Starting phenix.real_space_refine on Sat Jul 4 14:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hi1_34809/07_2026/8hi1_34809.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hi1_34809/07_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_34809/07_2026/8hi1_34809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hi1_34809/07_2026/8hi1_34809.map" model { file = "/net/cci-nas-00/data/ceres_data/8hi1_34809/07_2026/8hi1_34809.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hi1_34809/07_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-dev-6108/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: 3.75, per 1000 atoms: 0.18 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: 2.01 Conformation dependent library (CDL) restraints added in 556.3 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: 3.43 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: 4.57 Time building geometry restraints manager: 2.77 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: 0.060 Construct map_model_manager: 0.120 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- 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 : 0.736 11.317 15328 Z= 0.510 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 0.73569 / 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 : 0.516 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: 0.2900 time to fit residues: 68.0287 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 : 0.545 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.213359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165984 restraints weight = 33222.441| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.42 r_work: 0.3754 rms_B_bonded: 2.80 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: 0.7604 moved from start: 0.1562 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 : 0.650 17.979 15328 Z= 0.376 Chirality : 0.043 0.248 1751 Planarity : 0.005 0.056 1760 Dihedral : 18.271 162.555 1971 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.06 % Allowed : 8.93 % 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 are not related in a simple way. whole: -4.87 (0.19), residues: 1214 helix: -2.60 (0.17), residues: 509 sheet: -2.75 (0.35), residues: 157 loop : -4.02 (0.21), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.012 0.001 TYR D 92 PHE 0.019 0.001 PHE A 176 TRP 0.006 0.001 TRP F 22 HIS 0.007 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (11161) covalent geometry : angle 0.65017 / 0.38 (15328) hydrogen bonds : bond 0.06000 / 4.11 ( 458) hydrogen bonds : angle 5.16663 / 3.54 ( 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 : 0.659 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7297 (t0) cc_final: 0.6895 (t0) REVERT: A 125 MET cc_start: 0.5956 (mtt) cc_final: 0.4180 (ttp) REVERT: A 224 ASP cc_start: 0.6280 (m-30) cc_final: 0.5950 (m-30) REVERT: B 54 MET cc_start: 0.8306 (mmt) cc_final: 0.7678 (mmt) REVERT: B 76 ASP cc_start: 0.8182 (t0) cc_final: 0.7951 (t0) REVERT: C 45 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7273 (mpp80) REVERT: C 76 ASP cc_start: 0.7672 (m-30) cc_final: 0.7402 (m-30) REVERT: C 140 MET cc_start: 0.3790 (ttt) cc_final: 0.2810 (tpt) outliers start: 11 outliers final: 7 residues processed: 117 average time/residue: 0.2510 time to fit residues: 41.2862 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 0.0470 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.211905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.163894 restraints weight = 33225.089| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.45 r_work: 0.3734 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11161 Z= 0.144 Angle : 0.595 18.530 15328 Z= 0.345 Chirality : 0.041 0.227 1751 Planarity : 0.004 0.073 1760 Dihedral : 18.314 163.482 1971 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.96 % Allowed : 10.66 % Favored : 88.38 % 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: -4.01 (0.20), residues: 1214 helix: -1.74 (0.20), residues: 510 sheet: -2.55 (0.33), residues: 181 loop : -3.63 (0.22), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 13 TYR 0.008 0.001 TYR D 92 PHE 0.015 0.001 PHE A 176 TRP 0.008 0.001 TRP F 22 HIS 0.007 0.001 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (11161) covalent geometry : angle 0.59515 / 0.34 (15328) hydrogen bonds : bond 0.05269 / 3.61 ( 458) hydrogen bonds : angle 4.76267 / 3.25 ( 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 121 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7398 (t0) cc_final: 0.6919 (t0) REVERT: A 125 MET cc_start: 0.6007 (mtt) cc_final: 0.4208 (ttp) REVERT: C 45 ARG cc_start: 0.7597 (mtt180) cc_final: 0.7241 (mpp80) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.2343 time to fit residues: 38.1986 Evaluate side-chains 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.202523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.155705 restraints weight = 33422.194| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.61 r_work: 0.3589 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2518 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= 0.204 Angle : 0.642 18.626 15328 Z= 0.368 Chirality : 0.043 0.238 1751 Planarity : 0.005 0.061 1760 Dihedral : 18.469 163.540 1971 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.73 % Allowed : 11.05 % Favored : 87.22 % 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: -3.80 (0.20), residues: 1214 helix: -1.54 (0.20), residues: 518 sheet: -2.54 (0.34), residues: 180 loop : -3.53 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 90 TYR 0.011 0.001 TYR D 92 PHE 0.015 0.002 PHE D 24 TRP 0.008 0.001 TRP F 22 HIS 0.015 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (11161) covalent geometry : angle 0.64210 / 0.37 (15328) hydrogen bonds : bond 0.05394 / 3.69 ( 458) hydrogen bonds : angle 4.67355 / 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 129 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7479 (t0) cc_final: 0.7044 (t0) REVERT: A 125 MET cc_start: 0.5974 (mtt) cc_final: 0.4197 (ttp) REVERT: C 45 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7173 (mpp80) REVERT: C 140 MET cc_start: 0.3645 (ttt) cc_final: 0.2703 (tpt) REVERT: C 240 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6451 (pt0) outliers start: 18 outliers final: 12 residues processed: 124 average time/residue: 0.2230 time to fit residues: 39.9674 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 45 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4378 r_free = 0.4378 target = 0.202606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155574 restraints weight = 33050.773| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.50 r_work: 0.3621 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11161 Z= 0.165 Angle : 0.598 18.674 15328 Z= 0.345 Chirality : 0.042 0.229 1751 Planarity : 0.004 0.053 1760 Dihedral : 18.462 164.578 1971 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.54 % Allowed : 12.49 % 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: -3.51 (0.21), residues: 1214 helix: -1.30 (0.21), residues: 522 sheet: -2.37 (0.34), residues: 180 loop : -3.40 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.010 0.001 TYR D 92 PHE 0.011 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 0.00365 / 0.17 (11161) covalent geometry : angle 0.59837 / 0.35 (15328) hydrogen bonds : bond 0.04945 / 3.36 ( 458) hydrogen bonds : angle 4.49409 / 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: 16 poor density : 95 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7429 (t0) cc_final: 0.6964 (t0) REVERT: A 125 MET cc_start: 0.5979 (mtt) cc_final: 0.4197 (ttp) REVERT: B 90 ARG cc_start: 0.7770 (mmp80) cc_final: 0.7560 (mmp80) REVERT: C 45 ARG cc_start: 0.7578 (mtt180) cc_final: 0.7187 (mpp80) REVERT: C 140 MET cc_start: 0.3808 (ttt) cc_final: 0.2808 (tpt) REVERT: C 240 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6469 (pt0) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.2209 time to fit residues: 34.2938 Evaluate side-chains 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 0.0980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.202157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.155012 restraints weight = 33443.672| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.61 r_work: 0.3647 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11161 Z= 0.164 Angle : 0.590 18.755 15328 Z= 0.341 Chirality : 0.042 0.229 1751 Planarity : 0.004 0.050 1760 Dihedral : 18.458 164.693 1971 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.73 % Allowed : 12.97 % Favored : 85.30 % 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: -3.35 (0.21), residues: 1214 helix: -1.16 (0.21), residues: 523 sheet: -2.10 (0.35), residues: 177 loop : -3.40 (0.22), residues: 514 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 0.010 0.001 PHE D 24 TRP 0.006 0.001 TRP F 22 HIS 0.009 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (11161) covalent geometry : angle 0.58984 / 0.34 (15328) hydrogen bonds : bond 0.04813 / 3.28 ( 458) hydrogen bonds : angle 4.39645 / 2.99 ( 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 115 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7456 (t0) cc_final: 0.6978 (t0) REVERT: A 125 MET cc_start: 0.5818 (mtt) cc_final: 0.4078 (ttp) REVERT: C 45 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7212 (mpp80) REVERT: C 140 MET cc_start: 0.3758 (ttt) cc_final: 0.2779 (tpt) REVERT: C 240 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6462 (pt0) REVERT: D 58 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7400 (mt) outliers start: 18 outliers final: 15 residues processed: 110 average time/residue: 0.2289 time to fit residues: 36.5567 Evaluate side-chains 111 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 244 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN F 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154294 restraints weight = 33486.440| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.59 r_work: 0.3588 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3181 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= 0.166 Angle : 0.587 18.846 15328 Z= 0.339 Chirality : 0.042 0.228 1751 Planarity : 0.004 0.048 1760 Dihedral : 18.483 164.812 1971 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.73 % Allowed : 13.54 % Favored : 84.73 % 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: -3.18 (0.21), residues: 1214 helix: -1.04 (0.21), residues: 525 sheet: -1.92 (0.35), residues: 177 loop : -3.33 (0.22), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 90 TYR 0.010 0.001 TYR D 92 PHE 0.011 0.002 PHE E 82 TRP 0.006 0.001 TRP F 22 HIS 0.012 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (11161) covalent geometry : angle 0.58682 / 0.34 (15328) hydrogen bonds : bond 0.04736 / 3.23 ( 458) hydrogen bonds : angle 4.31493 / 2.93 ( 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 119 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7452 (t0) cc_final: 0.6962 (t0) REVERT: A 125 MET cc_start: 0.5905 (mtt) cc_final: 0.4127 (ttp) REVERT: C 45 ARG cc_start: 0.7594 (mtt180) cc_final: 0.7196 (mpp80) REVERT: C 140 MET cc_start: 0.3764 (ttt) cc_final: 0.2778 (tpt) REVERT: C 240 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6462 (pt0) REVERT: D 58 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7390 (mt) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.2198 time to fit residues: 36.4620 Evaluate side-chains 108 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN 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 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 26 ILE 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: 0.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 244 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 = 0.4357 r_free = 0.4357 target = 0.201110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153940 restraints weight = 33082.912| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.55 r_work: 0.3664 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11161 Z= 0.127 Angle : 0.562 18.838 15328 Z= 0.325 Chirality : 0.041 0.266 1751 Planarity : 0.004 0.038 1760 Dihedral : 18.439 165.266 1971 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.34 % Allowed : 14.31 % Favored : 84.34 % 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: -2.85 (0.22), residues: 1214 helix: -0.74 (0.22), residues: 518 sheet: -1.72 (0.36), residues: 177 loop : -3.18 (0.23), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.008 0.001 TYR D 92 PHE 0.010 0.001 PHE A 176 TRP 0.006 0.001 TRP F 22 HIS 0.007 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (11161) covalent geometry : angle 0.56173 / 0.32 (15328) hydrogen bonds : bond 0.04321 / 2.95 ( 458) hydrogen bonds : angle 4.18023 / 2.83 ( 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: 14 poor density : 98 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7468 (t0) cc_final: 0.6965 (t0) REVERT: A 125 MET cc_start: 0.5913 (mtt) cc_final: 0.4134 (ttp) REVERT: C 45 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7246 (mpp80) REVERT: C 140 MET cc_start: 0.3647 (ttt) cc_final: 0.2596 (tpt) REVERT: C 240 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6440 (pt0) REVERT: D 58 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7334 (mt) outliers start: 14 outliers final: 12 residues processed: 109 average time/residue: 0.2121 time to fit residues: 34.5231 Evaluate side-chains 109 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN 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 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 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: 20.0000 chunk 41 optimal weight: 0.1980 chunk 123 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.201354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154047 restraints weight = 33429.086| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.53 r_work: 0.3595 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3415 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= 0.164 Angle : 0.580 18.830 15328 Z= 0.334 Chirality : 0.042 0.228 1751 Planarity : 0.004 0.038 1760 Dihedral : 18.496 164.831 1971 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.54 % Allowed : 14.60 % 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: -2.89 (0.22), residues: 1214 helix: -0.74 (0.22), residues: 520 sheet: -1.65 (0.36), residues: 177 loop : -3.28 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.008 0.001 TYR E 61 PHE 0.010 0.001 PHE E 3 TRP 0.006 0.001 TRP C 166 HIS 0.010 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11161) covalent geometry : angle 0.58009 / 0.33 (15328) hydrogen bonds : bond 0.04575 / 3.13 ( 458) hydrogen bonds : angle 4.21964 / 2.87 ( 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 114 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7502 (t0) cc_final: 0.7000 (t0) REVERT: A 125 MET cc_start: 0.5923 (mtt) cc_final: 0.4122 (ttp) REVERT: C 45 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7249 (mpp80) REVERT: C 140 MET cc_start: 0.3620 (ttt) cc_final: 0.2573 (tpt) REVERT: C 240 GLU cc_start: 0.6785 (tm-30) cc_final: 0.6428 (pt0) REVERT: D 58 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7360 (mt) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.2107 time to fit residues: 33.6963 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 : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLN 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 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 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: 2.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 20 optimal weight: 3.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4368 r_free = 0.4368 target = 0.201297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154804 restraints weight = 33190.144| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.63 r_work: 0.3486 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11161 Z= 0.155 Angle : 0.575 18.921 15328 Z= 0.331 Chirality : 0.042 0.263 1751 Planarity : 0.004 0.035 1760 Dihedral : 18.516 165.092 1971 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.34 % Allowed : 15.18 % Favored : 83.48 % 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: -2.75 (0.22), residues: 1214 helix: -0.69 (0.22), residues: 517 sheet: -1.57 (0.37), residues: 177 loop : -3.14 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.008 0.001 TYR D 92 PHE 0.010 0.001 PHE E 3 TRP 0.007 0.001 TRP C 166 HIS 0.009 0.002 HIS C 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (11161) covalent geometry : angle 0.57493 / 0.33 (15328) hydrogen bonds : bond 0.04472 / 3.05 ( 458) hydrogen bonds : angle 4.17396 / 2.84 ( 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 107 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7432 (t0) cc_final: 0.6924 (t0) REVERT: A 125 MET cc_start: 0.5838 (mtt) cc_final: 0.4068 (ttp) REVERT: C 45 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7248 (mpp80) REVERT: C 140 MET cc_start: 0.3630 (ttt) cc_final: 0.2584 (tpt) REVERT: C 240 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6407 (pt0) REVERT: D 58 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7319 (mt) outliers start: 14 outliers final: 12 residues processed: 104 average time/residue: 0.2048 time to fit residues: 31.4401 Evaluate side-chains 104 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 109 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4375 r_free = 0.4375 target = 0.202110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155424 restraints weight = 33036.105| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.62 r_work: 0.3649 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11161 Z= 0.136 Angle : 0.559 19.023 15328 Z= 0.323 Chirality : 0.041 0.226 1751 Planarity : 0.004 0.034 1760 Dihedral : 18.514 165.360 1971 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.25 % Allowed : 15.47 % Favored : 83.29 % 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: -2.66 (0.22), residues: 1214 helix: -0.56 (0.22), residues: 519 sheet: -1.45 (0.37), residues: 177 loop : -3.17 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 118 TYR 0.008 0.001 TYR D 92 PHE 0.010 0.001 PHE A 176 TRP 0.008 0.001 TRP C 166 HIS 0.007 0.001 HIS C 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11161) covalent geometry : angle 0.55932 / 0.32 (15328) hydrogen bonds : bond 0.04284 / 2.94 ( 458) hydrogen bonds : angle 4.08040 / 2.79 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6289.13 seconds wall clock time: 107 minutes 4.31 seconds (6424.31 seconds total)