 average time/residue: 0.4199 time to fit residues: 109.8520 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 : 3.508 ------------------------------------------------------------------------------- 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 B residue 112 ASP 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 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 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 319 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 214 GLU Chi-restraints excluded: chain H residue 112 ASP 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 214 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 258 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 176 optimal weight: 0.0170 chunk 1 optimal weight: 0.0870 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.094621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.063707 restraints weight = 93160.833| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 5.05 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1724 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= 0.102 Angle : 0.475 8.620 29312 Z= 0.239 Chirality : 0.034 0.155 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.269 13.598 2960 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.86 % Allowed : 19.38 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.17), residues: 2640 helix: 3.39 (0.12), residues: 1784 sheet: 2.06 (0.49), residues: 156 loop : -0.67 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 111 HIS 0.002 0.000 HIS B 189 PHE 0.009 0.001 PHE C 40 TYR 0.011 0.001 TYR C 123 ARG 0.007 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1454) hydrogen bonds : angle 3.37157 ( 4242) covalent geometry : bond 0.00204 (21664) covalent geometry : angle 0.47498 (29312) *********************** 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 172 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8499 (mtt180) REVERT: B 224 MET cc_start: 0.8792 (tpp) cc_final: 0.8406 (tpp) REVERT: D 224 MET cc_start: 0.8823 (tpp) cc_final: 0.8407 (tpp) REVERT: E 36 MET cc_start: 0.7778 (ppp) cc_final: 0.7516 (ppp) REVERT: F 224 MET cc_start: 0.8847 (tpp) cc_final: 0.8431 (tpp) REVERT: G 36 MET cc_start: 0.6126 (ppp) cc_final: 0.5816 (ppp) REVERT: H 224 MET cc_start: 0.8815 (tpp) cc_final: 0.8412 (tpp) REVERT: H 256 MET cc_start: 0.8841 (tmm) cc_final: 0.8479 (tpp) outliers start: 41 outliers final: 25 residues processed: 172 average time/residue: 0.3529 time to fit residues: 93.3471 Evaluate side-chains 155 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 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 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 161 VAL 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 154 THR 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 227 ILE 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 239 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 252 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 139 optimal weight: 0.0570 chunk 197 optimal weight: 30.0000 chunk 73 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 99 optimal weight: 50.0000 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.081608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054557 restraints weight = 80267.958| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.25 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21664 Z= 0.121 Angle : 0.498 8.824 29312 Z= 0.246 Chirality : 0.035 0.154 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.255 13.275 2960 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.63 % Allowed : 19.84 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.17), residues: 2640 helix: 3.44 (0.12), residues: 1788 sheet: 2.02 (0.49), residues: 156 loop : -0.67 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 32 HIS 0.002 0.001 HIS H 189 PHE 0.009 0.001 PHE H 181 TYR 0.011 0.001 TYR A 123 ARG 0.009 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 1454) hydrogen bonds : angle 3.37784 ( 4242) covalent geometry : bond 0.00259 (21664) covalent geometry : angle 0.49824 (29312) *********************** 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 166 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8370 (mtt180) REVERT: B 224 MET cc_start: 0.8852 (tpp) cc_final: 0.8373 (tpp) REVERT: C 97 MET cc_start: 0.8876 (mpp) cc_final: 0.8604 (mmm) REVERT: D 224 MET cc_start: 0.8876 (tpp) cc_final: 0.8447 (tpp) REVERT: D 256 MET cc_start: 0.8991 (tmm) cc_final: 0.8711 (tpp) REVERT: E 36 MET cc_start: 0.6839 (ppp) cc_final: 0.6454 (ppp) REVERT: F 224 MET cc_start: 0.8904 (tpp) cc_final: 0.8414 (tpp) REVERT: G 36 MET cc_start: 0.4179 (ppp) cc_final: 0.3864 (ppp) REVERT: H 224 MET cc_start: 0.8874 (tpp) cc_final: 0.8395 (tpp) outliers start: 36 outliers final: 30 residues processed: 165 average time/residue: 0.3392 time to fit residues: 88.2638 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 : 2.574 ------------------------------------------------------------------------------- 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 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 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 161 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 154 THR 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 244 THR Chi-restraints excluded: chain H residue 319 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 54 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 257 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN C 270 ASN E 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.079777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049475 restraints weight = 84334.473| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.74 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21664 Z= 0.231 Angle : 0.567 8.028 29312 Z= 0.285 Chirality : 0.037 0.158 3184 Planarity : 0.003 0.039 3840 Dihedral : 3.399 13.543 2960 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.63 % Allowed : 20.11 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.17), residues: 2640 helix: 3.48 (0.12), residues: 1764 sheet: 1.84 (0.49), residues: 156 loop : -0.66 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 111 HIS 0.003 0.001 HIS H 189 PHE 0.012 0.001 PHE D 181 TYR 0.011 0.002 TYR A 123 ARG 0.011 0.000 ARG G 317 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 1454) hydrogen bonds : angle 3.58676 ( 4242) covalent geometry : bond 0.00513 (21664) covalent geometry : angle 0.56681 (29312) *********************** 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 165 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8479 (mtp85) REVERT: B 88 MET cc_start: 0.8078 (mmp) cc_final: 0.7756 (mmp) REVERT: B 224 MET cc_start: 0.8833 (tpp) cc_final: 0.8353 (tpp) REVERT: C 97 MET cc_start: 0.8982 (mpp) cc_final: 0.8690 (mmm) REVERT: D 88 MET cc_start: 0.8079 (mmp) cc_final: 0.7836 (mmp) REVERT: D 224 MET cc_start: 0.8885 (tpp) cc_final: 0.8433 (tpp) REVERT: E 36 MET cc_start: 0.7428 (ppp) cc_final: 0.7137 (ppp) REVERT: F 88 MET cc_start: 0.8033 (mmp) cc_final: 0.7756 (mmp) REVERT: F 224 MET cc_start: 0.8894 (tpp) cc_final: 0.8398 (tpp) REVERT: G 36 MET cc_start: 0.5504 (ppp) cc_final: 0.5150 (ppp) REVERT: H 88 MET cc_start: 0.8027 (mmp) cc_final: 0.7742 (mmp) REVERT: H 224 MET cc_start: 0.8862 (tpp) cc_final: 0.8363 (tpp) outliers start: 36 outliers final: 33 residues processed: 165 average time/residue: 0.3823 time to fit residues: 100.6004 Evaluate side-chains 161 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 4.065 ------------------------------------------------------------------------------- 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 C residue 215 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 161 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 154 THR 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 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 243 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 241 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 257 optimal weight: 0.7980 chunk 196 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 270 ASN E 270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.080848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053481 restraints weight = 80551.781| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.43 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21664 Z= 0.134 Angle : 0.515 8.103 29312 Z= 0.255 Chirality : 0.035 0.154 3184 Planarity : 0.003 0.038 3840 Dihedral : 3.365 13.210 2960 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.68 % Allowed : 20.02 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.17), residues: 2640 helix: 3.50 (0.12), residues: 1764 sheet: 1.94 (0.49), residues: 156 loop : -0.67 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.003 0.001 HIS B 189 PHE 0.009 0.001 PHE H 181 TYR 0.012 0.001 TYR A 123 ARG 0.005 0.000 ARG C 155 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1454) hydrogen bonds : angle 3.42832 ( 4242) covalent geometry : bond 0.00291 (21664) covalent geometry : angle 0.51452 (29312) *********************** 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 167 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8419 (mtt180) REVERT: B 88 MET cc_start: 0.8141 (mmp) cc_final: 0.7867 (mmp) REVERT: B 224 MET cc_start: 0.8864 (tpp) cc_final: 0.8359 (tpp) REVERT: C 97 MET cc_start: 0.8910 (mpp) cc_final: 0.8594 (mmm) REVERT: D 88 MET cc_start: 0.8165 (mmp) cc_final: 0.7842 (mmp) REVERT: D 224 MET cc_start: 0.8874 (tpp) cc_final: 0.8334 (tpp) REVERT: E 36 MET cc_start: 0.6710 (ppp) cc_final: 0.6397 (ppp) REVERT: E 272 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.9132 (mt0) REVERT: F 88 MET cc_start: 0.8112 (mmp) cc_final: 0.7905 (mmp) REVERT: F 224 MET cc_start: 0.8903 (tpp) cc_final: 0.8378 (tpp) REVERT: G 36 MET cc_start: 0.4513 (ppp) cc_final: 0.4118 (ppp) REVERT: G 68 MET cc_start: 0.8779 (ttp) cc_final: 0.8164 (ptp) REVERT: H 88 MET cc_start: 0.8086 (mmp) cc_final: 0.7872 (mmp) REVERT: H 224 MET cc_start: 0.8849 (tpp) cc_final: 0.8327 (tpp) outliers start: 37 outliers final: 33 residues processed: 167 average time/residue: 0.3454 time to fit residues: 90.1953 Evaluate side-chains 163 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 C residue 215 VAL 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 161 VAL Chi-restraints excluded: chain E residue 272 GLN 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 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 29 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.081181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.054076 restraints weight = 80370.227| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.26 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1937 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= 0.121 Angle : 0.512 8.908 29312 Z= 0.253 Chirality : 0.035 0.153 3184 Planarity : 0.003 0.040 3840 Dihedral : 3.332 16.556 2960 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.54 % Allowed : 20.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.17), residues: 2640 helix: 3.55 (0.12), residues: 1764 sheet: 1.99 (0.50), residues: 156 loop : -0.69 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 111 HIS 0.002 0.001 HIS B 189 PHE 0.010 0.001 PHE C 153 TYR 0.011 0.001 TYR A 123 ARG 0.012 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1454) hydrogen bonds : angle 3.35071 ( 4242) covalent geometry : bond 0.00260 (21664) covalent geometry : angle 0.51192 (29312) ********************** 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 163 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8387 (mtt180) REVERT: A 85 ARG cc_start: 0.9279 (mmp80) cc_final: 0.9056 (mmp80) REVERT: B 88 MET cc_start: 0.8037 (mmp) cc_final: 0.7827 (mmp) REVERT: B 224 MET cc_start: 0.8876 (tpp) cc_final: 0.8365 (tpp) REVERT: C 68 MET cc_start: 0.8790 (ttp) cc_final: 0.8345 (ptm) REVERT: C 97 MET cc_start: 0.8920 (mpp) cc_final: 0.8623 (mmm) REVERT: D 224 MET cc_start: 0.8908 (tpp) cc_final: 0.8366 (tpp) REVERT: E 36 MET cc_start: 0.6663 (ppp) cc_final: 0.6354 (ppp) REVERT: E 68 MET cc_start: 0.8790 (ttp) cc_final: 0.8237 (ptp) REVERT: F 224 MET cc_start: 0.8925 (tpp) cc_final: 0.8406 (tpp) REVERT: G 36 MET cc_start: 0.4474 (ppp) cc_final: 0.4063 (ppp) REVERT: H 224 MET cc_start: 0.8895 (tpp) cc_final: 0.8371 (tpp) outliers start: 34 outliers final: 31 residues processed: 163 average time/residue: 0.3442 time to fit residues: 88.7246 Evaluate side-chains 161 residues out of total 2208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 C residue 215 VAL 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 161 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 244 THR Chi-restraints excluded: chain H residue 319 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 173 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 31 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 257 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 164 optimal weight: 50.0000 chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.081629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.054538 restraints weight = 80596.291| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 4.46 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21664 Z= 0.104 Angle : 0.506 10.695 29312 Z= 0.248 Chirality : 0.034 0.152 3184 Planarity : 0.003 0.037 3840 Dihedral : 3.286 16.557 2960 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.31 % Allowed : 20.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.17), residues: 2640 helix: 3.51 (0.12), residues: 1788 sheet: 2.00 (0.50), residues: 156 loop : -0.71 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 111 HIS 0.002 0.000 HIS D 189 PHE 0.010 0.001 PHE G 153 TYR 0.011 0.001 TYR C 123 ARG 0.008 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1454) hydrogen bonds : angle 3.27640 ( 4242) covalent geometry : bond 0.00213 (21664) covalent geometry : angle 0.50572 (29312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8849.16 seconds wall clock time: 156 minutes 18.87 seconds (9378.87 seconds total)