Starting phenix.real_space_refine on Sun Aug 24 16:45:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.map" model { file = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2025/8hi1_34809.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1054 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 31 5.16 5 C 6728 2.51 5 N 1916 2.21 5 O 2125 1.98 5 H 10143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4568 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain: "B" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3576 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "C" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4379 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 6, 'TRANS': 278} Chain: "D" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3731 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 2 Chain: "E" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1475 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "F" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1483 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 826 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 960 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.16, per 1000 atoms: 0.20 Number of scatterers: 20998 At special positions: 0 Unit cell: (109.65, 117.3, 148.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 55 15.00 O 2125 8.00 N 1916 7.00 C 6728 6.00 H 10143 1.00 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: 2.10 Conformation dependent library (CDL) restraints added in 871.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 17 sheets defined 46.1% alpha, 10.0% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.666A pdb=" N VAL A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.536A pdb=" N SER A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.792A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 139 through 163 removed outlier: 3.505A pdb=" N ARG A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 205 removed outlier: 3.938A pdb=" N SER A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.799A pdb=" N LEU A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.200A pdb=" N THR A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.963A pdb=" N ASN A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.099A pdb=" N ARG A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.951A pdb=" N ARG A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'B' and resid 68 through 76 removed outlier: 4.154A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.313A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.651A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 203 Processing helix chain 'B' and resid 219 through 243 removed outlier: 3.721A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'C' and resid 68 through 75 removed outlier: 4.158A pdb=" N LEU C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.559A pdb=" N SER C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.597A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.115A pdb=" N ALA C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.735A pdb=" N MET C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 129' Processing helix chain 'C' and resid 139 through 162 removed outlier: 4.182A pdb=" N ARG C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.033A pdb=" N GLY C 179 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 205 removed outlier: 4.158A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.566A pdb=" N TYR C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 233 " --> pdb=" O TYR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 244 removed outlier: 4.188A pdb=" N GLU C 240 " --> pdb=" O PRO C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 4.148A pdb=" N ARG C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 278 removed outlier: 3.739A pdb=" N ILE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.865A pdb=" N LEU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 removed outlier: 4.152A pdb=" N ASN D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.928A pdb=" N GLY D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 219 through 244 removed outlier: 3.894A pdb=" N ASP D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.641A pdb=" N LYS D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 removed outlier: 4.363A pdb=" N VAL D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 4.225A pdb=" N ASN E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 48 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 48 removed outlier: 4.196A pdb=" N ASN F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.511A pdb=" N ALA A 30 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.763A pdb=" N ILE A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.717A pdb=" N TRP A 83 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.925A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.611A pdb=" N MET B 81 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.676A pdb=" N VAL C 82 " --> pdb=" O LEU C 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.593A pdb=" N ILE D 66 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.558A pdb=" N ILE D 25 " --> pdb=" O LEU D 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.559A pdb=" N ASN D 33 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 83 removed outlier: 4.131A pdb=" N TRP D 83 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 91 " --> pdb=" O TRP D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27 removed outlier: 7.046A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE E 3 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 56 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 73 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 82 removed outlier: 3.592A pdb=" N SER E 78 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 85 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 24 through 27 removed outlier: 3.849A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE F 3 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 56 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 82 removed outlier: 3.605A pdb=" N ILE F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 5.39 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10143 1.03 - 1.23: 40 1.23 - 1.42: 4676 1.42 - 1.62: 6383 1.62 - 1.81: 62 Bond restraints: 21304 Sorted by residual: bond pdb=" CB ILE D 74 " pdb=" CG2 ILE D 74 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB GLN F 24 " pdb=" CG GLN F 24 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB VAL E 32 " pdb=" CG1 VAL E 32 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" C ASP C 65 " pdb=" N ILE C 66 " ideal model delta sigma weight residual 1.329 1.300 0.029 2.19e-02 2.09e+03 1.74e+00 bond pdb=" CG LEU D 60 " pdb=" CD1 LEU D 60 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.61: 38372 10.61 - 21.23: 1 21.23 - 31.84: 0 31.84 - 42.45: 0 42.45 - 53.06: 2 Bond angle restraints: 38375 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 124.38 71.32 53.06 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CA LEU C 295 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 114.08 61.54 52.54 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" CA LEU C 295 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" N VAL C 121 " pdb=" CA VAL C 121 " pdb=" C VAL C 121 " ideal model delta sigma weight residual 112.43 108.68 3.75 9.20e-01 1.18e+00 1.66e+01 angle pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N GLN C 141 " ideal model delta sigma weight residual 118.42 122.66 -4.24 1.31e+00 5.83e-01 1.05e+01 ... (remaining 38370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 9134 31.74 - 63.48: 588 63.48 - 95.23: 11 95.23 - 126.97: 0 126.97 - 158.71: 2 Dihedral angle restraints: 9735 sinusoidal: 5645 harmonic: 4090 Sorted by residual: dihedral pdb=" CA ARG B 90 " pdb=" C ARG B 90 " pdb=" N GLN B 91 " pdb=" CA GLN B 91 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN E 36 " pdb=" C ASN E 36 " pdb=" N SER E 37 " pdb=" CA SER E 37 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C4' DT H 29 " pdb=" C3' DT H 29 " pdb=" O3' DT H 29 " pdb=" P DT H 30 " ideal model delta sinusoidal sigma weight residual 220.00 61.29 158.71 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1070 0.033 - 0.066: 457 0.066 - 0.099: 170 0.099 - 0.131: 45 0.131 - 0.164: 9 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL C 35 " pdb=" N VAL C 35 " pdb=" C VAL C 35 " pdb=" CB VAL C 35 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ILE B 25 " pdb=" N ILE B 25 " pdb=" C ILE B 25 " pdb=" CB ILE B 25 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1748 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 207 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 208 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 207 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 208 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 207 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 208 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.024 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1038 2.17 - 2.78: 39824 2.78 - 3.38: 53178 3.38 - 3.99: 70414 3.99 - 4.60: 112154 Nonbonded interactions: 276608 Sorted by model distance: nonbonded pdb="HH22 ARG B 49 " pdb=" OE1 GLU E 25 " model vdw 1.562 2.450 nonbonded pdb=" HH TYR D 229 " pdb=" OD2 ASP D 275 " model vdw 1.601 2.450 nonbonded pdb="HH12 ARG C 169 " pdb=" OP1 DG H 28 " model vdw 1.627 2.450 nonbonded pdb="HH11 ARG C 123 " pdb=" O SER C 136 " model vdw 1.628 2.450 nonbonded pdb="HH22 ARG C 169 " pdb=" OG SER C 187 " model vdw 1.629 2.450 ... (remaining 276603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2)) or (resid 247 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2)) or (resid 248 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 249 through 250 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 251 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2 or name CD1)) or (resid 252 and (name N or name CA or name C or name O or name \ HA2 or name HA3)) or resid 253 through 296 or (resid 297 through 298 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 299 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 300 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 301 and ( \ name N or name CA or name C or name O or name CB or name CG or name SD or name C \ E )) or (resid 302 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 303 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 304 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) o \ r (resid 305 and (name N or name CA or name C or name O or name CB or name CG or \ name ND1 or name CD2 or name CE1 or name NE2)) or (resid 306 and (name N or nam \ e CA or name C or name O )))) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 24 through \ 74 or (resid 75 and (name N or name CA or name C or name O or name HA2 or name H \ A3)) or resid 76 through 306)) } ncs_group { reference = (chain 'B' and (resid 4 through 85 or (resid 86 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 8 \ 7 through 88 or (resid 89 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or (resid 90 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ )) or (resid 91 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or (resid 92 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or (resid 93 and (name N or name CA or name C or na \ me O or name CB )) or resid 94 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 or \ name HG )) or resid 102 through 281)) selection = (chain 'D' and (resid 4 through 140 or resid 181 through 281)) } ncs_group { reference = (chain 'E' and resid 2 through 92) selection = (chain 'F' and resid 2 through 92) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.090 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 : 0.005 0.048 11161 Z= 0.215 Angle : 0.694 11.317 15328 Z= 0.413 Chirality : 0.043 0.164 1751 Planarity : 0.004 0.064 1760 Dihedral : 17.864 158.710 4263 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.18 (0.16), residues: 1214 helix: -3.79 (0.14), residues: 511 sheet: -3.40 (0.34), residues: 135 loop : -4.63 (0.18), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 40 TYR 0.013 0.001 TYR F 61 PHE 0.014 0.002 PHE E 82 TRP 0.007 0.001 TRP E 22 HIS 0.010 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00508 (11161) covalent geometry : angle 0.69383 (15328) hydrogen bonds : bond 0.17387 ( 458) hydrogen bonds : angle 6.77442 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7279 (t0) cc_final: 0.7019 (t0) REVERT: A 125 MET cc_start: 0.6258 (mtt) cc_final: 0.4586 (ttp) REVERT: C 76 ASP cc_start: 0.7224 (m-30) cc_final: 0.6991 (m-30) REVERT: C 140 MET cc_start: 0.3824 (ttt) cc_final: 0.3269 (tpt) REVERT: D 76 ASP cc_start: 0.6943 (t70) cc_final: 0.6729 (t0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3380 time to fit residues: 77.6084 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN B 127 GLN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 100 HIS D 277 GLN E 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.212396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164111 restraints weight = 33206.692| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.51 r_work: 0.3716 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11161 Z= 0.151 Angle : 0.626 17.930 15328 Z= 0.351 Chirality : 0.041 0.147 1751 Planarity : 0.004 0.053 1760 Dihedral : 18.180 161.422 1971 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.96 % Allowed : 9.03 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.72 (0.19), residues: 1214 helix: -2.45 (0.18), residues: 511 sheet: -2.89 (0.32), residues: 172 loop : -3.89 (0.21), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 13 TYR 0.014 0.001 TYR D 92 PHE 0.020 0.001 PHE A 176 TRP 0.006 0.001 TRP F 22 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00346 (11161) covalent geometry : angle 0.62554 (15328) hydrogen bonds : bond 0.05283 ( 458) hydrogen bonds : angle 4.98713 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7340 (t0) cc_final: 0.6919 (t0) REVERT: A 125 MET cc_start: 0.6047 (mtt) cc_final: 0.4270 (ttp) REVERT: A 224 ASP cc_start: 0.6168 (m-30) cc_final: 0.5912 (m-30) REVERT: B 54 MET cc_start: 0.8275 (mmt) cc_final: 0.7580 (mmt) REVERT: B 76 ASP cc_start: 0.8227 (t0) cc_final: 0.7942 (t0) REVERT: C 45 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7290 (mpp80) REVERT: C 76 ASP cc_start: 0.7700 (m-30) cc_final: 0.7376 (m-30) REVERT: D 76 ASP cc_start: 0.7999 (t70) cc_final: 0.7771 (t0) outliers start: 10 outliers final: 6 residues processed: 118 average time/residue: 0.2344 time to fit residues: 39.0738 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.203815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156723 restraints weight = 33387.202| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.59 r_work: 0.3542 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11161 Z= 0.166 Angle : 0.602 18.553 15328 Z= 0.339 Chirality : 0.042 0.151 1751 Planarity : 0.004 0.053 1760 Dihedral : 18.210 161.191 1971 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.54 % Allowed : 10.18 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.20), residues: 1214 helix: -1.65 (0.20), residues: 518 sheet: -2.61 (0.32), residues: 187 loop : -3.57 (0.22), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.011 0.001 TYR D 92 PHE 0.016 0.001 PHE A 176 TRP 0.007 0.001 TRP C 166 HIS 0.011 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00383 (11161) covalent geometry : angle 0.60226 (15328) hydrogen bonds : bond 0.04845 ( 458) hydrogen bonds : angle 4.61681 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7403 (t0) cc_final: 0.6940 (t0) REVERT: A 125 MET cc_start: 0.5975 (mtt) cc_final: 0.4219 (ttp) REVERT: C 45 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7217 (mpp80) REVERT: C 140 MET cc_start: 0.3938 (ttt) cc_final: 0.2960 (tpt) REVERT: C 240 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6445 (pt0) outliers start: 16 outliers final: 10 residues processed: 125 average time/residue: 0.2132 time to fit residues: 37.1534 Evaluate side-chains 105 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.201662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154407 restraints weight = 33392.677| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.62 r_work: 0.3496 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11161 Z= 0.185 Angle : 0.610 18.668 15328 Z= 0.343 Chirality : 0.042 0.155 1751 Planarity : 0.005 0.076 1760 Dihedral : 18.277 162.476 1971 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.11 % Allowed : 11.72 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.21), residues: 1214 helix: -1.26 (0.21), residues: 521 sheet: -2.38 (0.34), residues: 177 loop : -3.44 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 123 TYR 0.011 0.001 TYR D 92 PHE 0.012 0.002 PHE D 24 TRP 0.007 0.001 TRP C 166 HIS 0.013 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00430 (11161) covalent geometry : angle 0.60950 (15328) hydrogen bonds : bond 0.04833 ( 458) hydrogen bonds : angle 4.48967 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7464 (t0) cc_final: 0.6988 (t0) REVERT: A 125 MET cc_start: 0.5854 (mtt) cc_final: 0.4115 (ttp) REVERT: C 45 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7222 (mpp80) REVERT: C 140 MET cc_start: 0.3762 (ttt) cc_final: 0.2701 (tpt) REVERT: C 240 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6498 (pt0) REVERT: D 58 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7391 (mt) outliers start: 22 outliers final: 15 residues processed: 120 average time/residue: 0.1964 time to fit residues: 33.3610 Evaluate side-chains 110 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.199845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152680 restraints weight = 33247.224| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.55 r_work: 0.3643 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11161 Z= 0.208 Angle : 0.625 18.624 15328 Z= 0.351 Chirality : 0.043 0.165 1751 Planarity : 0.005 0.049 1760 Dihedral : 18.316 162.655 1971 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.73 % Allowed : 14.31 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.21), residues: 1214 helix: -1.19 (0.21), residues: 525 sheet: -2.21 (0.35), residues: 177 loop : -3.49 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.010 0.001 TYR D 92 PHE 0.013 0.002 PHE D 24 TRP 0.006 0.001 TRP F 22 HIS 0.012 0.002 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00493 (11161) covalent geometry : angle 0.62464 (15328) hydrogen bonds : bond 0.04937 ( 458) hydrogen bonds : angle 4.43793 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7480 (t0) cc_final: 0.7003 (t0) REVERT: A 125 MET cc_start: 0.5957 (mtt) cc_final: 0.4166 (ttp) REVERT: C 45 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7250 (mpp80) REVERT: C 140 MET cc_start: 0.4161 (ttt) cc_final: 0.3015 (tpt) REVERT: C 240 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6520 (pt0) REVERT: D 58 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7401 (mt) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.1956 time to fit residues: 30.8934 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 55 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.200081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152777 restraints weight = 33292.679| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.58 r_work: 0.3458 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11161 Z= 0.182 Angle : 0.600 18.832 15328 Z= 0.339 Chirality : 0.042 0.144 1751 Planarity : 0.004 0.045 1760 Dihedral : 18.280 163.149 1971 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.63 % Allowed : 16.23 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.21), residues: 1214 helix: -1.05 (0.21), residues: 525 sheet: -1.92 (0.36), residues: 177 loop : -3.38 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.010 0.001 TYR D 92 PHE 0.013 0.002 PHE C 24 TRP 0.005 0.001 TRP F 22 HIS 0.011 0.002 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00426 (11161) covalent geometry : angle 0.59977 (15328) hydrogen bonds : bond 0.04617 ( 458) hydrogen bonds : angle 4.31751 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7403 (t0) cc_final: 0.6902 (t0) REVERT: A 125 MET cc_start: 0.5859 (mtt) cc_final: 0.4083 (ttp) REVERT: B 76 ASP cc_start: 0.8656 (t0) cc_final: 0.8455 (t0) REVERT: B 227 ASP cc_start: 0.7831 (m-30) cc_final: 0.7577 (m-30) REVERT: C 33 ASN cc_start: 0.7487 (OUTLIER) cc_final: 0.7076 (t0) REVERT: C 45 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7263 (mpp80) REVERT: C 140 MET cc_start: 0.4135 (ttt) cc_final: 0.2971 (tpt) REVERT: C 141 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6523 (tm-30) REVERT: C 237 LEU cc_start: 0.7345 (tp) cc_final: 0.7043 (mt) REVERT: C 240 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6475 (pt0) REVERT: D 58 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7282 (mt) REVERT: E 42 LYS cc_start: 0.7086 (mtpp) cc_final: 0.6728 (mptt) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.2062 time to fit residues: 36.0572 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 110 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.208890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162203 restraints weight = 32878.902| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.51 r_work: 0.3640 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11161 Z= 0.111 Angle : 0.547 19.326 15328 Z= 0.309 Chirality : 0.040 0.208 1751 Planarity : 0.003 0.035 1760 Dihedral : 18.122 163.013 1971 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.15 % Allowed : 16.23 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.22), residues: 1214 helix: -0.50 (0.22), residues: 518 sheet: -1.57 (0.36), residues: 180 loop : -3.15 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.007 0.001 TYR B 92 PHE 0.010 0.001 PHE F 3 TRP 0.006 0.001 TRP C 166 HIS 0.004 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00250 (11161) covalent geometry : angle 0.54656 (15328) hydrogen bonds : bond 0.03693 ( 458) hydrogen bonds : angle 4.00292 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7440 (t0) cc_final: 0.6887 (t0) REVERT: A 125 MET cc_start: 0.5850 (mtt) cc_final: 0.4007 (ttp) REVERT: C 45 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7220 (mpp80) REVERT: C 126 TYR cc_start: 0.7621 (m-80) cc_final: 0.7371 (m-80) REVERT: C 140 MET cc_start: 0.3913 (ttt) cc_final: 0.2782 (tpt) REVERT: C 240 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6290 (pt0) REVERT: D 58 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7328 (mt) REVERT: E 42 LYS cc_start: 0.7027 (mtpp) cc_final: 0.6739 (mptt) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.1969 time to fit residues: 34.1488 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain F residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.199475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151811 restraints weight = 33280.893| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.57 r_work: 0.3616 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11161 Z= 0.162 Angle : 0.578 19.083 15328 Z= 0.325 Chirality : 0.041 0.196 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.191 162.792 1971 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.34 % Allowed : 17.00 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.22), residues: 1214 helix: -0.53 (0.22), residues: 521 sheet: -1.49 (0.37), residues: 177 loop : -3.21 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.008 0.001 TYR F 68 PHE 0.013 0.001 PHE E 3 TRP 0.007 0.001 TRP C 166 HIS 0.009 0.002 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00380 (11161) covalent geometry : angle 0.57782 (15328) hydrogen bonds : bond 0.04279 ( 458) hydrogen bonds : angle 4.04966 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7422 (t0) cc_final: 0.6874 (t0) REVERT: A 125 MET cc_start: 0.5833 (mtt) cc_final: 0.4021 (ttp) REVERT: B 5 ASN cc_start: 0.7158 (t0) cc_final: 0.6719 (t0) REVERT: B 218 ASP cc_start: 0.8115 (t0) cc_final: 0.7717 (t0) REVERT: C 33 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7087 (t0) REVERT: C 45 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7235 (mpp80) REVERT: C 140 MET cc_start: 0.4153 (ttt) cc_final: 0.2921 (tpt) REVERT: C 237 LEU cc_start: 0.7244 (tp) cc_final: 0.6976 (mt) REVERT: C 240 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6390 (pt0) REVERT: D 58 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7402 (mt) REVERT: E 42 LYS cc_start: 0.7068 (mtpp) cc_final: 0.6761 (mptt) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.1850 time to fit residues: 30.6251 Evaluate side-chains 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 120 optimal weight: 2.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.206244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.159068 restraints weight = 33186.932| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.56 r_work: 0.3473 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11161 Z= 0.148 Angle : 0.568 19.154 15328 Z= 0.321 Chirality : 0.041 0.150 1751 Planarity : 0.004 0.065 1760 Dihedral : 18.189 163.296 1971 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.54 % Allowed : 16.91 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.22), residues: 1214 helix: -0.37 (0.22), residues: 517 sheet: -1.37 (0.38), residues: 174 loop : -3.12 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 156 TYR 0.008 0.001 TYR D 92 PHE 0.011 0.001 PHE E 3 TRP 0.007 0.001 TRP C 166 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00345 (11161) covalent geometry : angle 0.56817 (15328) hydrogen bonds : bond 0.04079 ( 458) hydrogen bonds : angle 3.97697 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7446 (t0) cc_final: 0.6898 (t0) REVERT: A 125 MET cc_start: 0.5793 (mtt) cc_final: 0.3987 (ttp) REVERT: B 5 ASN cc_start: 0.7130 (t0) cc_final: 0.6740 (t0) REVERT: B 218 ASP cc_start: 0.8085 (t0) cc_final: 0.7686 (t0) REVERT: C 33 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7068 (t0) REVERT: C 45 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7224 (mpp80) REVERT: C 140 MET cc_start: 0.4081 (ttt) cc_final: 0.2912 (tpt) REVERT: C 141 GLN cc_start: 0.6647 (tm-30) cc_final: 0.6431 (tm-30) REVERT: C 237 LEU cc_start: 0.7283 (tp) cc_final: 0.6996 (mt) REVERT: C 240 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6340 (pt0) REVERT: D 58 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7305 (mt) REVERT: D 257 GLN cc_start: 0.4226 (mp10) cc_final: 0.3966 (tp-100) REVERT: E 42 LYS cc_start: 0.7037 (mtpp) cc_final: 0.6734 (mptt) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.1926 time to fit residues: 33.2142 Evaluate side-chains 118 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.206917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159123 restraints weight = 32920.847| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.56 r_work: 0.3478 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11161 Z= 0.133 Angle : 0.555 19.239 15328 Z= 0.313 Chirality : 0.041 0.216 1751 Planarity : 0.004 0.046 1760 Dihedral : 18.170 163.175 1971 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.44 % Allowed : 17.00 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.22), residues: 1214 helix: -0.20 (0.22), residues: 517 sheet: -1.22 (0.39), residues: 174 loop : -3.07 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.007 0.001 TYR D 92 PHE 0.011 0.001 PHE E 3 TRP 0.008 0.001 TRP C 166 HIS 0.007 0.001 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00309 (11161) covalent geometry : angle 0.55475 (15328) hydrogen bonds : bond 0.03899 ( 458) hydrogen bonds : angle 3.90672 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7419 (t0) cc_final: 0.6879 (t0) REVERT: A 125 MET cc_start: 0.5739 (mtt) cc_final: 0.3980 (ttp) REVERT: B 5 ASN cc_start: 0.7223 (t0) cc_final: 0.6645 (t0) REVERT: C 33 ASN cc_start: 0.7468 (OUTLIER) cc_final: 0.7062 (t0) REVERT: C 45 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7210 (mpp80) REVERT: C 237 LEU cc_start: 0.7241 (tp) cc_final: 0.6940 (mt) REVERT: C 240 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6222 (pt0) REVERT: D 58 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7311 (mt) REVERT: D 87 ARG cc_start: 0.8237 (mtp180) cc_final: 0.7984 (mtp180) REVERT: D 257 GLN cc_start: 0.4246 (mp10) cc_final: 0.4015 (tp-100) REVERT: E 42 LYS cc_start: 0.6989 (mtpp) cc_final: 0.6690 (mptt) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.2077 time to fit residues: 36.0811 Evaluate side-chains 115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.195910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147182 restraints weight = 33313.803| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.70 r_work: 0.3471 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11161 Z= 0.193 Angle : 0.603 18.932 15328 Z= 0.339 Chirality : 0.043 0.181 1751 Planarity : 0.004 0.049 1760 Dihedral : 18.286 163.229 1971 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.63 % Allowed : 17.20 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.22), residues: 1214 helix: -0.35 (0.22), residues: 516 sheet: -1.43 (0.40), residues: 166 loop : -3.11 (0.22), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 156 TYR 0.010 0.001 TYR D 92 PHE 0.016 0.002 PHE E 3 TRP 0.008 0.001 TRP C 166 HIS 0.011 0.002 HIS C 29 Details of bonding type rmsd covalent geometry : bond 0.00460 (11161) covalent geometry : angle 0.60300 (15328) hydrogen bonds : bond 0.04577 ( 458) hydrogen bonds : angle 4.08645 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6032.07 seconds wall clock time: 102 minutes 38.57 seconds (6158.57 seconds total)