Starting phenix.real_space_refine on Fri Aug 7 11:25:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hi1_34809/08_2026/8hi1_34809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hi1_34809/08_2026/8hi1_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_2026/8hi1_34809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2026/8hi1_34809.map" model { file = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2026/8hi1_34809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hi1_34809/08_2026/8hi1_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-2.2rc3-6140/lib/python3.11/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: 3.18, per 1000 atoms: 0.15 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: 1.99 Conformation dependent library (CDL) restraints added in 553.1 milliseconds 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: 3.37 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: 4.34 Time building geometry restraints manager: 2.79 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=" C1' DT G 24 " pdb=" N1 DT G 24 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" C1' DC H 15 " pdb=" N1 DC H 15 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C3' DA G 1 " pdb=" C2' DA G 1 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DG H 12 " pdb=" C2' DG H 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.04e+00 bond pdb=" C3' DC H 11 " pdb=" C2' DC H 11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.88e+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=" N3 DT G 16 " pdb=" C4 DT G 16 " pdb=" O4 DT G 16 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT H 4 " pdb=" C4 DT H 4 " pdb=" O4 DT H 4 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.11e+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 - 0.039: 1190 0.039 - 0.077: 371 0.077 - 0.116: 117 0.116 - 0.155: 60 0.155 - 0.193: 13 Chirality restraints: 1751 Sorted by residual: chirality pdb=" C3' DT H 23 " pdb=" C4' DT H 23 " pdb=" O3' DT H 23 " pdb=" C2' DT H 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" C3' DC G 4 " pdb=" C4' DC G 4 " pdb=" O3' DC G 4 " pdb=" C2' DC G 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" C3' DA G 5 " pdb=" C4' DA G 5 " pdb=" O3' DA G 5 " pdb=" C2' DA G 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.83e-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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.090 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.810 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 0.051 11161 Z= 0.319 Angle : 0.737 11.317 15328 Z= 0.511 Chirality : 0.048 0.193 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 are 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/Z covalent geometry : bond 0.00547 / 0.32 (11161) covalent geometry : angle 0.73683 / 0.51 (15328) hydrogen bonds : bond 0.17387 / 11.78 ( 458) hydrogen bonds : angle 6.77442 / 4.76 ( 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 : 0.450 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: 0.2581 time to fit residues: 60.5937 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 : 0.326 ------------------------------------------------------------------------------- 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: 0.0170 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 5 ASN B 127 GLN ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 277 GLN E 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165898 restraints weight = 33226.915| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.42 r_work: 0.3752 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11161 Z= 0.158 Angle : 0.653 18.113 15328 Z= 0.377 Chirality : 0.043 0.256 1751 Planarity : 0.005 0.056 1760 Dihedral : 18.273 162.215 1971 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.06 % Allowed : 9.03 % Favored : 89.91 % 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 are not related in a simple way. whole: -4.82 (0.19), residues: 1214 helix: -2.56 (0.18), residues: 510 sheet: -2.72 (0.35), residues: 157 loop : -4.00 (0.21), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.012 0.001 TYR D 92 PHE 0.018 0.001 PHE A 176 TRP 0.006 0.001 TRP C 166 HIS 0.007 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (11161) covalent geometry : angle 0.65343 / 0.38 (15328) hydrogen bonds : bond 0.05851 / 4.01 ( 458) hydrogen bonds : angle 5.12910 / 3.51 ( 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: 11 poor density : 112 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7309 (t0) cc_final: 0.6901 (t0) REVERT: A 125 MET cc_start: 0.5968 (mtt) cc_final: 0.4191 (ttp) REVERT: A 224 ASP cc_start: 0.6277 (m-30) cc_final: 0.5938 (m-30) REVERT: B 54 MET cc_start: 0.8303 (mmt) cc_final: 0.7677 (mmt) REVERT: B 76 ASP cc_start: 0.8185 (t0) cc_final: 0.7959 (t0) REVERT: C 45 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7279 (mpp80) REVERT: C 76 ASP cc_start: 0.7678 (m-30) cc_final: 0.7409 (m-30) REVERT: C 140 MET cc_start: 0.3766 (ttt) cc_final: 0.2778 (tpt) REVERT: D 76 ASP cc_start: 0.7983 (t70) cc_final: 0.7765 (t0) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.2427 time to fit residues: 40.2013 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 72 GLU 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 C residue 290 VAL Chi-restraints excluded: chain D residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 0.0470 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.208256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160413 restraints weight = 33376.606| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.59 r_work: 0.3673 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11161 Z= 0.192 Angle : 0.640 18.273 15328 Z= 0.367 Chirality : 0.043 0.245 1751 Planarity : 0.005 0.076 1760 Dihedral : 18.410 163.279 1971 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.15 % Allowed : 11.05 % Favored : 87.80 % 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 are not related in a simple way. whole: -4.24 (0.20), residues: 1214 helix: -1.97 (0.19), residues: 519 sheet: -2.69 (0.32), residues: 186 loop : -3.73 (0.22), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 13 TYR 0.010 0.001 TYR D 92 PHE 0.013 0.002 PHE D 24 TRP 0.009 0.001 TRP F 22 HIS 0.011 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (11161) covalent geometry : angle 0.64029 / 0.37 (15328) hydrogen bonds : bond 0.05725 / 3.92 ( 458) hydrogen bonds : angle 4.86043 / 3.32 ( 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 123 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7440 (t0) cc_final: 0.7010 (t0) REVERT: A 125 MET cc_start: 0.6009 (mtt) cc_final: 0.4206 (ttp) REVERT: B 54 MET cc_start: 0.8392 (mmt) cc_final: 0.7756 (mmt) REVERT: C 45 ARG cc_start: 0.7628 (mtt180) cc_final: 0.7241 (mpp80) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.2143 time to fit residues: 36.8365 Evaluate side-chains 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR 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 89 VAL Chi-restraints excluded: chain E residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 ASN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.154289 restraints weight = 33537.439| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.57 r_work: 0.3657 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2563 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= 0.179 Angle : 0.619 18.691 15328 Z= 0.356 Chirality : 0.043 0.248 1751 Planarity : 0.004 0.056 1760 Dihedral : 18.444 163.877 1971 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.54 % Allowed : 11.82 % Favored : 86.65 % 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 are not related in a simple way. whole: -3.89 (0.20), residues: 1214 helix: -1.62 (0.20), residues: 519 sheet: -2.60 (0.33), residues: 180 loop : -3.57 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 123 TYR 0.010 0.001 TYR D 92 PHE 0.012 0.001 PHE D 24 TRP 0.007 0.001 TRP F 22 HIS 0.011 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (11161) covalent geometry : angle 0.61902 / 0.36 (15328) hydrogen bonds : bond 0.05216 / 3.56 ( 458) hydrogen bonds : angle 4.67120 / 3.18 ( 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 119 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7455 (t0) cc_final: 0.7028 (t0) REVERT: A 125 MET cc_start: 0.5985 (mtt) cc_final: 0.4193 (ttp) REVERT: C 45 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7184 (mpp80) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.2102 time to fit residues: 34.4828 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 89 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.203653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156648 restraints weight = 33254.617| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.59 r_work: 0.3676 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11161 Z= 0.146 Angle : 0.587 18.754 15328 Z= 0.340 Chirality : 0.041 0.242 1751 Planarity : 0.004 0.048 1760 Dihedral : 18.437 164.437 1971 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.44 % Allowed : 12.58 % Favored : 85.98 % 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 are not related in a simple way. whole: -3.59 (0.21), residues: 1214 helix: -1.33 (0.21), residues: 519 sheet: -2.41 (0.34), residues: 180 loop : -3.48 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 90 TYR 0.009 0.001 TYR D 92 PHE 0.009 0.001 PHE A 176 TRP 0.007 0.001 TRP F 22 HIS 0.008 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (11161) covalent geometry : angle 0.58705 / 0.34 (15328) hydrogen bonds : bond 0.04844 / 3.29 ( 458) hydrogen bonds : angle 4.49444 / 3.04 ( 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 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7411 (t0) cc_final: 0.6954 (t0) REVERT: A 125 MET cc_start: 0.5925 (mtt) cc_final: 0.4173 (ttp) REVERT: C 45 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7185 (mpp80) REVERT: C 140 MET cc_start: 0.3638 (ttt) cc_final: 0.2587 (tpt) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.2107 time to fit residues: 33.7086 Evaluate side-chains 106 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 89 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.0040 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.153766 restraints weight = 33275.050| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.54 r_work: 0.3638 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11161 Z= 0.199 Angle : 0.628 18.760 15328 Z= 0.360 Chirality : 0.043 0.246 1751 Planarity : 0.005 0.050 1760 Dihedral : 18.531 164.375 1971 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.83 % Allowed : 13.16 % Favored : 85.01 % 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 are not related in a simple way. whole: -3.50 (0.21), residues: 1214 helix: -1.30 (0.21), residues: 521 sheet: -2.12 (0.35), residues: 176 loop : -3.48 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 90 TYR 0.009 0.001 TYR E 61 PHE 0.013 0.002 PHE D 24 TRP 0.007 0.001 TRP F 22 HIS 0.015 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (11161) covalent geometry : angle 0.62753 / 0.36 (15328) hydrogen bonds : bond 0.05154 / 3.51 ( 458) hydrogen bonds : angle 4.50412 / 3.06 ( 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 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7526 (t0) cc_final: 0.7071 (t0) REVERT: A 125 MET cc_start: 0.5885 (mtt) cc_final: 0.4116 (ttp) REVERT: B 4 LYS cc_start: 0.6418 (ttpp) cc_final: 0.6149 (ttpt) REVERT: C 45 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7206 (mpp80) REVERT: C 140 MET cc_start: 0.3767 (ttt) cc_final: 0.2694 (tpt) REVERT: D 58 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7474 (mt) REVERT: D 140 MET cc_start: -0.1562 (tpt) cc_final: -0.1797 (ppp) outliers start: 19 outliers final: 14 residues processed: 108 average time/residue: 0.2245 time to fit residues: 35.5083 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 : 0.548 ------------------------------------------------------------------------------- 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 14 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 87 ARG 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN D 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.201353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.154197 restraints weight = 33301.314| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.55 r_work: 0.3658 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11161 Z= 0.159 Angle : 0.588 18.774 15328 Z= 0.340 Chirality : 0.042 0.244 1751 Planarity : 0.004 0.045 1760 Dihedral : 18.497 165.058 1971 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.92 % Allowed : 13.93 % Favored : 84.15 % 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 are not related in a simple way. whole: -3.28 (0.21), residues: 1214 helix: -1.11 (0.21), residues: 524 sheet: -1.94 (0.36), residues: 177 loop : -3.41 (0.22), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.010 0.001 TYR D 92 PHE 0.011 0.001 PHE D 24 TRP 0.006 0.001 TRP F 22 HIS 0.010 0.002 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (11161) covalent geometry : angle 0.58772 / 0.34 (15328) hydrogen bonds : bond 0.04732 / 3.22 ( 458) hydrogen bonds : angle 4.36802 / 2.96 ( 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: 20 poor density : 101 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7511 (t0) cc_final: 0.7025 (t0) REVERT: A 125 MET cc_start: 0.5988 (mtt) cc_final: 0.4183 (ttp) REVERT: B 4 LYS cc_start: 0.6327 (ttpp) cc_final: 0.6059 (ttpt) REVERT: C 45 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7200 (mpp80) REVERT: C 140 MET cc_start: 0.3792 (ttt) cc_final: 0.2697 (tpt) REVERT: D 58 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7414 (mt) REVERT: D 140 MET cc_start: -0.1715 (tpt) cc_final: -0.1917 (ppp) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.2245 time to fit residues: 37.8750 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU 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 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 F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155645 restraints weight = 32983.121| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.54 r_work: 0.3694 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11161 Z= 0.116 Angle : 0.560 19.026 15328 Z= 0.324 Chirality : 0.041 0.238 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.439 165.379 1971 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.44 % Allowed : 14.70 % Favored : 83.86 % 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 are not related in a simple way. whole: -2.95 (0.22), residues: 1214 helix: -0.82 (0.21), residues: 523 sheet: -1.72 (0.35), residues: 180 loop : -3.29 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.007 0.001 TYR D 92 PHE 0.010 0.001 PHE A 176 TRP 0.006 0.001 TRP F 22 HIS 0.005 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11161) covalent geometry : angle 0.56044 / 0.32 (15328) hydrogen bonds : bond 0.04243 / 2.89 ( 458) hydrogen bonds : angle 4.20063 / 2.84 ( 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 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7469 (t0) cc_final: 0.6963 (t0) REVERT: A 125 MET cc_start: 0.5969 (mtt) cc_final: 0.4168 (ttp) REVERT: B 4 LYS cc_start: 0.6267 (ttpp) cc_final: 0.6040 (ttpt) REVERT: C 45 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7234 (mpp80) REVERT: C 140 MET cc_start: 0.3644 (ttt) cc_final: 0.2572 (tpt) REVERT: D 58 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7347 (mt) REVERT: D 140 MET cc_start: -0.1487 (tpt) cc_final: -0.1761 (ppp) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.2049 time to fit residues: 32.8499 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU 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 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL 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: 10.0000 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.202552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155155 restraints weight = 33407.984| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.57 r_work: 0.3478 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11161 Z= 0.140 Angle : 0.569 18.873 15328 Z= 0.328 Chirality : 0.042 0.304 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.466 164.987 1971 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.44 % Allowed : 15.18 % Favored : 83.38 % 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 are not related in a simple way. whole: -2.88 (0.22), residues: 1214 helix: -0.75 (0.21), residues: 523 sheet: -1.63 (0.36), residues: 177 loop : -3.29 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.007 0.001 TYR D 92 PHE 0.010 0.001 PHE A 176 TRP 0.005 0.001 TRP C 166 HIS 0.009 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11161) covalent geometry : angle 0.56929 / 0.33 (15328) hydrogen bonds : bond 0.04353 / 2.98 ( 458) hydrogen bonds : angle 4.17985 / 2.82 ( 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 112 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.609 Fit side-chains 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: 0.5840 (mtt) cc_final: 0.4076 (ttp) REVERT: B 4 LYS cc_start: 0.6078 (ttpp) cc_final: 0.5873 (ttpt) REVERT: C 45 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7177 (mpp80) REVERT: C 140 MET cc_start: 0.3539 (ttt) cc_final: 0.2463 (tpt) REVERT: C 160 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5981 (mm-30) REVERT: D 58 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7299 (mt) REVERT: D 140 MET cc_start: -0.1516 (tpt) cc_final: -0.1783 (ppp) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.2042 time to fit residues: 33.2411 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU 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 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 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: 4.9990 chunk 104 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 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: 2.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.201145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.153988 restraints weight = 33170.483| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.53 r_work: 0.3653 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11161 Z= 0.159 Angle : 0.582 18.885 15328 Z= 0.334 Chirality : 0.042 0.241 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.503 164.924 1971 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.44 % Allowed : 15.66 % Favored : 82.90 % 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 are not related in a simple way. whole: -2.86 (0.22), residues: 1214 helix: -0.74 (0.22), residues: 523 sheet: -1.60 (0.36), residues: 177 loop : -3.27 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.009 0.001 TYR D 92 PHE 0.010 0.001 PHE E 3 TRP 0.006 0.001 TRP C 166 HIS 0.009 0.002 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (11161) covalent geometry : angle 0.58153 / 0.33 (15328) hydrogen bonds : bond 0.04481 / 3.06 ( 458) hydrogen bonds : angle 4.20362 / 2.85 ( 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 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7452 (t0) cc_final: 0.6938 (t0) REVERT: A 125 MET cc_start: 0.5968 (mtt) cc_final: 0.4151 (ttp) REVERT: B 4 LYS cc_start: 0.6317 (ttpp) cc_final: 0.6094 (ttpt) REVERT: C 45 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7257 (mpp80) REVERT: C 140 MET cc_start: 0.3875 (ttt) cc_final: 0.2782 (tpt) REVERT: D 58 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7382 (mt) REVERT: E 42 LYS cc_start: 0.7046 (mtpp) cc_final: 0.6768 (mptt) outliers start: 15 outliers final: 14 residues processed: 110 average time/residue: 0.2040 time to fit residues: 33.5206 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain B residue 72 GLU 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 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 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 10 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** 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 = 0.4360 r_free = 0.4360 target = 0.200415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.153316 restraints weight = 33127.043| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.58 r_work: 0.3672 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11161 Z= 0.179 Angle : 0.600 18.848 15328 Z= 0.342 Chirality : 0.042 0.243 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.547 165.020 1971 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 1.54 % Allowed : 15.85 % 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 are not related in a simple way. whole: -2.90 (0.22), residues: 1214 helix: -0.77 (0.21), residues: 523 sheet: -1.55 (0.37), residues: 177 loop : -3.31 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.009 0.001 TYR D 92 PHE 0.013 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/Z covalent geometry : bond 0.00405 / 0.18 (11161) covalent geometry : angle 0.59979 / 0.34 (15328) hydrogen bonds : bond 0.04680 / 3.20 ( 458) hydrogen bonds : angle 4.22362 / 2.88 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6093.00 seconds wall clock time: 103 minutes 44.80 seconds (6224.80 seconds total)